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Ly A, Garcia V, Blenman KRM, Ehinger A, Elfer K, Hanna MG, Li X, Peeters DJE, Birmingham R, Dudgeon S, Gardecki E, Gupta R, Lennerz J, Pan T, Saltz J, Wharton KA, Ehinger D, Acs B, Dequeker EMC, Salgado R, Gallas BD. Training pathologists to assess stromal tumour-infiltrating lymphocytes in breast cancer synergises efforts in clinical care and scientific research. Histopathology 2024. [PMID: 38433289 DOI: 10.1111/his.15140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/15/2023] [Accepted: 12/31/2023] [Indexed: 03/05/2024]
Abstract
A growing body of research supports stromal tumour-infiltrating lymphocyte (TIL) density in breast cancer to be a robust prognostic and predicive biomarker. The gold standard for stromal TIL density quantitation in breast cancer is pathologist visual assessment using haematoxylin and eosin-stained slides. Artificial intelligence/machine-learning algorithms are in development to automate the stromal TIL scoring process, and must be validated against a reference standard such as pathologist visual assessment. Visual TIL assessment may suffer from significant interobserver variability. To improve interobserver agreement, regulatory science experts at the US Food and Drug Administration partnered with academic pathologists internationally to create a freely available online continuing medical education (CME) course to train pathologists in assessing breast cancer stromal TILs using an interactive format with expert commentary. Here we describe and provide a user guide to this CME course, whose content was designed to improve pathologist accuracy in scoring breast cancer TILs. We also suggest subsequent steps to translate knowledge into clinical practice with proficiency testing.
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Affiliation(s)
- Amy Ly
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Victor Garcia
- Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging, Diagnostics, and Software Reliability, US Food and Drug Administration, Silver Spring, MD, USA
| | - Kim R M Blenman
- Department of Internal Medicine, Section of Medical Oncology and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Computer Science, Yale School of Engineering and Applied Science, New Haven, CT, USA
| | - Anna Ehinger
- Department of Genetics, Pathology and Molecular Diagnostics, Laboratory Medicine, Region Skane, Lund University, Lund, Sweden
| | - Katherine Elfer
- Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging, Diagnostics, and Software Reliability, US Food and Drug Administration, Silver Spring, MD, USA
| | - Matthew G Hanna
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiaoxian Li
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Dieter J E Peeters
- Department of Pathology, University Hospital Antwerp, Edegem, Belgium
- Department of Pathology, Algemeen Ziekenhuis (AZ) Sint-Maarten, Mechelen, Belgium
| | - Ryan Birmingham
- Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging, Diagnostics, and Software Reliability, US Food and Drug Administration, Silver Spring, MD, USA
- Department of Biomedical Informatics, Emory University, Atlanta, GA, USA
| | - Sarah Dudgeon
- Center for Computational Health, Yale School of Medicine, New Haven, CT, USA
| | - Emma Gardecki
- Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging, Diagnostics, and Software Reliability, US Food and Drug Administration, Silver Spring, MD, USA
| | - Rajarsi Gupta
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Jochen Lennerz
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA, USA
| | - Tony Pan
- Department of Biomedical Informatics, Emory University, Atlanta, GA, USA
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | | | - Daniel Ehinger
- Department of Clinical Sciences, Division of Oncology, Lund University, Lund, Sweden
- Department of Genetics, Pathology, and Molecular Diagnostics, Skane University Hospital, Lund, Sweden
| | - Balazs Acs
- Department of Oncology and Pathology, Cancer Centre Karolinska, Karolinksa Institutet, Stockholm, Sweden
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Elisabeth M C Dequeker
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, University of Leuven, Leuven, Belgium
| | - Roberto Salgado
- Department of Pathology, Gasthuiszusters Antwerpen-Ziekenhuis Netwerk Antwerpen (GZA-ZNA) Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Brandon D Gallas
- Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging, Diagnostics, and Software Reliability, US Food and Drug Administration, Silver Spring, MD, USA
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Meng P, Dalal H, Chen Y, Brueffer C, Gladchuk S, Alcaide M, Ehinger A, Saal LH. Digital PCR quantification of ultrahigh ERBB2 copy number identifies poor breast cancer survival after trastuzumab. NPJ Breast Cancer 2024; 10:14. [PMID: 38374091 PMCID: PMC10876644 DOI: 10.1038/s41523-024-00621-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
HER2/ERBB2 evaluation is necessary for treatment decision-making in breast cancer (BC), however current methods have limitations and considerable variability exists. DNA copy number (CN) evaluation by droplet digital PCR (ddPCR) has complementary advantages for HER2/ERBB2 diagnostics. In this study, we developed a single-reaction multiplex ddPCR assay for determination of ERBB2 CN in reference to two control regions, CEP17 and a copy-number-stable region of chr. 2p13.1, validated CN estimations to clinical in situ hybridization (ISH) HER2 status, and investigated the association of ERBB2 CN with clinical outcomes. 909 primary BC tissues were evaluated and the area under the curve for concordance to HER2 status was 0.93 and 0.96 for ERBB2 CN using either CEP17 or 2p13.1 as reference, respectively. The accuracy of ddPCR ERBB2 CN was 93.7% and 94.1% in the training and validation groups, respectively. Positive and negative predictive value for the classic HER2 amplification and non-amplification groups was 97.2% and 94.8%, respectively. An identified biological "ultrahigh" ERBB2 ddPCR CN group had significantly worse survival within patients treated with adjuvant trastuzumab for both recurrence-free survival (hazard ratio, HR: 3.3; 95% CI 1.1-9.6; p = 0.031, multivariable Cox regression) and overall survival (HR: 3.6; 95% CI 1.1-12.6; p = 0.041). For validation using RNA-seq data as a surrogate, in a population-based SCAN-B cohort (NCT02306096) of 682 consecutive patients receiving adjuvant trastuzumab, the ultrahigh-ERBB2 mRNA group had significantly worse survival. Multiplex ddPCR is useful for ERBB2 CN estimation and ultrahigh ERBB2 may be a predictive factor for decreased long-term survival after trastuzumab treatment.
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Affiliation(s)
- Pei Meng
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
| | - Hina Dalal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
| | - Yilun Chen
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Christian Brueffer
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Sergii Gladchuk
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Miguel Alcaide
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
- Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, Lund, Sweden
| | - Lao H Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden.
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Elfer K, Gardecki E, Garcia V, Ly A, Hytopoulos E, Wen S, Hanna MG, Peeters DJE, Saltz J, Ehinger A, Dudgeon SN, Li X, Blenman KRM, Chen W, Green U, Birmingham R, Pan T, Lennerz JK, Salgado R, Gallas BD. Reproducible Reporting of the Collection and Evaluation of Annotations for Artificial Intelligence Models. Mod Pathol 2024; 37:100439. [PMID: 38286221 DOI: 10.1016/j.modpat.2024.100439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/14/2023] [Accepted: 01/21/2024] [Indexed: 01/31/2024]
Abstract
This work puts forth and demonstrates the utility of a reporting framework for collecting and evaluating annotations of medical images used for training and testing artificial intelligence (AI) models in assisting detection and diagnosis. AI has unique reporting requirements, as shown by the AI extensions to the Consolidated Standards of Reporting Trials (CONSORT) and Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) checklists and the proposed AI extensions to the Standards for Reporting Diagnostic Accuracy (STARD) and Transparent Reporting of a Multivariable Prediction model for Individual Prognosis or Diagnosis (TRIPOD) checklists. AI for detection and/or diagnostic image analysis requires complete, reproducible, and transparent reporting of the annotations and metadata used in training and testing data sets. In an earlier work by other researchers, an annotation workflow and quality checklist for computational pathology annotations were proposed. In this manuscript, we operationalize this workflow into an evaluable quality checklist that applies to any reader-interpreted medical images, and we demonstrate its use for an annotation effort in digital pathology. We refer to this quality framework as the Collection and Evaluation of Annotations for Reproducible Reporting of Artificial Intelligence (CLEARR-AI).
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Affiliation(s)
- Katherine Elfer
- United States Food and Drug Administration, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging Diagnostics and Software Reliability, Silver Spring, Maryland; National Institutes of Health, National Cancer Institute, Division of Cancer Prevention, Cancer Prevention Fellowship Program, Bethesda, Maryland.
| | - Emma Gardecki
- United States Food and Drug Administration, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging Diagnostics and Software Reliability, Silver Spring, Maryland
| | - Victor Garcia
- United States Food and Drug Administration, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging Diagnostics and Software Reliability, Silver Spring, Maryland
| | - Amy Ly
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Si Wen
- United States Food and Drug Administration, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging Diagnostics and Software Reliability, Silver Spring, Maryland
| | - Matthew G Hanna
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dieter J E Peeters
- Department of Pathology, University Hospital Antwerp/University of Antwerp, Antwerp, Belgium; Department of Pathology, Sint-Maarten Hospital, Mechelen, Belgium
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York
| | - Anna Ehinger
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Laboratory Medicine, Lund University, Lund, Sweden
| | - Sarah N Dudgeon
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Xiaoxian Li
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Kim R M Blenman
- Department of Internal Medicine, Section of Medical Oncology, Yale School of Medicine and Yale Cancer Center, Yale University, New Haven, Connecticut; Department of Computer Science, School of Engineering and Applied Science, Yale University, New Haven, Connecticut
| | - Weijie Chen
- United States Food and Drug Administration, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging Diagnostics and Software Reliability, Silver Spring, Maryland
| | - Ursula Green
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, Georgia
| | - Ryan Birmingham
- United States Food and Drug Administration, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging Diagnostics and Software Reliability, Silver Spring, Maryland; Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, Georgia
| | - Tony Pan
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, Georgia
| | - Jochen K Lennerz
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Roberto Salgado
- Division of Research, Peter Mac Callum Cancer Centre, Melbourne, Australia; Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
| | - Brandon D Gallas
- United States Food and Drug Administration, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging Diagnostics and Software Reliability, Silver Spring, Maryland
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Sigurjonsdottir G, De Marchi T, Ehinger A, Hartman J, Bosch A, Staaf J, Killander F, Niméus E. Comparison of SP142 and 22C3 PD-L1 assays in a population-based cohort of triple-negative breast cancer patients in the context of their clinically established scoring algorithms. Breast Cancer Res 2023; 25:123. [PMID: 37817263 PMCID: PMC10566164 DOI: 10.1186/s13058-023-01724-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/02/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Immunohistochemical (IHC) PD-L1 expression is commonly employed as predictive biomarker for checkpoint inhibitors in triple-negative breast cancer (TNBC). However, IHC evaluation methods are non-uniform and further studies are needed to optimize clinical utility. METHODS We compared the concordance, prognostic value and gene expression between PD-L1 IHC expression by SP142 immune cell (IC) score and 22C3 combined positive score (CPS; companion IHC diagnostic assays for atezolizumab and pembrolizumab, respectively) in a population-based cohort of 232 early-stage TNBC patients. RESULTS The expression rates of PD-L1 for SP142 IC ≥ 1%, 22C3 CPS ≥ 10, 22C3 CPS ≥ 1 and 22C3 IC ≥ 1% were 50.9%, 27.2%, 53.9% and 41.8%, respectively. The analytical concordance (kappa values) between SP142 IC+ and these three different 22C3 scorings were 73.7% (0.48, weak agreement), 81.5% (0.63) and 86.6% (0.73), respectively. The SP142 assay was better at identifying 22C3 positive tumors than the 22C3 assay was at detecting SP142 positive tumors. PD-L1 (CD274) gene expression (mRNA) showed a strong positive association with all two-categorical IHC scorings of the PD-L1 expression, irrespective of antibody and cut-off (Spearman Rho ranged from 0.59 to 0.62; all p-values < 0.001). PD-L1 IHC positivity and abundance of tumor infiltrating lymphocytes were of positive prognostic value in univariable regression analyses in patients treated with (neo)adjuvant chemotherapy, where it was strongest for 22C3 CPS ≥ 10 and distant relapse-free interval (HR = 0.18, p = 0.019). However, PD-L1 status was not independently prognostic when adjusting for abundance of tumor infiltrating lymphocytes in multivariable analyses. CONCLUSION Our findings support that the SP142 and 22C3 IHC assays, with their respective clinically applied scoring algorithms, are not analytically equivalent where they identify partially non-overlapping subpopulations of TNBC patients and cannot be substituted with one another regarding PD-L1 detection. Trial registration The Swedish Cancerome Analysis Network - Breast (SCAN-B) study, retrospectively registered 2nd Dec 2014 at ClinicalTrials.gov; ID NCT02306096.
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Affiliation(s)
- Gudbjörg Sigurjonsdottir
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Tommaso De Marchi
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Laboratory Medicine, Region Skåne, Lund, Sweden
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Ana Bosch
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Lund, Sweden
| | - Fredrika Killander
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Emma Niméus
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
- Divison of Surgery, Department of Clinical Sciences Lund, Lund University, Sölvegatan 19 - BMC I12, 22184, Lund, Sweden.
- Department of Surgery, Skåne University Hospital, Malmö, Sweden.
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Lehn S, Pekar G, Balbas PB, Staaf J, Möller C, Lövgren K, Ehinger A, Campos AB, Borg Å, Pietras K. Abstract P6-01-05: Platelet-derived growth factor-CC expression in primary triple-negative breast cancer is associated with the basal-like molecular subtype and increased immune infiltrate. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p6-01-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Around 10-15% of all breast cancers are categorized clinically as triple-negative breast cancer (TNBC). TNBC is defined by lack of protein expression or over expression of treatment targets such as the Estrogen Receptor α (ER) and Human Epidermal Growth Factor Receptor-2 (HER2), and the prognostic factor PR (Progesterone Receptor). The negative definition of TNBC results in a heterogeneous mix of tumors with variable molecular characteristics and prognosis. Defining TNBC molecular subtypes in detail is of importance to improve prognostication and find new treatment options. Expression of Platelet-derived growth factor-CC (PDGF-CC) has previously been correlated with the TNBC subtype, and paracrine PDGF-CC signaling has been reported to be of importance for maintaining TNBC tumor cell phenotype. We aimed to characterize PDGF-CC expression within the TNBC patient population by combining studies of PDGF-CC in tissue microarrays (TMAs) with matching RNAseq data and clinical follow-up; all variables originating from the SCAN-B (Sweden Cancerome Analysis Network – Breast) clinical study (ClinicalTrials.gov: NCT02306096). TMAs constructed of primary TNBC patient samples were stained for PDGF-CC using the Dako PT Autostainer system. Tumor cell-specific expression of PDGF-CC intensity was scored as either absent (N=11), weak (N=86), intermediate (N=81) or strong (N=70), and the scores were used to create corresponding TNBC PDGF-CC subgroups. We then explored associations of these subgroups with clinicopathological variables and time-to-event outcomes. Intermediate and strong PDGF-CC scores were associated with Nottingham Histological Grade 3 (p=0.001), increased proliferation (p< 0.001) and younger patient age at diagnosis (p=0.002). RNAseq data corresponding to tumors included in the TMAs was then retrieved, and differentially expressed genes were identified and used to perform Gene Set Enrichment Analysis (GSEA) comparing the TMA-derived PDGF-CC subgroups. Immune-related signatures were found to be enriched in the strong PDGF-CC subgroup vs. intermediate. Interestingly, strong PDGF-CC intensity was associated with a decreased risk of recurrence in the chemotherapy treated patient group (HR 0.28, 95% CI 0.10-0.80, p=0.017). Finally, patient samples were assigned a PAM50 subtype and a TNBC molecular subtype by the TNBCtype algorithm. Ninety-four percent of tumors in the strong PDGF-CC subgroup were classified as basal-like, whereas the corresponding number in the weak and intermediate PDGF-CC subgroups were 51% and 84%, respectively. The TNBC molecular subtype termed ‘Immunomodulatory’ was more frequently represented in the strong PDGF-CC subgroup compared to weak and intermediate (33% vs. 13% and 16%, respectively). In conclusion, strong PDGF-CC protein expression identified basal-like TNBCs, with an increase in immune cell infiltrate shown by RNAseq analysis. Whether or not PDGF-CC has a direct effect on influx of immune cells into tumors remains to be investigated. Analyses are currently ongoing to better understand the improved outcome associated with strong PDGF-CC intensity and on the contrary, the worse outcome associated with weak and intermediate PDGF-CC intensity, and if paracrine PDGF-CC signaling may explain the discrepancy observed.
Citation Format: Sophie Lehn, Gyula Pekar, Paulina Bolivar Balbas, Johan Staaf, Christina Möller, Kristina Lövgren, Anna Ehinger, Ana Bosch Campos, Åke Borg, Kristian Pietras. Platelet-derived growth factor-CC expression in primary triple-negative breast cancer is associated with the basal-like molecular subtype and increased immune infiltrate [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-01-05.
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Affiliation(s)
| | | | | | | | | | | | | | - Ana Bosch Campos
- 8Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden, Sweden
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Antonello D, von Mering C, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, 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Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, 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George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV. Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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Staaf J, Häkkinen J, Hegardt C, Saal LH, Kimbung S, Hedenfalk I, Lien T, Sørlie T, Naume B, Russnes H, Marcone R, Ayyanan A, Brisken C, Malterling RR, Asking B, Olofsson H, Lindman H, Bendahl PO, Ehinger A, Larsson C, Loman N, Rydén L, Malmberg M, Borg Å, Vallon-Christersson J. RNA sequencing-based single sample predictors of molecular subtype and risk of recurrence for clinical assessment of early-stage breast cancer. NPJ Breast Cancer 2022; 8:94. [PMID: 35974007 PMCID: PMC9381586 DOI: 10.1038/s41523-022-00465-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/20/2022] [Indexed: 11/09/2022] Open
Abstract
Multigene assays for molecular subtypes and biomarkers can aid management of early invasive breast cancer. Using RNA-sequencing we aimed to develop single-sample predictor (SSP) models for clinical markers, subtypes, and risk of recurrence (ROR). A cohort of 7743 patients was divided into training and test set. We trained SSPs for subtypes and ROR assigned by nearest-centroid (NC) methods and SSPs for biomarkers from histopathology. Classifications were compared with Prosigna in two external cohorts (ABiM, n = 100 and OSLO2-EMIT0, n = 103). Prognostic value was assessed using distant recurrence-free interval. Agreement between SSP and NC for PAM50 (five subtypes) was high (85%, Kappa = 0.78) for Subtype (four subtypes) very high (90%, Kappa = 0.84) and for ROR risk category high (84%, Kappa = 0.75, weighted Kappa = 0.90). Prognostic value was assessed as equivalent and clinically relevant. Agreement with histopathology was very high or high for receptor status, while moderate for Ki67 status and poor for Nottingham histological grade. SSP and Prosigna concordance was high for subtype (OSLO-EMIT0 83%, Kappa = 0.73 and ABiM 80%, Kappa = 0.72) and moderate and high for ROR risk category (68 and 84%, Kappa = 0.50 and 0.70, weighted Kappa = 0.70 and 0.78). Pooled concordance for emulated treatment recommendation dichotomized for chemotherapy was high (85%, Kappa = 0.66). Retrospective evaluation suggested that SSP application could change chemotherapy recommendations for up to 17% of postmenopausal ER+/HER2-/N0 patients with balanced escalation and de-escalation. Results suggest that NC and SSP models are interchangeable on a group-level and nearly so on a patient level and that SSP models can be derived to closely match clinical tests.
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Affiliation(s)
- Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden.
| | - Jari Häkkinen
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Cecilia Hegardt
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Lao H Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Siker Kimbung
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Tonje Lien
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, POB 4953 Nydalen N-0424, Oslo, Norway.,Department of Pathology, Oslo University Hospital, POB 4953 Nydalen N-0424, Oslo, Norway
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, POB 4953 Nydalen N-0424, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Bjørn Naume
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, POB 4953 Nydalen N-0424, Oslo, Norway
| | - Hege Russnes
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, POB 4953 Nydalen N-0424, Oslo, Norway.,Department of Pathology, Oslo University Hospital, POB 4953 Nydalen N-0424, Oslo, Norway
| | - Rachel Marcone
- ISREC-Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1005, Lausanne, Switzerland
| | - Ayyakkannu Ayyanan
- ISREC-Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Cathrin Brisken
- ISREC-Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | | | - Bengt Asking
- Department of Surgery, Region Jönköping County, Jönköping, Sweden
| | - Helena Olofsson
- Department of Clinical Pathology, Akademiska Hospital, Uppsala, Sweden.,Department of Pathology, Centre for Clinical Research of Uppsala University, Vastmanland´s Hospital Västerås, Västerås, Sweden
| | - Henrik Lindman
- Department of Immunology, Genetics and Pathology, Uppsala University Hospital, Uppsala, Sweden
| | - Pär-Ola Bendahl
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden.,Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, Lund, Sweden
| | - Christer Larsson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Niklas Loman
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden.,Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Lisa Rydén
- Division of Surgery, Department of Clinical Sciences, Lund University, Lund, Sweden.,Department of Surgery and Gastroenterology, Skåne University Hospital Malmö, Malmö, Sweden
| | - Martin Malmberg
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Johan Vallon-Christersson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden.
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9
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Elfer K, Dudgeon S, Garcia V, Blenman K, Hytopoulos E, Wen S, Li X, Ly A, Werness B, Sheth MS, Amgad M, Gupta R, Saltz J, Hanna MG, Ehinger A, Peeters D, Salgado R, Gallas BD. Pilot study to evaluate tools to collect pathologist annotations for validating machine learning algorithms. J Med Imaging (Bellingham) 2022; 9:047501. [PMID: 35911208 PMCID: PMC9326105 DOI: 10.1117/1.jmi.9.4.047501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/28/2022] [Indexed: 11/14/2022] Open
Abstract
Purpose: Validation of artificial intelligence (AI) algorithms in digital pathology with a reference standard is necessary before widespread clinical use, but few examples focus on creating a reference standard based on pathologist annotations. This work assesses the results of a pilot study that collects density estimates of stromal tumor-infiltrating lymphocytes (sTILs) in breast cancer biopsy specimens. This work will inform the creation of a validation dataset for the evaluation of AI algorithms fit for a regulatory purpose. Approach: Collaborators and crowdsourced pathologists contributed glass slides, digital images, and annotations. Here, "annotations" refer to any marks, segmentations, measurements, or labels a pathologist adds to a report, image, region of interest (ROI), or biological feature. Pathologists estimated sTILs density in 640 ROIs from hematoxylin and eosin stained slides of 64 patients via two modalities: an optical light microscope and two digital image viewing platforms. Results: The pilot study generated 7373 sTILs density estimates from 29 pathologists. Analysis of annotations found the variability of density estimates per ROI increases with the mean; the root mean square differences were 4.46, 14.25, and 26.25 as the mean density ranged from 0% to 10%, 11% to 40%, and 41% to 100%, respectively. The pilot study informs three areas of improvement for future work: technical workflows, annotation platforms, and agreement analysis methods. Upgrades to the workflows and platforms will improve operability and increase annotation speed and consistency. Conclusions: Exploratory data analysis demonstrates the need to develop new statistical approaches for agreement. The pilot study dataset and analysis methods are publicly available to allow community feedback. The development and results of the validation dataset will be publicly available to serve as an instructive tool that can be replicated by developers and researchers.
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Affiliation(s)
- Katherine Elfer
- United States Food and Drug Administration, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging Diagnostics & Software Reliability, Silver Spring, Maryland, United States
- National Institutes of Health, National Cancer Institute, Division of Cancer Prevention, Cancer Prevention Fellowship Program, Bethesda, Maryland, United States
| | - Sarah Dudgeon
- Yale University Computational Biology and Bioinformatics, New Haven, Connecticut, United States
- Yale New Haven Hospital, Center for Outcomes Research and Evaluation, New Haven, Connecticut, United States
| | - Victor Garcia
- United States Food and Drug Administration, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging Diagnostics & Software Reliability, Silver Spring, Maryland, United States
| | - Kim Blenman
- School of Medicine, Yale Cancer Center, Department of Internal Medicine, Section of Medical Oncology, New Haven, Connecticut, United States
- Yale University, School of Engineering and Applied Science, Department of Computer Science, New Haven, Connecticut, United States
| | | | - Si Wen
- United States Food and Drug Administration, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging Diagnostics & Software Reliability, Silver Spring, Maryland, United States
| | - Xiaoxian Li
- Emory University School of Medicine, Department of Pathology and Laboratory Medicine, Atlanta, Georgia, United States
| | - Amy Ly
- Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Bruce Werness
- Inova Health System Department of Pathology, Falls Church, Virginia, United States
- Arrive Bio LLC, San Francisco, California, United States
| | - Manasi S. Sheth
- United States Food and Drug Administration (FDA), Center for Devices and Radiologic Health, Office of Product Evaluation and Quality, Office of Clinical Evidence and Analysis, Division of Biostatistics, White Oak, Maryland, United States
| | - Mohamed Amgad
- Northwestern University Feinberg School of Medicine, Department of Pathology, Chicago, Illinois, United States
| | - Rajarsi Gupta
- SUNY Stony Brook Medicine, Department of Biomedical Informatics, Stony Brook, New York, United States
| | - Joel Saltz
- SUNY Stony Brook Medicine, Department of Biomedical Informatics, Stony Brook, New York, United States
- SUNY Stony Brook Medicine, Department of Pathology, Stony Brook, New York, United States
| | - Matthew G. Hanna
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Anna Ehinger
- Lund University, Laboratory Medicine, Region Skåne, Department of Genetics and Pathology, Lund, Sweden
| | - Dieter Peeters
- Sint-Maarten Hospital, Department of Pathology, Mechelen, Belgium
- University of Antwerp, Department of Biomedical Sciences, Antwerp, Belgium
| | - Roberto Salgado
- Peter Mac Callum Cancer Centre, Division of Research, Melbourne, Australia
- GZA-ZNA Hospitals, Department of Pathology, Antwerp, Belgium
| | - Brandon D. Gallas
- United States Food and Drug Administration, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging Diagnostics & Software Reliability, Silver Spring, Maryland, United States
- Address all correspondence to Brandon D. Gallas,
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10
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Elfer KN, Blenman K, Dudgeon SN, Garcia V, Ehinger A, Li X, Ly A, Peeters D, Werness B, Hanna M, Salgado R. Abstract 460: Tools for collecting pathologist annotations and understanding interobserver variability. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The High Throughput Truthing (HTT) project is assessing pathologist agreement estimates of stromal tumor-infiltrating lymphocytes (sTILs) density in hematoxylin and eosin (H&E) stained breast cancer biopsy slides. The HTT project will create a validation dataset for artificial intelligence and machine learning (AI/ML) algorithms in digital pathology fit for a training, proficiency testing, and regulatory purpose.
Methods: The pilot study crowdsourced pathologists to estimate sTIL density in 640 regions of interest (ROIs) across 64 slides via two modalities: an optical microscope (eeDAP) and two digital platforms (caMicroscope and PathPresenter). eeDAP is a hardware-software interface that presents the observer with pre-defined fields of view on H&E slides that corresponds to the ROI on a whole slide image. The PathPresenter and caMicroscope web-applications replicate the eeDAP workflow on the whole slide image without microscope hardware. In the workflow, pathologists evaluated the eligibility of an ROI for sTILs content then estimated the densities of tumor-associated stroma and sTILs in the ROI. Inter-pathologist agreement within ROIs was characterized with the root mean-squared difference. Using 72 of the highest variability ROIs selected from the pilot study, seven practicing pathologists participated in a subsequent focus group to improve the clinical training and data-collection workflows.
Results: The pilot study collected 7,373 sTIL density estimates from 35 pathologists between February 2020 and May 2021. The focus group provided an additional 411 evaluations on 72 ROIs and in-depth discussions to identify pitfalls, gaps in training, and workflow improvements. Installation of eeDAP for physical data collection guided improvements in documentation and operation capabilities. Updated training materials refine the definition of tumor-associated stroma, provide reference images to differentiate sTILs from other cell types, and provide feedback during training. Digital and microscope platforms benefitted from enforcing registration and training, standardizing workflows, and accelerating eeDAP slide-image registration.
Conclusions: The slides, images, and annotations provided by volunteer collaborators and participants for our pilot study led to improvements in data collection tools and crowdsourcing workflows to ensure consistency and minimize annotation variability. Our pilot dataset and analysis methods are available on a public HTT Github repository to allow open access to our methodology and feedback from the digital pathology and statistics communities. These data-collection and analysis methods are applicable to other quantitative biomarkers for validation of AI/ML algorithms. The lessons learned from this work will be applied to the HTT pivotal study and inform future quality data-collection methods of pathologist annotations.
Citation Format: Katherine N. Elfer, Kim Blenman, Sarah N. Dudgeon, Victor Garcia, Anna Ehinger, Xiaoxian Li, Amy Ly, Dieter Peeters, Bruce Werness, Matthew Hanna, Roberto Salgado. Tools for collecting pathologist annotations and understanding interobserver variability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 460.
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Affiliation(s)
- Katherine N. Elfer
- 1National Cancer Institute, Cancer Prevention Fellowship Program; United States Food and Drug Administration, Center for Devices and Radiologic Health, Office of Science and Engineering Laboratories, Division of Imaging Diagnostics & Software Reliability, Bethesda; White Oak, MD
| | - Kim Blenman
- 2Yale University: School of Medicine and Yale Cancer Center; School of Engineering and Applied Science, New Haven, CT
| | | | - Victor Garcia
- 4United States Food and Drug Administration, Center for Devices and Radiologic Health, Office of Science and Engineering Laboratories, Division of Imaging Diagnostics & Software Reliability, Bethesda, MD
| | - Anna Ehinger
- 5Lund University, Skåne University Hospital, Lund, Sweden
| | - Xiaoxian Li
- 6Emory University School of Medicine, Atlanta, GA
| | - Amy Ly
- 7Massachusetts General Hospital, Boston, MA
| | - Dieter Peeters
- 8Sint-Maarten Hospital; University of Antwerp, Mechelen; Antwerp, Belgium
| | - Bruce Werness
- 9Inova Health System; Arrive Bio, Falls Church, VA; San Francisco, CA
| | - Matthew Hanna
- 10Memorial Sloan Kettering Cancer Center, New York, NY
| | - Roberto Salgado
- 11Peter Mac Callum Cancer Centre, Division of Research, Melbourne, Australia; GZA-ZNA Hospitals, Antwerp, Belgium
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11
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Vallon-Christersson J, Staaf J, Häkkinen J, Hegardt C, Saal L, Ehinger A, Larsson C, Loman N, Rydén L, Malmberg M, Borg Å. 52P RNA sequencing-based single sample predictors of molecular subtype and risk of recurrence for clinical assessment of early-stage breast cancer. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.03.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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12
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Saghir H, Veerla S, Malmberg M, Rydén L, Ehinger A, Saal L, Vallon-Christersson J, Borg Å, Hegardt C, Hedenfalk I, Dieroff-Hay S, Larsson C, Loman N, Kimbung S. Abstract P2-08-11: How reliable are biomarkers assessed on a core needle biopsy? A study of paired core needle biopsies and surgical specimens in early breast cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p2-08-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The conventional biomarkers estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG) are used to classify breast cancer into its molecular subtypes, determine prognosis, and guide treatment. A preoperative core needle biopsy (CNB) is used to confirm the diagnosis and invasiveness of a breast lesion and forms the basis for characterizing the tumor in the case of neoadjuvant primary treatment, emphasizing the importance of obtaining reliable biomarker assessment from a diagnostic CNB. Aim: The aim of this study was to determine the similarity between biomarker status assessed on a CNB compared to a medically untreated surgical specimen. Methods: Paired CNB and surgical specimens from 267 patients that were part of the prospective Sweden Cancerome Analysis Network- Breast (SCAN-B) cohort were studied. The concordance for the five biomarkers: ER, PgR, Ki67, HER2 and molecular subtype, between paired CNB and surgical specimen were investigated using immunohistochemistry (IHC) and gene expression-based analytical methods (GEX). IHC data were collected from patient medical records and gene expression was measured by RNA sequencing. Cohen’s kappa and Mcnemar’s test were used to compare the concordance of biomarkers.Results: Moderate to very good levels of concordance were observed between the biomarker status obtained on a CNB compared with the paired surgical specimen for IHC (κappa range 0.474-0.917) and GEX (κappa range 0.528-0.776), respectively. However, a significant drift from low to high Ki67 status and from negative to positive HER2 status between the CNB and surgical specimen was observed when using IHC and GEX, respectively (McNemar p < 0.05 for both comparisons). Moderate to good concordance levels of biomarker status were generally obtained when comparing GEX and IHC status measured from the same type of sample (κappa range 0.484-0.649) except for Ki67 which consistently displayed poor concordance levels between IHC and GEX for both CNB and surgical specimen comparisons (κappa range 0.158-0.198). Notably, a significant shift from positive to negative ER status and high to low Ki67 status was observed when comparing IHC with GEX classification (McNemar p <0.001 for both comparisons). Conclusion: The tissue sampling and the method of biomarker analysis may affect the results of biomarker status and ultimately affect treatment decisions. The implications of using a preoperative CNB to determine biomarker status, prognosis, and treatment choice should be taken into consideration in neoadjuvant treatment settings.
Citation Format: Hani Saghir, Srinivas Veerla, Martin Malmberg, Lisa Rydén, Anna Ehinger, Lao Saal, Johan Vallon-Christersson, Åke Borg, Cecilia Hegardt, Ingrid Hedenfalk, Susanne Dieroff-Hay, Christer Larsson, Niklas Loman, Siker Kimbung. How reliable are biomarkers assessed on a core needle biopsy? A study of paired core needle biopsies and surgical specimens in early breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-08-11.
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Affiliation(s)
- Hani Saghir
- Division of Oncology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Srinivas Veerla
- Division of Oncology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Martin Malmberg
- Dept. of Hematology, Oncology and Radiation Physics, Lund University Hospital, Lund, Sweden
| | - Lisa Rydén
- Division of Oncology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Lao Saal
- Division of Oncology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | | | - Åke Borg
- Division of Oncology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Cecilia Hegardt
- Division of Oncology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | | | - Christer Larsson
- Division of Translational Cancer Research, Dept. of Laboratory Medicine, Lund University, Lund, Sweden
| | - Niklas Loman
- Dept. of Hematology, Oncology and Radiation Physics, Lund University Hospital, Lund, Sweden
| | - Siker Kimbung
- Division of Oncology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
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13
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El Bairi K, Haynes HR, Blackley E, Fineberg S, Shear J, Turner S, de Freitas JR, Sur D, Amendola LC, Gharib M, Kallala A, Arun I, Azmoudeh-Ardalan F, Fujimoto L, Sua LF, Liu SW, Lien HC, Kirtani P, Balancin M, El Attar H, Guleria P, Yang W, Shash E, Chen IC, Bautista V, Do Prado Moura JF, Rapoport BL, Castaneda C, Spengler E, Acosta-Haab G, Frahm I, Sanchez J, Castillo M, Bouchmaa N, Md Zin RR, Shui R, Onyuma T, Yang W, Husain Z, Willard-Gallo K, Coosemans A, Perez EA, Provenzano E, Ericsson PG, Richardet E, Mehrotra R, Sarancone S, Ehinger A, Rimm DL, Bartlett JMS, Viale G, Denkert C, Hida AI, Sotiriou C, Loibl S, Hewitt SM, Badve S, Symmans WF, Kim RS, Pruneri G, Goel S, Francis PA, Inurrigarro G, Yamaguchi R, Garcia-Rivello H, Horlings H, Afqir S, Salgado R, Adams S, Kok M, Dieci MV, Michiels S, Demaria S, Loi S. The tale of TILs in breast cancer: A report from The International Immuno-Oncology Biomarker Working Group. NPJ Breast Cancer 2021; 7:150. [PMID: 34853355 PMCID: PMC8636568 DOI: 10.1038/s41523-021-00346-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 09/28/2021] [Indexed: 02/08/2023] Open
Abstract
The advent of immune-checkpoint inhibitors (ICI) in modern oncology has significantly improved survival in several cancer settings. A subgroup of women with breast cancer (BC) has immunogenic infiltration of lymphocytes with expression of programmed death-ligand 1 (PD-L1). These patients may potentially benefit from ICI targeting the programmed death 1 (PD-1)/PD-L1 signaling axis. The use of tumor-infiltrating lymphocytes (TILs) as predictive and prognostic biomarkers has been under intense examination. Emerging data suggest that TILs are associated with response to both cytotoxic treatments and immunotherapy, particularly for patients with triple-negative BC. In this review from The International Immuno-Oncology Biomarker Working Group, we discuss (a) the biological understanding of TILs, (b) their analytical and clinical validity and efforts toward the clinical utility in BC, and (c) the current status of PD-L1 and TIL testing across different continents, including experiences from low-to-middle-income countries, incorporating also the view of a patient advocate. This information will help set the stage for future approaches to optimize the understanding and clinical utilization of TIL analysis in patients with BC.
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Affiliation(s)
- Khalid El Bairi
- Department of Medical Oncology, Mohammed VI University Hospital, Faculty of Medicine and Pharmacy, Mohammed Ist University, Oujda, Morocco.
| | - Harry R Haynes
- Department of Cellular Pathology, Great Western Hospital, Swindon, UK
- Translational Health Sciences, University of Bristol, Bristol, UK
| | - Elizabeth Blackley
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Susan Fineberg
- Department of Pathology, Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jeffrey Shear
- Chief Information Officer, WISS & Company, LLP and President J. Shear Consulting, LLC-Ardsley, Ardsley, NY, USA
| | | | - Juliana Ribeiro de Freitas
- Department of Pathology and Legal Medicine, Medical School of the Federal University of Bahia, Salvador, Brazil
| | - Daniel Sur
- Department of Medical Oncology, University of Medicine "I. Hatieganu", Cluj Napoca, Romania
| | | | - Masoumeh Gharib
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Indu Arun
- Department of Histopathology, Tata Medical Center, Kolkata, India
| | - Farid Azmoudeh-Ardalan
- Department of Pathology, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Luciana Fujimoto
- Pathology and Legal Medicine, Amazon Federal University, Belém, Brazil
| | - Luz F Sua
- Department of Pathology and Laboratory Medicine, Fundacion Valle del Lili, and Faculty of Health Sciences, Universidad ICESI, Cali, Colombia
| | | | - Huang-Chun Lien
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Pawan Kirtani
- Department of Histopathology, Manipal Hospitals Dwarka, New Delhi, India
| | - Marcelo Balancin
- Department of Pathology, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | | | - Prerna Guleria
- Army Hospital Research and Referral, Delhi Cantt, New Delhi, India
| | | | - Emad Shash
- Breast Cancer Comprehensive Center, National Cancer Institute, Cairo University, Cairo, Egypt
| | - I-Chun Chen
- Department of Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Veronica Bautista
- Department of Pathology, Breast Cancer Center FUCAM, Mexico City, Mexico
| | | | - Bernardo L Rapoport
- The Medical Oncology Centre of Rosebank, Johannesburg, South Africa
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, corner Doctor Savage Road and Bophelo Road, Pretoria, 0002, South Africa
| | - Carlos Castaneda
- Department of Medical Oncology, Instituto Nacional de Enfermedades Neoplásicas, Lima, 15038, Peru
- Faculty of Health Sciences, Universidad Cientifica del Sur, Lima, Peru
| | - Eunice Spengler
- Departmento de Patologia, Hospital Universitario Austral, Pilar, Argentina
| | - Gabriela Acosta-Haab
- Department of Pathology, Hospital de Oncología Maria Curie, Buenos Aires, Argentina
| | - Isabel Frahm
- Department of Pathology, Sanatorio Mater Dei, Buenos Aires, Argentina
| | - Joselyn Sanchez
- Department of Research, Instituto Nacional de Enfermedades Neoplasicas, Lima, 15038, Peru
| | - Miluska Castillo
- Department of Research, Instituto Nacional de Enfermedades Neoplasicas, Lima, 15038, Peru
| | - Najat Bouchmaa
- Institute of Biological Sciences, Mohammed VI Polytechnic University (UM6P), 43 150, Ben-Guerir, Morocco
| | - Reena R Md Zin
- Department of Pathology, Faculty of Medicine, UKM Medical Centre, Kuala Lumpur, Malaysia
| | - Ruohong Shui
- Department of Pathology, Fudan University Cancer Center, Shanghai, China
| | | | - Wentao Yang
- Department of Pathology, Fudan University Cancer Center, Shanghai, China
| | | | - Karen Willard-Gallo
- Molecular Immunology Unit, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - An Coosemans
- Laboratory of Tumour Immunology and Immunotherapy, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Edith A Perez
- Department of Hematology/Oncology, Mayo Clinic, Jacksonville, FL, USA
| | - Elena Provenzano
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Paula Gonzalez Ericsson
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eduardo Richardet
- Clinical Oncology Unit, Instituto Oncológico Córdoba, Córdoba, Argentina
| | - Ravi Mehrotra
- India Cancer Research Consortium-ICMR, Department of Health Research, New Delhi, India
| | - Sandra Sarancone
- Department of Pathology, Laboratorio QUANTUM, Rosario, Argentina
| | - Anna Ehinger
- Department of Clinical Genetics and Pathology, Skåne University Hospital, Lund University, Lund, Sweden
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - John M S Bartlett
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Canada
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Giuseppe Viale
- Department of Pathology, Istituto Europeo di Oncologia IRCCS, and University of Milan, Milan, Italy
| | - Carsten Denkert
- Institute of Pathology, Universitätsklinikum Gießen und Marburg GmbH, Standort Marburg and Philipps-Universität Marburg, Marburg, Germany
| | - Akira I Hida
- Department of Pathology, Matsuyama Shimin Hospital, Matsuyama, Japan
| | - Christos Sotiriou
- Department of Medical Oncology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Stephen M Hewitt
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sunil Badve
- Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, USA
| | - William Fraser Symmans
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Rim S Kim
- National Surgical Adjuvant Breast and Bowel Project (NSABP)/NRG Oncology, Pittsburgh, PA, USA
| | - Giancarlo Pruneri
- Department of Pathology, RCCS Fondazione Istituto Nazionale Tumori and University of Milan, School of Medicine, Milan, Italy
| | - Shom Goel
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Prudence A Francis
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Medical Oncology Department, Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Rin Yamaguchi
- Department of Pathology and Laboratory Medicine, Kurume University Medical Center, Kurume, Fukuoka, Japan
| | - Hernan Garcia-Rivello
- Servicio de Anatomía Patológica, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Hugo Horlings
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Said Afqir
- Department of Medical Oncology, Mohammed VI University Hospital, Faculty of Medicine and Pharmacy, Mohammed Ist University, Oujda, Morocco
| | - Roberto Salgado
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
| | - Sylvia Adams
- Perlmutter Cancer Center, New York University Medical School, New York, NY, USA
| | - Marleen Kok
- Divisions of Medical Oncology, Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maria Vittoria Dieci
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
- Medical Oncology 2, Istituto Oncologico Veneto IOV-IRCCS, Padova, Italy
| | - Stefan Michiels
- Service de Biostatistique et d'Epidémiologie, Gustave Roussy, Oncostat U1018, Inserm, University Paris-Saclay, labeled Ligue Contre le Cancer, Villejuif, France
| | - Sandra Demaria
- Department of Radiation Oncology, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
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14
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Andersson A, Larsson L, Stenbeck L, Salmén F, Ehinger A, Wu SZ, Al-Eryani G, Roden D, Swarbrick A, Borg Å, Frisén J, Engblom C, Lundeberg J. Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions. Nat Commun 2021; 12:6012. [PMID: 34650042 PMCID: PMC8516894 DOI: 10.1038/s41467-021-26271-2] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra- and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. By integration with single cell data, we spatially map tumor-associated cell types to find tertiary lymphoid-like structures, and a type I interferon response overlapping with regions of T-cell and macrophage subset colocalization. We construct a predictive model to infer presence of tertiary lymphoid-like structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define a high resolution map of cellular interactions in tumors and provide tools generalizing across tissues and diseases.
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Affiliation(s)
- Alma Andersson
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ludvig Larsson
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Linnea Stenbeck
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Salmén
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.,Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Cancer Genomics Netherlands, Utrecht, the Netherlands
| | - Anna Ehinger
- Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden.,Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Sunny Z Wu
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia.,St Vincent's Clinical School, Faculty of Medicine, Sydney, Australia
| | - Ghamdan Al-Eryani
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia.,St Vincent's Clinical School, Faculty of Medicine, Sydney, Australia
| | - Daniel Roden
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia.,St Vincent's Clinical School, Faculty of Medicine, Sydney, Australia
| | - Alex Swarbrick
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia.,St Vincent's Clinical School, Faculty of Medicine, Sydney, Australia
| | - Åke Borg
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Engblom
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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15
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Bai Y, Cole K, Martinez-Morilla S, Ahmed FS, Zugazagoitia J, Staaf J, Bosch A, Ehinger A, Niméus E, Hartman J, Acs B, Rimm DL. An Open Source, Automated Tumor Infiltrating Lymphocyte Algorithm for Prognosis in Triple-Negative Breast Cancer. Clin Cancer Res 2021; 27:5557-5565. [PMID: 34088723 DOI: 10.1158/1078-0432.ccr-21-0325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/29/2021] [Accepted: 06/02/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Although tumor infiltrating lymphocytes (TIL) assessment has been acknowledged to have both prognostic and predictive importance in triple negative breast cancer (TNBC), it is subject to inter and intra-observer variability that has prevented widespread adoption. Here we constructed a machine-learning based breast cancer TIL scoring approach and validated its prognostic potential in multiple TNBC cohorts. EXPERIMENTAL DESIGN Using the QuPath open source software, we built a neural-network classifier for tumor cells, lymphocytes, fibroblasts and "other" cells on hematoxylin-eosin (H&E) stained sections. We analyzed the classifier-derived TIL measurements with five unique constructed TIL variables. A retrospective collection of 171 TNBC cases was used as the discovery set to identify the optimal association of machine-read TIL variables with patient outcome. For validation we evaluated a retrospective collection of 749 TNBC patients comprised of four independent validation subsets. RESULTS We found that all five machine TIL variables had significant prognostic association with outcomes (p{less than or equal to}0.01 for all comparisons) but showed cell specific variation in validation sets. Cox regression analysis demonstrated that all five TIL variables were independently associated with improved overall survival after adjusting for clinicopathological factors including stage, age and histological grade (p{less than or equal to}0.003 for all analyses). CONCLUSIONS Neural net driven cell classifier defined TIL variables were robust and independent prognostic factors in several independent validation cohorts of TNBC patients. These objective, open source TIL variables are freely available to download and can now be considered for testing in a prospective setting to assess clinical utility.
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Affiliation(s)
| | | | | | | | | | | | - Ana Bosch
- Department of Clinical Sciences. Division of Oncology, Lund University
| | - Anna Ehinger
- Clinical Genetics and Pathology, Lund University
| | - Emma Niméus
- Oncology and Pathology, Clinical Sciences, Lund University
| | - Johan Hartman
- Dept of Oncology and Pathology, Karolinska Institute
| | - Balazs Acs
- Department of Oncology-Pathology, Karolinska Institute
| | - David L Rimm
- Department of Pathology, Yale School of Medicine
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16
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Dahlgren M, George AM, Brueffer C, Gladchuk S, Chen Y, Vallon-Christersson J, Hegardt C, Häkkinen J, Rydén L, Malmberg M, Larsson C, Gruvberger-Saal SK, Ehinger A, Loman N, Borg Å, Saal LH. Preexisting Somatic Mutations of Estrogen Receptor Alpha ( ESR1) in Early-Stage Primary Breast Cancer. JNCI Cancer Spectr 2021; 5:pkab028. [PMID: 33937624 PMCID: PMC8060794 DOI: 10.1093/jncics/pkab028] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/29/2021] [Accepted: 03/26/2021] [Indexed: 01/26/2023] Open
Abstract
Background More than three-quarters of primary breast cancers are positive for estrogen receptor alpha (ER; encoded by the gene ESR1), the most important factor for directing anti-estrogenic endocrine therapy (ET). Recently, mutations in ESR1 were identified as acquired mechanisms of resistance to ET, found in 12% to 55% of metastatic breast cancers treated previously with ET. Methods We analyzed 3217 population-based invasive primary (nonmetastatic) breast cancers (within the SCAN-B study, ClinicalTrials.gov NCT02306096), sampled from initial diagnosis prior to any treatment, for the presence of ESR1 mutations using RNA sequencing. Mutations were verified by droplet digital polymerase chain reaction on tumor and normal DNA. Patient outcomes were analyzed using Kaplan-Meier estimation and a series of 2-factor Cox regression multivariable analyses. Results We identified ESR1 resistance mutations in 30 tumors (0.9%), of which 29 were ER positive (1.1%). In ET-treated disease, presence of ESR1 mutation was associated with poor relapse-free survival and overall survival (2-sided log-rank test P < .001 and P = .008, respectively), with hazard ratios of 3.00 (95% confidence interval = 1.56 to 5.88) and 2.51 (95% confidence interval = 1.24 to 5.07), respectively, which remained statistically significant when adjusted for other prognostic factors. Conclusions These population-based results indicate that ESR1 mutations at diagnosis of primary breast cancer occur in about 1% of women and identify for the first time in the adjuvant setting that such preexisting mutations are associated to eventual resistance to standard hormone therapy. If replicated, tumor ESR1 screening should be considered in ER-positive primary breast cancer, and for patients with mutated disease, ER degraders such as fulvestrant or other therapeutic options may be considered as more appropriate.
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Affiliation(s)
- Malin Dahlgren
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Anthony M George
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Christian Brueffer
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Sergii Gladchuk
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Yilun Chen
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Johan Vallon-Christersson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Cecilia Hegardt
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Jari Häkkinen
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Lisa Rydén
- Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Martin Malmberg
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Christer Larsson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Sofia K Gruvberger-Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Current affiliation: Center for Molecular Diagnostics, Skåne University Hospital, Lund, Sweden (SKG-S)
| | - Anna Ehinger
- Department of Pathology, Skåne University Hospital, Lund, Sweden
| | - Niklas Loman
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Lao H Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
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17
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Aine M, Boyaci C, Hartman J, Häkkinen J, Mitra S, Campos AB, Nimeus E, Ehinger A, Vallon-Christersson J, Borg Å, Staaf J. Correction to: Molecular analyses of triple-negative breast cancer in the young and elderly. Breast Cancer Res 2021; 23:28. [PMID: 33627140 PMCID: PMC7903710 DOI: 10.1186/s13058-021-01405-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Mattias Aine
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Ceren Boyaci
- Department of Clinical Pathology and Cytology, Karolinska University Laboratory, Stockholm, Sweden
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
| | - Jari Häkkinen
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Shamik Mitra
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ana Bosch Campos
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Emma Nimeus
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden.,Division of Surgery, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden.,Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, Lund, Sweden
| | - Johan Vallon-Christersson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden.
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18
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Kaminska K, Akrap N, Staaf J, Alves CL, Ehinger A, Ebbesson A, Hedenfalk I, Beumers L, Veerla S, Harbst K, Ehmsen S, Borgquist S, Borg Å, Pérez-Fidalgo A, Ditzel HJ, Bosch A, Honeth G. Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer. Breast Cancer Res 2021; 23:26. [PMID: 33602273 PMCID: PMC7893923 DOI: 10.1186/s13058-021-01402-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/31/2021] [Indexed: 11/23/2022] Open
Abstract
Background Resistance to endocrine treatment in metastatic breast cancer is a major clinical challenge. Clinical tools to predict both drug resistance and possible treatment combination approaches to overcome it are lacking. This unmet need is mainly due to the heterogeneity underlying both the mechanisms involved in resistance development and breast cancer itself. Methods To study the complexity of the mechanisms involved in the resistance to the selective estrogen receptor degrader (SERD) fulvestrant, we performed comprehensive biomarker analyses using several in vitro models that recapitulate the heterogeneity of developed resistance. We further corroborated our findings in tissue samples from patients treated with fulvestrant. Results We found that different in vitro models of fulvestrant resistance show variable stability in their phenotypes, which corresponded with distinct genomic alterations. Notably, the studied models presented adaptation at different cell cycle nodes to facilitate progression through the cell cycle and responded differently to CDK inhibitors. Cyclin E2 overexpression was identified as a biomarker of a persistent fulvestrant-resistant phenotype. Comparison of pre- and post-treatment paired tumor biopsies from patients treated with fulvestrant revealed an upregulation of cyclin E2 upon development of resistance. Moreover, overexpression of this cyclin was found to be a prognostic factor determining resistance to fulvestrant and shorter progression-free survival. Conclusions These data highlight the complexity of estrogen receptor positive breast cancer and suggest that the development of diverse resistance mechanisms dictate levels of ER independence and potentially cross-resistance to CDK inhibitors. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-021-01402-1.
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Affiliation(s)
- Kamila Kaminska
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Nina Akrap
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Carla L Alves
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Division of Clinical Genetics and Pathology, Department of Laboratory Medicine, Skåne University Hospital, Lund, Sweden
| | - Anna Ebbesson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Lukas Beumers
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Srinivas Veerla
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Katja Harbst
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Sidse Ehmsen
- Department of Oncology, Odense University Hospital, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Signe Borgquist
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Aarhus University Hospital, Aarhus, Denmark
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | | | - Henrik J Ditzel
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Ana Bosch
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. .,Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden.
| | - Gabriella Honeth
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
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19
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Aine M, Boyaci C, Hartman J, Häkkinen J, Mitra S, Campos AB, Nimeus E, Ehinger A, Vallon-Christersson J, Borg Å, Staaf J. Molecular analyses of triple-negative breast cancer in the young and elderly. Breast Cancer Res 2021; 23:20. [PMID: 33568222 PMCID: PMC7874480 DOI: 10.1186/s13058-021-01392-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/11/2021] [Indexed: 01/09/2023] Open
Abstract
Background Breast cancer in young adults has been implicated with a worse outcome. Analyses of genomic traits associated with age have been heterogenous, likely because of an incomplete accounting for underlying molecular subtypes. We aimed to resolve whether triple-negative breast cancer (TNBC) in younger versus older patients represent similar or different molecular diseases in the context of genetic and transcriptional subtypes and immune cell infiltration. Patients and methods In total, 237 patients from a reported population-based south Swedish TNBC cohort profiled by RNA sequencing and whole-genome sequencing (WGS) were included. Patients were binned in 10-year intervals. Complimentary PD-L1 and CD20 immunohistochemistry and estimation of tumor-infiltrating lymphocytes (TILs) were performed. Cases were analyzed for differences in patient outcome, genomic, transcriptional, and immune landscape features versus age at diagnosis. Additionally, 560 public WGS breast cancer profiles were used for validation. Results Median age at diagnosis was 62 years (range 26–91). Age was not associated with invasive disease-free survival or overall survival after adjuvant chemotherapy. Among the BRCA1-deficient cases (82/237), 90% were diagnosed before the age of 70 and were predominantly of the basal-like subtype. In the full TNBC cohort, reported associations of patient age with changes in Ki67 expression, PIK3CA mutations, and a luminal androgen receptor subtype were confirmed. Within DNA repair deficiency or gene expression defined molecular subgroups, age-related alterations in, e.g., overall gene expression, immune cell marker gene expression, genetic mutational and rearrangement signatures, amount of copy number alterations, and tumor mutational burden did, however, not appear distinct. Similar non-significant associations for genetic alterations with age were obtained for other breast cancer subgroups in public WGS data. Consistent with age-related immunosenescence, TIL counts decreased linearly with patient age across different genetic TNBC subtypes. Conclusions Age-related alterations in TNBC, as well as breast cancer in general, need to be viewed in the context of underlying genomic phenotypes. Based on this notion, age at diagnosis alone does not appear to provide an additional layer of biological complexity above that of proposed genetic and transcriptional phenotypes of TNBC. Consequently, treatment decisions should be less influenced by age and more driven by tumor biology. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-021-01392-0.
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Affiliation(s)
- Mattias Aine
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Ceren Boyaci
- Department of Clinical Pathology and Cytology, Karolinska University Laboratory, Stockholm, Sweden
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
| | - Jari Häkkinen
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Shamik Mitra
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ana Bosch Campos
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Emma Nimeus
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden.,Division of Surgery, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden.,Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, Lund, Sweden
| | - Johan Vallon-Christersson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden.
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20
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Ericson Lindquist K, Ciornei C, Westbom-Fremer S, Gudinaviciene I, Ehinger A, Mylona N, Urdar R, Lianou M, Svensson F, Seidal T, Haglund F, Dobra K, Béndek M, Bardóczi E, Szablewska A, Witkowski M, Ramnefjell M, De Las Casas LE, Gulyas M, Hegedus A, Micke P, Brunnström H. Difficulties in diagnostics of lung tumours in biopsies: an interpathologist concordance study evaluating the international diagnostic guidelines. J Clin Pathol 2021; 75:302-309. [PMID: 33547095 PMCID: PMC9046746 DOI: 10.1136/jclinpath-2020-207257] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/29/2020] [Accepted: 01/20/2021] [Indexed: 12/19/2022]
Abstract
AIMS Accurate and reliable diagnosis is essential for lung cancer treatment. The study aim was to investigate interpathologist diagnostic concordance for pulmonary tumours according to WHO diagnostic criteria. METHODS Fifty-two unselected lung and bronchial biopsies were diagnosed by a thoracic pathologist based on a broad spectrum of immunohistochemical (IHC) stainings, molecular data and clinical/radiological information. Slides stained with H&E, thyroid transcription factor-1 (TTF-1) clone SPT24 and p40 were scanned and provided digitally to 20 pathologists unaware of reference diagnoses. The pathologists independently diagnosed the cases and stated if further diagnostic markers were deemed necessary. RESULTS In 31 (60%) of the cases, ≥80% of the pathologists agreed with each other and with the reference diagnosis. Lower agreement was seen in non-small cell neuroendocrine tumours and in squamous cell carcinoma with diffuse TTF-1 positivity. Agreement with the reference diagnosis ranged from 26 to 45 (50%-87%) for the individual pathologists. The pathologists requested additional IHC staining in 15-44 (29%-85%) of the 52 cases. In nearly half (17 of 36) of the malignant cases, one or more pathologist advocated for a different final diagnosis than the reference without need of additional IHC markers, potentially leading to different clinical treatment. CONCLUSIONS Interpathologist diagnostic agreement is moderate for small unselected bronchial and lung biopsies based on a minimal panel of markers. Neuroendocrine morphology is sometimes missed and TTF-1 clone SPT24 should be interpreted with caution. Our results suggest an intensified education need for thoracic pathologists and a more generous use of diagnostic IHC markers.
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Affiliation(s)
- Kajsa Ericson Lindquist
- Department of Clinical Sciences Lund, Division of Pathology, Lund University, Lund, Sweden.,Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
| | - Cristina Ciornei
- Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
| | - Sofia Westbom-Fremer
- Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden.,Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Inga Gudinaviciene
- Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
| | - Anna Ehinger
- Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden.,Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Nektaria Mylona
- Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
| | - Rodrigo Urdar
- Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
| | - Maria Lianou
- Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
| | - Franziska Svensson
- Department of Pathology and Cytology, Halland Hospital Halmstad, Halmstad, Sweden
| | - Tomas Seidal
- Department of Pathology and Cytology, Halland Hospital Halmstad, Halmstad, Sweden
| | - Felix Haglund
- Department of Clinical Pathology and Cytology, Karolinska University Hospital Solna, Stockholm, Sweden.,Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Katalin Dobra
- Department of Pathology, Division of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Clinical Pathology and Cytology, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Mátyás Béndek
- Department of Clinical Pathology and Cytology, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Erika Bardóczi
- Department of Clinical Pathology and Cytology, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Aneta Szablewska
- Department of Pathology and Cytology, Blekinge Hospital Karlskrona, Karlskrona, Sweden
| | - Marek Witkowski
- Department of Pathology, Kalmar County Hospital, Kalmar, Sweden
| | - Maria Ramnefjell
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Luis E De Las Casas
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Miklos Gulyas
- Department of Immunology, Genetics and Pathology, Uppsala University and Uppsala University Hospital, Uppsala, Sweden
| | - Agnes Hegedus
- Department of Immunology, Genetics and Pathology, Uppsala University and Uppsala University Hospital, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University and Uppsala University Hospital, Uppsala, Sweden
| | - Hans Brunnström
- Department of Clinical Sciences Lund, Division of Pathology, Lund University, Lund, Sweden .,Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
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21
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Brueffer C, Gladchuk S, Winter C, Vallon-Christersson J, Hegardt C, Häkkinen J, George AM, Chen Y, Ehinger A, Larsson C, Loman N, Malmberg M, Rydén L, Borg Å, Saal LH. The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome. EMBO Mol Med 2020; 12:e12118. [PMID: 32926574 PMCID: PMC7539222 DOI: 10.15252/emmm.202012118] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 08/08/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is a disease of genomic alterations, of which the panorama of somatic mutations and how these relate to subtypes and therapy response is incompletely understood. Within SCAN‐B (ClinicalTrials.gov: NCT02306096), a prospective study elucidating the transcriptomic profiles for thousands of breast cancers, we developed a RNA‐seq pipeline for detection of SNVs/indels and profiled a real‐world cohort of 3,217 breast tumors. We describe the mutational landscape of primary breast cancer viewed through the transcriptome of a large population‐based cohort and relate it to patient survival. We demonstrate that RNA‐seq can be used to call mutations in genes such as PIK3CA,TP53, and ERBB2, as well as the status of molecular pathways and mutational burden, and identify potentially druggable mutations in 86.8% of tumors. To make this rich dataset available for the research community, we developed an open source web application, the SCAN‐B MutationExplorer (http://oncogenomics.bmc.lu.se/MutationExplorer). These results add another dimension to the use of RNA‐seq as a clinical tool, where both gene expression‐ and mutation‐based biomarkers can be interrogated in real‐time within 1 week of tumor sampling.
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Affiliation(s)
- Christian Brueffer
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden
| | - Sergii Gladchuk
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden
| | - Christof Winter
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden
| | - Johan Vallon-Christersson
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden.,CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Cecilia Hegardt
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden.,CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Jari Häkkinen
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden
| | - Anthony M George
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden
| | - Yilun Chen
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden.,Department of Pathology, Skåne University Hospital, Lund, Sweden
| | - Christer Larsson
- Lund University Cancer Center, Lund, Sweden.,Division of Molecular Pathology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Niklas Loman
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden.,Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Martin Malmberg
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Lisa Rydén
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden.,Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden.,CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Lao H Saal
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund University Cancer Center, Lund, Sweden.,CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
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22
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Dahlgren M, George AM, Brueffer C, Gladchuk S, Chen Y, Vallon-Christersson J, Hegardt C, Häkkinen J, Rydén L, Malmberg M, Larsson C, Gruvberger-Saal SK, Ehinger A, Loman N, Borg Å, Saal LH. Abstract CT074: Pre-existing ESR1 mutations in early-stage primary breast cancer predict failure of endocrine therapy and poor survival. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-ct074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: More than three-quarters of primary breast cancers are positive for estrogen receptor alpha (ER; encoded by the gene ESR1), the most important factor for directing anti-estrogenic endocrine therapy. Although mutation in ESR1 is known as an acquired mechanism of resistance to endocrine therapy (ET), found in 12-55% of metastatic breast cancers treated previously with ET, the impact of ESR1 mutation on therapy response in primary breast cancer is unclear. Patients and methods: In this study we analyzed 3217 real-world and population-based early-stage primary breast cancers (within the SCAN-B study, ClinicalTrials.gov NCT02306096). Tissues were sampled from initial diagnosis prior to any treatment and analyzed for the presence of ESR1 mutations using RNA sequencing. Mutations were verified by SAGAsafe droplet digital PCR. Results: We identified ESR1 resistance mutations in 30 cases (0.9%), of which 29 were ER-positive (1.1%). In ER-positive disease, presence of ESR1 mutation was significantly associated to poor relapse-free survival (RFS) and overall survival (OS) (p=0.011 and p=0.019, respectively), and moreover predicted poor RFS and OS within the patient group that received ET (p=0.007 and p=0.010, respectively). Conclusions: These results indicate that ESR1 mutations at diagnosis of untreated primary breast cancer are rare, however we confirm for the first time that such early mutations predict eventual resistance to standard hormone therapy in the adjuvant setting. If replicated, tumor ESR1 screening may be considered in ER-positive primary breast cancer and, in mutated cases, ER-degraders such as fulvestrant or other therapeutic options may be considered as more appropriate.
Citation Format: Malin Dahlgren, Anthony M. George, Christian Brueffer, Sergii Gladchuk, Yilun Chen, Johan Vallon-Christersson, Cecilia Hegardt, Jari Häkkinen, Lisa Rydén, Martin Malmberg, Christer Larsson, Sofia K. Gruvberger-Saal, Anna Ehinger, Niklas Loman, Åke Borg, Lao H. Saal. Pre-existing ESR1 mutations in early-stage primary breast cancer predict failure of endocrine therapy and poor survival [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr CT074.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lisa Rydén
- 2Skåne University Hospital, Lund, Sweden
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23
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Glodzik D, Bosch A, Hartman J, Aine M, Vallon-Christersson J, Reuterswärd C, Karlsson A, Mitra S, Niméus E, Holm K, Häkkinen J, Hegardt C, Saal LH, Larsson C, Malmberg M, Rydén L, Ehinger A, Loman N, Kvist A, Ehrencrona H, Nik-Zainal S, Borg Å, Staaf J. Comprehensive molecular comparison of BRCA1 hypermethylated and BRCA1 mutated triple negative breast cancers. Nat Commun 2020; 11:3747. [PMID: 32719340 PMCID: PMC7385112 DOI: 10.1038/s41467-020-17537-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/02/2020] [Indexed: 02/08/2023] Open
Abstract
Homologous recombination deficiency (HRD) is a defining characteristic in BRCA-deficient breast tumors caused by genetic or epigenetic alterations in key pathway genes. We investigated the frequency of BRCA1 promoter hypermethylation in 237 triple-negative breast cancers (TNBCs) from a population-based study using reported whole genome and RNA sequencing data, complemented with analyses of genetic, epigenetic, transcriptomic and immune infiltration phenotypes. We demonstrate that BRCA1 promoter hypermethylation is twice as frequent as BRCA1 pathogenic variants in early-stage TNBC and that hypermethylated and mutated cases have similarly improved prognosis after adjuvant chemotherapy. BRCA1 hypermethylation confers an HRD, immune cell type, genome-wide DNA methylation, and transcriptional phenotype similar to TNBC tumors with BRCA1-inactivating variants, and it can be observed in matched peripheral blood of patients with tumor hypermethylation. Hypermethylation may be an early event in tumor development that progress along a common pathway with BRCA1-mutated disease, representing a promising DNA-based biomarker for early-stage TNBC.
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Affiliation(s)
- Dominik Glodzik
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA, Cambridge, UK
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ana Bosch
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Department of Oncology, Skåne University Hospital, SE-22184, Lund, Sweden
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institute, SE-17177, Stockholm, Sweden
| | - Mattias Aine
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund University, SE-22184, Lund, Sweden
| | - Johan Vallon-Christersson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Christel Reuterswärd
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Anna Karlsson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Shamik Mitra
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Emma Niméus
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Division of Surgery, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | - Karolina Holm
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Jari Häkkinen
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Cecilia Hegardt
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Lao H Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Christer Larsson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Martin Malmberg
- Department of Oncology, Skåne University Hospital, SE-22184, Lund, Sweden
| | - Lisa Rydén
- Division of Surgery, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, SE-22184, Lund, Sweden
| | - Niklas Loman
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Department of Oncology, Skåne University Hospital, SE-22184, Lund, Sweden
| | - Anders Kvist
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Hans Ehrencrona
- Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, SE-22184, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-22184, Lund, Sweden
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, CB2 0QQ, Cambridge, UK
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden.
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24
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Larsson C, Ehinger A, Winslow S, Leandersson K, Klintman M, Dahl L, Vallon-Christersson J, Häkkinen J, Hegardt C, Manjer J, Saal L, Rydén L, Malmberg M, Borg Å, Loman N. Prognostic implications of the expression levels of different immunoglobulin heavy chain-encoding RNAs in early breast cancer. NPJ Breast Cancer 2020; 6:28. [PMID: 32656317 PMCID: PMC7338507 DOI: 10.1038/s41523-020-0170-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/02/2020] [Indexed: 12/22/2022] Open
Abstract
The extent and composition of the immune response in a breast cancer is one important prognostic factor for the disease. The aim of the current work was to refine the analysis of the humoral component of an immune response in breast tumors by quantifying mRNA expression of different immunoglobulin classes and study their association with prognosis. We used RNA-Seq data from two local population-based breast cancer cohorts to determine the expression of IGJ and immunoglobulin heavy (IGH) chain-encoding RNAs. The association with prognosis was investigated and public data sets were used to corroborate the findings. Except for IGHE and IGHD, mRNAs encoding heavy chains were generally detected at substantial levels and correlated with other immune-related genes. High IGHG1 mRNA was associated with factors related to poor prognosis such as estrogen receptor negativity, HER2 amplification, and high grade, whereas high IGHA2 mRNA levels were primarily associated with lower age at diagnosis. High IGHA2 and IGJ mRNA levels were associated with a more favorable prognosis both in univariable and multivariable Cox models. When adjusting for other prognostic factors, high IGHG1 mRNA levels were positively associated with improved prognosis. To our knowledge, these results are the first to demonstrate that expression of individual Ig class types has prognostic implications in breast cancer.
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Affiliation(s)
- Christer Larsson
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anna Ehinger
- Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Sofia Winslow
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Karin Leandersson
- Cancer Immunology, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Marie Klintman
- Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Ludvig Dahl
- Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | | | - Jari Häkkinen
- Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Cecilia Hegardt
- Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Jonas Manjer
- Surgery, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Lao Saal
- Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Lisa Rydén
- Surgery, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Martin Malmberg
- Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Åke Borg
- Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Niklas Loman
- Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
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25
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Brueffer C, Gladchuk S, Winter C, Vallon-Christersson J, Hegardt C, Häkkinen J, George AM, Chen Y, Ehinger A, Larsson C, Loman N, Malmberg M, Rydén L, Borg Å, Saal LH. Defining the mutational landscape of 3,217 primary breast cancer transcriptomes through large-scale RNA-seq within the Sweden Cancerome Analysis Network: Breast Project (SCAN-B; NCT03430492). J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
518 Background: Breast cancer is a disease of genomic alterations, of which the complete panorama of somatic mutations and how these relate to molecular subtypes and therapy response is incompletely understood. The Sweden Cancerome Analysis Network-Breast project (SCAN-B; ClinicalTrials.gov NCT02306096) is a multi-center population-based ongoing prospective observational study elucidating the global transcriptomic profiles for thousands of patients and tumors using RNA sequencing. Since September 2010, over 15,000 patients with breast cancer have been enrolled at 9 hospitals across a wide geography of Sweden, comprising greater than 90% of all eligible patients in the catchment area. Methods: Within SCAN-B, we developed an optimized bioinformatics pipeline for detection of single nucleotide variants and small insertions and deletions from RNA-seq data. From this, we describe the mutational landscape of 3,217 primary breast cancer transcriptomes, and relate it to patient overall survival in a real-world setting (median follow-up 75 months, range 2-105 months). Results: We demonstrate that RNA-seq can be used to call mutations in important breast cancer genes such as PIK3CA, TP53, ESR1, and ERBB2, as well as mutation status of key molecular pathways and tumor mutational burden, identify mutations in one or more potentially druggable genes in 85.3% percent of cases, and reveal significant relationships to patient outcome within specific treatment groups. To make this rich and growing mutational portraiture of breast cancer available for the wider research community, we developed an open source interactive web application, SCAN-B MutationExplorer, publicly accessible at http://oncogenomics.bmc.lu.se/MutationExplorer . Conclusions: These results add another dimension to the use of RNA-seq as a potential clinical tool, where both gene expression-based signatures and gene mutation-based biomarkers can be interrogated simultaneously and in real-time within one week of tumor sampling.
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Affiliation(s)
| | | | | | | | | | | | | | - Yilun Chen
- Lund University, Division of Oncology, Lund, Sweden
| | - Anna Ehinger
- Skåne University Hospital, Department of Pathology, Lund, Sweden
| | | | - Niklas Loman
- Skåne University Hospital, Department of Oncology, Lund, Sweden
| | - Martin Malmberg
- Skåne University Hospital, Department of Oncology, Helsingborg, Sweden
| | - Lisa Rydén
- Skåne University Hospital, Department of Surgery, Lund, Sweden
| | - Åke Borg
- Lund University, Division of Oncology, Lund, Sweden
| | - Lao H. Saal
- Lund University, Division of Oncology, Lund, Sweden
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26
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Kos Z, Roblin E, Kim RS, Michiels S, Gallas BD, Chen W, van de Vijver KK, Goel S, Adams S, Demaria S, Viale G, Nielsen TO, Badve SS, Symmans WF, Sotiriou C, Rimm DL, Hewitt S, Denkert C, Loibl S, Luen SJ, Bartlett JMS, Savas P, Pruneri G, Dillon DA, Cheang MCU, Tutt A, Hall JA, Kok M, Horlings HM, Madabhushi A, van der Laak J, Ciompi F, Laenkholm AV, Bellolio E, Gruosso T, Fox SB, Araya JC, Floris G, Hudeček J, Voorwerk L, Beck AH, Kerner J, Larsimont D, Declercq S, Van den Eynden G, Pusztai L, Ehinger A, Yang W, AbdulJabbar K, Yuan Y, Singh R, Hiley C, Bakir MA, Lazar AJ, Naber S, Wienert S, Castillo M, Curigliano G, Dieci MV, André F, Swanton C, Reis-Filho J, Sparano J, Balslev E, Chen IC, Stovgaard EIS, Pogue-Geile K, Blenman KRM, Penault-Llorca F, Schnitt S, Lakhani SR, Vincent-Salomon A, Rojo F, Braybrooke JP, Hanna MG, Soler-Monsó MT, Bethmann D, Castaneda CA, Willard-Gallo K, Sharma A, Lien HC, Fineberg S, Thagaard J, Comerma L, Gonzalez-Ericsson P, Brogi E, Loi S, Saltz J, Klaushen F, Cooper L, Amgad M, Moore DA, Salgado R. Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer. NPJ Breast Cancer 2020; 6:17. [PMID: 32411819 PMCID: PMC7217863 DOI: 10.1038/s41523-020-0156-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 03/02/2020] [Indexed: 02/08/2023] Open
Abstract
Stromal tumor-infiltrating lymphocytes (sTILs) are important prognostic and predictive biomarkers in triple-negative (TNBC) and HER2-positive breast cancer. Incorporating sTILs into clinical practice necessitates reproducible assessment. Previously developed standardized scoring guidelines have been widely embraced by the clinical and research communities. We evaluated sources of variability in sTIL assessment by pathologists in three previous sTIL ring studies. We identify common challenges and evaluate impact of discrepancies on outcome estimates in early TNBC using a newly-developed prognostic tool. Discordant sTIL assessment is driven by heterogeneity in lymphocyte distribution. Additional factors include: technical slide-related issues; scoring outside the tumor boundary; tumors with minimal assessable stroma; including lymphocytes associated with other structures; and including other inflammatory cells. Small variations in sTIL assessment modestly alter risk estimation in early TNBC but have the potential to affect treatment selection if cutpoints are employed. Scoring and averaging multiple areas, as well as use of reference images, improve consistency of sTIL evaluation. Moreover, to assist in avoiding the pitfalls identified in this analysis, we developed an educational resource available at www.tilsinbreastcancer.org/pitfalls.
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Affiliation(s)
- Zuzana Kos
- Department of Pathology, BC Cancer - Vancouver, Vancouver, BC Canada
| | - Elvire Roblin
- Department of Biostatistics and Epidemiology, Gustave Roussy, University Paris-Saclay, Villejuif, France
- Oncostat U1018, Inserm, University Paris-Saclay, labeled Ligue Contre le Cancer, Villejuif, France
| | - Rim S. Kim
- National Surgical Adjuvant Breast and Bowel Project (NSABP)/NRG Oncology, Pittsburgh, PA USA
| | - Stefan Michiels
- Department of Biostatistics and Epidemiology, Gustave Roussy, University Paris-Saclay, Villejuif, France
- Oncostat U1018, Inserm, University Paris-Saclay, labeled Ligue Contre le Cancer, Villejuif, France
| | - Brandon D. Gallas
- Division of Imaging, Diagnostics, and Software Reliability (DIDSR); Office of Science and Engineering Laboratories (OSEL); Center for Devices and Radiological Health (CDRH), US Food and Drug Administration (US FDA), Silver Spring, MD USA
| | - Weijie Chen
- Division of Imaging, Diagnostics, and Software Reliability (DIDSR); Office of Science and Engineering Laboratories (OSEL); Center for Devices and Radiological Health (CDRH), US Food and Drug Administration (US FDA), Silver Spring, MD USA
| | - Koen K. van de Vijver
- Department of Pathology, University Hospital Antwerp, Antwerp, Belgium
- Department of Pathology, Ghent University Hospital, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Shom Goel
- The Sir Peter MacCallum Cancer Centre, Melbourne, VIC Australia
- Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria Australia
| | - Sylvia Adams
- Perlmutter Cancer Center, New York University Medical School, New York, NY USA
| | - Sandra Demaria
- Departments of Radiation Oncology and Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY USA
| | - Giuseppe Viale
- Department of Pathology, Istituto Europeo di Oncologia, University of Milan, Milan, Italy
| | - Torsten O. Nielsen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Sunil S. Badve
- Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, USA
| | - W. Fraser Symmans
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Christos Sotiriou
- Department of Medical Oncology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - David L. Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT USA
| | - Stephen Hewitt
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, MD USA
| | - Carsten Denkert
- Institute of Pathology, Universitätsklinikum Gießen und Marburg GmbH, Standort Marburg and Philipps-Universität Marburg, Marburg, Germany
| | | | - Stephen J. Luen
- Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria Australia
- Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC Australia
| | - John M. S. Bartlett
- Ontario Institute for Cancer Research, Toronto, ON Canada
- University of Edinburgh Cancer Research Centre, Edinburgh, UK
| | - Peter Savas
- Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria Australia
- Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC Australia
| | - Giancarlo Pruneri
- Department of Pathology, IRCCS Fondazione Instituto Nazionale Tumori and University of Milan, School of Medicine, Milan, Italy
| | - Deborah A. Dillon
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA USA
- Department of Pathology, Dana Farber Cancer Institute, Boston, MA USA
| | - Maggie Chon U. Cheang
- Institute of Cancer Research Clinical Trials and Statistics Unit, The Institute of Cancer Research, Surrey, UK
| | - Andrew Tutt
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Marleen Kok
- Department of Medical Oncology and Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hugo M. Horlings
- Department of Pathology, University Hospital Antwerp, Antwerp, Belgium
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH USA
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH USA
| | - Jeroen van der Laak
- Computational Pathology Group, Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Francesco Ciompi
- Computational Pathology Group, Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Enrique Bellolio
- Departamento de Anatomía Patológica, Universidad de La Frontera, Temuco, Chile
| | | | - Stephen B. Fox
- The Sir Peter MacCallum Cancer Centre, Melbourne, VIC Australia
- Department of Pathology, Peter MacCallum Cancer Centre Department of Pathology, Melbourne, VIC Australia
| | | | - Giuseppe Floris
- KU Leuven- Univerisity of Leuven, Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and KU Leuven- University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - Jan Hudeček
- Department of Research IT, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Leonie Voorwerk
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | - Denis Larsimont
- Department of Pathology, Jules Bordet Institute, Brussels, Belgium
| | | | | | - Lajos Pusztai
- Department of Internal Medicine, Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT USA
| | - Anna Ehinger
- Department of Clinical Genetics and Pathology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Wentao Yang
- Department of Pathology, Fudan University Shanghai Cancer Centre, Shanghai, China
| | - Khalid AbdulJabbar
- Centre for Evolution and Cancer; Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Yinyin Yuan
- Centre for Evolution and Cancer; Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Rajendra Singh
- Icahn School of Medicine at Mt. Sinai, New York, NY 10029 USA
| | - Crispin Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
| | - Maise al Bakir
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
| | - Alexander J. Lazar
- Departments of Pathology, Genomic Medicine, Dermatology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Stephen Naber
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, USA
| | - Stephan Wienert
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Charitéplatz 1, 10117 Berlin, Germany
| | - Miluska Castillo
- Department of Medical Oncology and Research, Instituto Nacional de Enfermedades Neoplasicas, Lima, 15038 Peru
| | | | - Maria-Vittoria Dieci
- Medical Oncology 2, Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Fabrice André
- Department of Medical Oncology, Institut Gustave Roussy, Villejuif, France
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
- Francis Crick Institute, Midland Road, London, UK
| | - Jorge Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Joseph Sparano
- Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY USA
| | - Eva Balslev
- Department of Pathology, Herlev and Gentofte Hospital, Herlev, Denmark
| | - I-Chun Chen
- Department of Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | | | - Katherine Pogue-Geile
- National Surgical Adjuvant Breast and Bowel Project (NSABP)/NRG Oncology, Pittsburgh, PA USA
| | - Kim R. M. Blenman
- Department of Internal Medicine, Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT USA
| | | | - Stuart Schnitt
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA USA
| | - Sunil R. Lakhani
- The University of Queensland Centre for Clinical Research and Pathology Queensland, Brisbane, QLD Australia
| | - Anne Vincent-Salomon
- Institut Curie, Paris Sciences Lettres Université, Inserm U934, Department of Pathology, Paris, France
| | - Federico Rojo
- Pathology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD) - CIBERONC, Madrid, Spain
- GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain
| | - Jeremy P. Braybrooke
- Nuffield Department of Population Health, University of Oxford, Oxford and Department of Medical Oncology, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Matthew G. Hanna
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - M. Teresa Soler-Monsó
- Department of Pathology, Bellvitge University Hospital, IDIBELL. Breast Unit. Catalan Institut of Oncology. L ‘Hospitalet del Llobregat’, Barcelona, 08908 Catalonia Spain
| | - Daniel Bethmann
- University Hospital Halle (Saale), Institute of Pathology, Halle (Saale), Germany
| | - Carlos A. Castaneda
- Department of Medical Oncology and Research, Instituto Nacional de Enfermedades Neoplasicas, Lima, 15038 Peru
| | - Karen Willard-Gallo
- Molecular Immunology Unit, Institut Jules Bordet, Universitè Libre de Bruxelles, Brussels, Belgium
| | - Ashish Sharma
- Department of Biomedical Informatics, Emory University, Atlanta, GA USA
| | - Huang-Chun Lien
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Susan Fineberg
- Department of Pathology, Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY USA
| | - Jeppe Thagaard
- DTU Compute, Department of Applied Mathematics, Technical University of Denmark; Visiopharm A/S, Hørsholm, Denmark
| | - Laura Comerma
- GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain
- Pathology Department, Hospital del Mar, Parc de Salut Mar, Barcelona, Spain
| | - Paula Gonzalez-Ericsson
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN USA
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Sherene Loi
- Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria Australia
- Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC Australia
| | - Joel Saltz
- Biomedical Informatics Department, Stony Brook University, Stony Brook, NY USA
| | - Frederick Klaushen
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Lee Cooper
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Mohamed Amgad
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA USA
| | - David A. Moore
- Department of Pathology, UCL Cancer Institute, UCL, London, UK
- University College Hospitals NHS Trust, London, UK
| | - Roberto Salgado
- Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC Australia
- Department of Pathology, GZA-ZNA, Antwerp, Belgium
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Gonzalez-Ericsson PI, Stovgaard ES, Sua LF, Reisenbichler E, Kos Z, Carter JM, Michiels S, Le Quesne J, Nielsen TO, Laenkholm AV, Fox SB, Adam J, Bartlett JM, Rimm DL, Quinn C, Peeters D, Dieci MV, Vincent-Salomon A, Cree I, Hida AI, Balko JM, Haynes HR, Frahm I, Acosta-Haab G, Balancin M, Bellolio E, Yang W, Kirtani P, Sugie T, Ehinger A, Castaneda CA, Kok M, McArthur H, Siziopikou K, Badve S, Fineberg S, Gown A, Viale G, Schnitt SJ, Pruneri G, Penault-Llorca F, Hewitt S, Thompson EA, Allison KH, Symmans WF, Bellizzi AM, Brogi E, Moore DA, Larsimont D, Dillon DA, Lazar A, Lien H, Goetz MP, Broeckx G, El Bairi K, Harbeck N, Cimino-Mathews A, Sotiriou C, Adams S, Liu SW, Loibl S, Chen IC, Lakhani SR, Juco JW, Denkert C, Blackley EF, Demaria S, Leon-Ferre R, Gluz O, Zardavas D, Emancipator K, Ely S, Loi S, Salgado R, Sanders M. The path to a better biomarker: application of a risk management framework for the implementation of PD-L1 and TILs as immuno-oncology biomarkers in breast cancer clinical trials and daily practice. J Pathol 2020; 250:667-684. [PMID: 32129476 DOI: 10.1002/path.5406] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 02/18/2020] [Indexed: 02/05/2023]
Abstract
Immune checkpoint inhibitor therapies targeting PD-1/PD-L1 are now the standard of care in oncology across several hematologic and solid tumor types, including triple negative breast cancer (TNBC). Patients with metastatic or locally advanced TNBC with PD-L1 expression on immune cells occupying ≥1% of tumor area demonstrated survival benefit with the addition of atezolizumab to nab-paclitaxel. However, concerns regarding variability between immunohistochemical PD-L1 assay performance and inter-reader reproducibility have been raised. High tumor-infiltrating lymphocytes (TILs) have also been associated with response to PD-1/PD-L1 inhibitors in patients with breast cancer (BC). TILs can be easily assessed on hematoxylin and eosin-stained slides and have shown reliable inter-reader reproducibility. As an established prognostic factor in early stage TNBC, TILs are soon anticipated to be reported in daily practice in many pathology laboratories worldwide. Because TILs and PD-L1 are parts of an immunological spectrum in BC, we propose the systematic implementation of combined PD-L1 and TIL analyses as a more comprehensive immuno-oncological biomarker for patient selection for PD-1/PD-L1 inhibition-based therapy in patients with BC. Although practical and regulatory considerations differ by jurisdiction, the pathology community has the responsibility to patients to implement assays that lead to optimal patient selection. We propose herewith a risk-management framework that may help mitigate the risks of suboptimal patient selection for immuno-therapeutic approaches in clinical trials and daily practice based on combined TILs/PD-L1 assessment in BC. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Elisabeth S Stovgaard
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Herlev, Denmark
| | - Luz F Sua
- Department of Pathology and Laboratory Medicine, Fundación Valle del Lili, and Faculty of Health Sciences, Universidad ICESI, Cali, Colombia
| | | | - Zuzana Kos
- Department of Pathology, BC Cancer Agency, Vancouver, Canada
| | - Jodi M Carter
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Stefan Michiels
- Biostatistics and Epidemiology Service, Centre de Recherche en Epidémiologie et Santé des Populations, Gustave Roussy, Université Paris-Sud, Villejuif, France
| | - John Le Quesne
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- MRC Toxicology Unit, University of Cambridge, Leicester, UK
| | - Torsten O Nielsen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | | | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Julien Adam
- Department of Pathology, Gustave Roussy, Grand Paris, France
| | - John Ms Bartlett
- Ontario Institute for Cancer Research, Toronto, Canada
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Edinburgh, UK
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Cecily Quinn
- Department of Pathology, St Vincent's University Hospital and University College Dublin, Dublin, Ireland
| | - Dieter Peeters
- HistoGeneX NV, Antwerp, Belgium
- AZ Sint-Maarten Hospital, Mechelen, Belgium
| | - Maria V Dieci
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
- Medical Oncology 2, Istituto Oncologico Veneto - IRCCS, Padova, Italy
| | | | - Ian Cree
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Akira I Hida
- Department of Pathology, Matsuyama Shimin Hospital, Matsuyama, Japan
| | - Justin M Balko
- Breast Cancer Research Program, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Harry R Haynes
- Department of Cellular Pathology, North Bristol NHS Trust, Bristol, UK
- Translational Health Sciences, University of Bristol, Bristol, UK
| | - Isabel Frahm
- Department of Pathology, Sanatorio Mater Dei, Buenos Aires, Argentina
| | - Gabriela Acosta-Haab
- Department of Pathology, Hospital de Oncología Maria Curie, Buenos Aires, Argentina
| | - Marcelo Balancin
- Department of Pathology, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Enrique Bellolio
- Department of Pathology, Universidad de La Frontera, Temuco, Chile
| | - Wentao Yang
- Department of Pathology, Fudan University Shanghai Cancer Centre, Shanghai, PR China
| | - Pawan Kirtani
- Department of Histopathology, Manipal Hospitals Dwarka, New Delhi, India
| | - Tomoharu Sugie
- Breast Surgery, Kansai Medical University Hospital, Hirakata, Japan
| | - Anna Ehinger
- Department of Clinical Genetics and Pathology, Skane University Hospital, Lund University, Lund, Sweden
| | - Carlos A Castaneda
- Department of Medical Oncology, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Marleen Kok
- Divisions of Medical Oncology, Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Heather McArthur
- Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kalliopi Siziopikou
- Department of Pathology, Breast Pathology Section, Northwestern University, Chicago, IL, USA
| | - Sunil Badve
- Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN, USA
| | - Susan Fineberg
- Department of Pathology, Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY, USA
| | - Allen Gown
- PhenoPath Laboratories, Seattle, WA, USA
| | - Giuseppe Viale
- Department of Pathology, Istituto Europeo di Oncologia IRCCS, Milan, Italy
- University of Milan, Milan, Italy
| | - Stuart J Schnitt
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Giancarlo Pruneri
- University of Milan, Milan, Italy
- Department of Pathology, IRCCS Fondazione Instituto Nazionale Tumori, Milan, Italy
| | - Frederique Penault-Llorca
- Department of Biology and Pathology, Centre Jean Perrin, Clermont Ferrand, France
- UMR INSERM 1240, Université Clermont Auvergne, Clermont Ferrand, France
| | - Stephen Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - William F Symmans
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew M Bellizzi
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David A Moore
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, and Department of Cellular Pathology, UCLH, London, UK
| | - Denis Larsimont
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Deborah A Dillon
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander Lazar
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Huangchun Lien
- Graduate Institute of Pathology, National Taiwan University, Taipei, Taiwan
| | | | - Glenn Broeckx
- Department of Pathology, University Hospital Antwerp, Edegem, Belgium
| | - Khalid El Bairi
- Cancer Biomarkers Working Group, Faculty of Medicine and Pharmacy, Mohamed Ist University, Oujda, Morocco
| | - Nadia Harbeck
- Breast Center, Department of OB&GYN and CCC (LMU), University of Munich, Munich, Germany
| | - Ashley Cimino-Mathews
- Department of Pathology and Oncology, The Johns Hopkins Hospital, Baltimore, MD, USA
| | - Christos Sotiriou
- Department of Medical Oncology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Sylvia Adams
- Perlmutter Cancer Center, New York University Medical School, New York, NY, USA
| | | | | | - I-Chun Chen
- Department of Medical Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Sunil R Lakhani
- The University of Queensland, Centre for Clinical Research, and Pathology Queensland, Royal Brisbane and Women's Hospital, Herston, Australia
| | - Jonathan W Juco
- Translational Medicine, Merck & Co, Inc, Kenilworth, NJ, USA
| | - Carsten Denkert
- Institute of Pathology, Universitätsklinikum Gießen und Marburg GmbH, Standort Marburg and Philipps-Universität Marburg, Marburg, Germany
| | - Elizabeth F Blackley
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Sandra Demaria
- Department of Radiation Oncology, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Oleg Gluz
- Johanniter GmbH - Evangelisches Krankenhaus Bethesda Mönchengladbach, West German Study Group, Mönchengladbach, Germany
| | | | | | - Scott Ely
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Sherene Loi
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Roberto Salgado
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
| | - Melinda Sanders
- Breast Cancer Research Program, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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Malmberg M, Larsson C, Vallon-Christersson J, Ehinger A, Hegardt C, Killander F, Ryden L, Saal LH, Loman N, Borg Å. Abstract P1-18-10: Preoperative treatment of HER2-positive breast cancer in South Sweden. A retrospective, comprehensive survey of neo-adjuvant treated HER2-positve breast cancer in the SCAN-B project 2010-2017. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p1-18-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Over the last few years, neoadjuvant therapy has become a standard of care in HER2-positive early breast cancer. This standard has recently been confirmed by the St. Gallen Consensus for stage II and III HER2-positive disease. In neoadjuvant treatment adding anti HER2 treatment almost doubled the pathological complete response (pCR) rate. Later studies have shown a better outcome for patients achieving a pCR compared with those with a non-pCR. The aim of this study is to present a comprehensive description of preoperative treatment in HER2-positive, according to ASCO and Swedish guidelines, breast cancer with detail treatment routines, choice of drugs and regimens as well as adherence to national guidelines and treatment changes over time.
Material: During the period October 2010 to December 2017 6572 patients with early breast cancer were diagnosed in the Skåne region of South Sweden and included in the SCAN-B project (Sweden Cancerome Analysis Network - Breast project, ClinicalTrials.gov identifier NCT02306096). The SCAN-B project is a population based study that during the period included 76.7% of all primary breast cancer patients in the catchment area. The majority of all tumors have been analyzed by NGS-based RNA sequencing, RNAseq.
Results: Of the 6572 patients 672 (10.2%) were HER2 positive and of these 101 (15%) were treated in a neoadjuvant setting with chemotherapy and HER2 directed antibodies. The proportion of HER2-positive patients receiving neoadjuvant treatment with trastuzumab increased from 9% in 2010 to 29% in 2017. Patient age was 27 to 89 years, median age 54 years. Pertuzumab was introduced in 2016 and in 2017 85% of patients received the combination of trastuzumab and pertuzumab. At diagnosis tumor stage T1, T2, T3 and T4d was 19%, 60%, 14% and 5% respectively and 50% were node negative at sentinel node biopsy pre treatment. Of tumors 52% were estrogen receptor positive (ie >10% stained nuclei). During the neoadjuvant treatment period 31 patients were hospitalized at median 2 times for toxicity and a total of medium 4.7 days. At surgery 62% had a mastectomy and 38% breast conserving surgery. Follow up time is median 3.9 years and overall survival 94%.
Conclusions: This retrospective analysis of neoadjuvant treated HER2-positive breast cancer patients shows a gradual increase of neoadjuvant treatment and a very fast implementation of pertuzumab when it became available in Sweden. Overall survival is high but the follow up time is short and the material to small to analyze subgroups. Data on tumor RNAseq will be presented.
Citation Format: Martin Malmberg, Christer Larsson, Johan Vallon-Christersson, Anna Ehinger, Cecilia Hegardt, Fredrika Killander, Lisa Ryden, Lao H. Saal, Niklas Loman, Åke Borg. Preoperative treatment of HER2-positive breast cancer in South Sweden. A retrospective, comprehensive survey of neo-adjuvant treated HER2-positve breast cancer in the SCAN-B project 2010-2017 [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P1-18-10.
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Affiliation(s)
| | | | | | - Anna Ehinger
- 4Department of Clinical Genetics and Pathology, Lund University Hospital, Sweden
| | - Cecilia Hegardt
- 5Lund University Cancer Center, Medicon Village, Lund University, Sweden
| | | | - Lisa Ryden
- 6Department of Surgery, Lund University Hospital, Sweden
| | - Lao H. Saal
- 5Lund University Cancer Center, Medicon Village, Lund University, Sweden
| | - Niklas Loman
- 1Dept. of Oncology, Lund University Hospital, Sweden
| | - Åke Borg
- 5Lund University Cancer Center, Medicon Village, Lund University, Sweden
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29
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Acs B, Leung SC, Kidwell KM, Arun I, Augulis R, Badve SS, Bai Y, Bane AL, Bartlett JM, Bayani J, Bigras G, Blank A, Borgquist S, Buikema H, Chang MC, Dietz RL, Dodson A, Ehinger A, Fineberg S, Focke CM, Gao D, Gown AM, Gutierrez C, Hartman J, Hugh JC, Kos Z, Lænkholm AV, Laurinavicius A, Levenson RM, Mahboubi-Ardakani R, Mastropasqua MG, Moriya T, Nofech-Mozes S, Osborne CK, Pantanowitz L, Penault-Llorca FM, Piper T, Quintayo MA, Rau TT, Reinhard S, Robertson S, Sakatani T, Salgado R, Spears M, Starczynski J, Sugie T, van der Vegt B, Viale G, Virk S, Zabaglo LA, Hayes DF, Dowsett M, Nielsen TO, Rimm DL. Abstract P5-02-01: Analytical validation and prognostic potential of an automated digital scoring protocol for Ki67: An International Ki67 Working Group study. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p5-02-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The nuclear proliferation biomarker Ki67 has multiple potential roles in breast cancer, including aiding decisions based on prognosis, but has unacceptable between-laboratory variability. Here we tested an open source and calibrated automated digital image analysis (DIA) platform to: (i) Assess inter-laboratory reproducibility of automated Ki67 measurement among 17 participating labs and compare those with standardized pathologist-based visual scoring. (ii) Investigate the comparability of Ki67 measurement across corresponding core biopsy and whole section cases. (iii) Test prognostic potential of the built Ki67 scoring algorithms on an independent cohort.
Methods: Two sets of 60 previously stained slides containing 30 core-cut biopsy and 30 corresponding whole tumor sections from 30 ER+ breast cancer cases were sent to 17 participating labs for automated assessment of average Ki67 expression. The blocks were centrally cut and stained for Ki67 using the Mib-1 antibody. The QuPath (open-source software) DIA platform was used to evaluate tumoral Ki67 expression. Calibration of the DIA method was performed in our previous study (Acs et al, Lab Invest 2019). A detailed guideline for building an automated Ki67 scoring algorithm was sent to the participating labs. Visual scoring of average Ki67 expression was performed by pathologists according to published standardized methods (Leung et al, NPJ Br Cancer 2016; Leung et al, Histopath 2019). Locked down DIA Ki67 scoring algorithms were applied to a validation cohort: 222 breast cancer cases from the Karolinska University Hospital in whole section format. Sufficient reproducibility to declare analytical validity was defined as an Intra Class Correlation (ICC) with lower limit of 95% credible interval (CI) >0.80. Markov Chain Monte Carlo routines for generalized linear mixed models were used to estimate ICCs and calculate corresponding CIs.
Results: The same-section ICC was 0.902 (CI: 0.852-0.949) across 17 labs using calibrated DIA platform on core biopsy slides and 0.845 (CI: 0.778-0.912) on whole sections. The different-section ICC across the 17 labs was 0.873 (CI: 0.806-0.932) scoring on core biopsy slides and 0.777 (CI: 0.670-0.874) on whole sections. The pathologist-based visual Ki67 scoring showed ICC of 0.860 for all comparisons, respectively (CI: 0.795-0.927). Similar to what was observed for visual Ki67 scoring, the DIA scores are higher for core biopsy slides compared to paired whole sections (p≤0.001; median difference: 5.31%; IQR: 11.50%). Ki67 scores of all locked down DIA algorithms correlates significantly (p≤0.023) with outcome on the validation cohort (observed hazard ratios range: 2.518-2.922).
Conclusions: Automated Ki67 evaluation using a calibrated, open-source DIA platform (QuPath) met the pre-specified criterion of success on core biopsies but not on whole sections in the multi-institutional setting. The systematic discrepancy between core biopsy and corresponding whole sections was likely due to pre-analytical factors (tissue handling, fixation) and intratumor heterogeneity. We found that different algorithms built according to calibrated DIA methods had similar prognostic potential. Assessment of clinical utility is planned.
Citation Format: Balazs Acs, Samuel C.Y. Leung, Kelley M. Kidwell, Indu Arun, Renaldas Augulis, Sunil S. Badve, Yalai Bai, Anita L. Bane, John M.S. Bartlett, Jane Bayani, Gilbert Bigras, Annika Blank, Signe Borgquist, Henk Buikema, Martin C. Chang, Robin L. Dietz, Andrew Dodson, Anna Ehinger, Susan Fineberg, Cornelia M. Focke, Dongxia Gao, Allen M. Gown, Carolina Gutierrez, Johan Hartman, Judith C. Hugh, Zuzana Kos, Anne-Vibeke Lænkholm, Arvydas Laurinavicius, Richard M. Levenson, Rustin Mahboubi-Ardakani, Mauro G. Mastropasqua, Takuya Moriya, Sharon Nofech-Mozes, C. Kent Osborne, Liron Pantanowitz, Frédérique M. Penault-Llorca, Tammy Piper, Mary Anne Quintayo, Tilman T. Rau, Stefan Reinhard, Stephanie Robertson, Takashi Sakatani, Roberto Salgado, Melanie Spears, Jane Starczynski, Tomoharu Sugie, Bert van der Vegt, Giuseppe Viale, Shakeel Virk, Lila A. Zabaglo, Daniel F. Hayes, Mitch Dowsett, Torsten O. Nielsen, David L. Rimm, International Ki67 in Breast Cancer Working Group, BIG-NABCG. Analytical validation and prognostic potential of an automated digital scoring protocol for Ki67: An International Ki67 Working Group study [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-02-01.
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Affiliation(s)
- Balazs Acs
- 1Department of Pathology, Yale University School of Medicine, New Haven, CT
| | | | - Kelley M. Kidwell
- 3Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Indu Arun
- 4Tata Medical Center, Kolkata, India
| | - Renaldas Augulis
- 5Vilnius University Faculty of Medicine and National Center of Pathology, Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Sunil S. Badve
- 6Indiana University Simon Cancer Center, Indianapolis, IN
| | - Yalai Bai
- 1Department of Pathology, Yale University School of Medicine, New Haven, CT
| | - Anita L. Bane
- 7Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada
| | | | - Jane Bayani
- 8Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gilbert Bigras
- 9Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Annika Blank
- 10Universität Bern Institut für Pathologie, Murtenstrasse, Switzerland
| | | | - Henk Buikema
- 12University Medical Center Groningen, Groningen, Netherlands
| | - Martin C. Chang
- 13Department of Pathology & Laboratory Medicine, University of Vermont Medical Center, Burlington, VT
| | - Robin L. Dietz
- 14Department of Pathology, University of Pittsburgh, Pittsburgh, PA
| | - Andrew Dodson
- 15UK NEQAS for Immunocytochemistry and In-Situ Hybridisation, London, United Kingdom
| | | | - Susan Fineberg
- 16Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY
| | | | - Dongxia Gao
- 2University of British Columbia, Vancouver, BC, Canada
| | | | - Carolina Gutierrez
- 19Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | | | | | - Zuzana Kos
- 22University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada
| | - Anne-Vibeke Lænkholm
- 23Department of Surgical Pathology, Zealand University Hospital, Slagelse, Denmark
| | - Arvydas Laurinavicius
- 5Vilnius University Faculty of Medicine and National Center of Pathology, Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Richard M. Levenson
- 24Department of Medical Pathology and Laboratory Medicine, University of California Davis Medical Center, Sacramento, CA
| | - Rustin Mahboubi-Ardakani
- 24Department of Medical Pathology and Laboratory Medicine, University of California Davis Medical Center, Sacramento, CA
| | | | | | - Sharon Nofech-Mozes
- 27University of Toronto Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - C. Kent Osborne
- 19Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | | | | | - Tammy Piper
- 29Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, United Kingdom
| | | | - Tilman T. Rau
- 10Universität Bern Institut für Pathologie, Murtenstrasse, Switzerland
| | - Stefan Reinhard
- 10Universität Bern Institut für Pathologie, Murtenstrasse, Switzerland
| | | | | | | | - Melanie Spears
- 8Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jane Starczynski
- 32Birmingham Heart of England, National Health Service, Birmingham, United Kingdom
| | | | | | | | - Shakeel Virk
- 35Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | | | | | - Mitch Dowsett
- 36The Institute of Cancer Research, London, United Kingdom
| | | | - David L. Rimm
- 1Department of Pathology, Yale University School of Medicine, New Haven, CT
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Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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Jögi A, Ehinger A, Hartman L, Alkner S. Expression of HIF-1α is related to a poor prognosis and tamoxifen resistance in contralateral breast cancer. PLoS One 2019; 14:e0226150. [PMID: 31821370 PMCID: PMC6903737 DOI: 10.1371/journal.pone.0226150] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/20/2019] [Indexed: 01/13/2023] Open
Abstract
Background Adjuvant endocrine treatment improves survival after estrogen receptor (ER) positive breast cancer. Recurrences occur, and most patients with metastatic breast cancer develop treatment resistance and incurable disease. An influential factor in relation to endocrine treatment resistance is tumor hypoxia and the hypoxia inducible transcription factors (HIFs). Poor perfusion makes tumors hypoxic and induces the HIFs, which promote cell survival. We previously showed that hypoxic breast cancer cells are tamoxifen-resistant, and that HIF-inhibition restored tamoxifen-sensitivity. We found that HIF-induced tamoxifen-resistance involve cross-talk with epithelial growth factor receptor (EGFR), which itself is linked to tamoxifen resistance. Contralateral breast cancer (CBC), i.e. development of a second breast cancer in the contralateral breast despite adjuvant tamoxifen treatment is in essence a human in vivo-model for tamoxifen-resistance that we explore here to find molecular pathways of tamoxifen-resistance. Methods We constructed a tissue-microarray including tumor-tissue from a large well-defined cohort of CBC-patients, a proportion of which got their second breast cancer despite ongoing adjuvant therapy. Using immunohistochemistry >500 patients were evaluable for HIF-1α and EGFR in both tumors, and correlations to treatment, patient outcome, prognostic and predictive factors were analyzed. Results We found an increased proportion of HIF-1α-positive tumors in tamoxifen-resistant (CBC during adjuvant tamoxifen) compared to naïve tumors (CBC without prior tamoxifen). Tumor HIF-1α-positivity correlated to increased breast cancer mortality, and negative prognostic factors including low age at diagnosis and ER-negativity. There was a covariance of HIF-1α- and EGFR-expression and also EGFR-expression correlated to poor prognosis. Conclusions The increased percentage of HIF-1α-positive tumors formed during adjuvant tamoxifen suggests a role for HIF-1α in escaping tamoxifen’s restraining effects on breast cancer. Implicating a potential benefit of HIF-inhibitors in targeting breast cancers resistant to endocrine therapy.
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Affiliation(s)
- Annika Jögi
- Department of Laboratory Medicine, Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden
- * E-mail:
| | - Anna Ehinger
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund, Sweden
- Lund University, Department of Clinical Genetics and Pathology, Medical Service, Regional Laboratories, Lund, Sweden
| | - Linda Hartman
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund, Sweden
| | - Sara Alkner
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund, Sweden
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32
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Lundgren C, Bendahl PO, Borg Å, Ehinger A, Hegardt C, Larsson C, Loman N, Malmberg M, Olofsson H, Saal LH, Sjöblom T, Lindman H, Klintman M, Häkkinen J, Vallon-Christersson J, Fernö M, Rydén L, Ekholm M. Agreement between molecular subtyping and surrogate subtype classification: a contemporary population-based study of ER-positive/HER2-negative primary breast cancer. Breast Cancer Res Treat 2019; 178:459-467. [PMID: 31432367 PMCID: PMC6797629 DOI: 10.1007/s10549-019-05378-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/24/2019] [Indexed: 12/31/2022]
Abstract
PURPOSE Oestrogen receptor-positive (ER+) and human epidermal receptor 2-negative (HER2-) breast cancers are classified as Luminal A or B based on gene expression, but immunohistochemical markers are used for surrogate subtyping. The aims of this study were to examine the agreement between molecular subtyping (MS) and surrogate subtyping and to identify subgroups consisting mainly of Luminal A or B tumours. METHODS The cohort consisted of 2063 patients diagnosed between 2013-2017, with primary ER+/HER2- breast cancer, analysed by RNA sequencing. Surrogate subtyping was performed according to three algorithms (St. Gallen 2013, Maisonneuve and our proposed Grade-based classification). Agreement (%) and kappa statistics (κ) were used as concordance measures and ROC analysis for luminal distinction. Ki67, progesterone receptor (PR) and histological grade (HG) were further investigated as surrogate markers. RESULTS The agreement rates between the MS and St. Gallen 2013, Maisonneuve and Grade-based classifications were 62% (κ = 0.30), 66% (κ = 0.35) and 70% (κ = 0.41), respectively. PR did not contribute to distinguishing Luminal A from B tumours (auROC = 0.56). By classifying HG1-2 tumours as Luminal A-like and HG3 as Luminal B-like, agreement with MS was 80% (κ = 0.46). Moreover, by combining HG and Ki67 status, a large subgroup of patients (51% of the cohort) having > 90% Luminal A tumours could be identified. CONCLUSIONS Agreement between MS and surrogate classifications was generally poor. However, a post hoc analysis showed that a combination of HG and Ki67 could identify patients very likely to have Luminal A tumours according to MS.
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Affiliation(s)
- Christine Lundgren
- Department of Oncology, Jönköping, Region Jönköping County, and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden.
| | - Pär-Ola Bendahl
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Åke Borg
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Anna Ehinger
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Cecilia Hegardt
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Christer Larsson
- Department of Laboratory Medicine Lund, Division of Translational Cancer Research, Lund University, Lund, Sweden
| | - Niklas Loman
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Martin Malmberg
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Helena Olofsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lao H Saal
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Henrik Lindman
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Marie Klintman
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Jari Häkkinen
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Johan Vallon-Christersson
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Mårten Fernö
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Lisa Rydén
- Department of Clinical Sciences Lund, Division of Surgery, Lund University, Lund, Sweden
| | - Maria Ekholm
- Department of Oncology, Jönköping, Region Jönköping County, and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
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33
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Staaf J, Glodzik D, Bosch A, Vallon-Christersson J, Reuterswärd C, Häkkinen J, Degasperi A, Amarante TD, Saal LH, Hegardt C, Stobart H, Ehinger A, Larsson C, Rydén L, Loman N, Malmberg M, Kvist A, Ehrencrona H, Davies HR, Borg Å, Nik-Zainal S. Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study. Nat Med 2019; 25:1526-1533. [PMID: 31570822 PMCID: PMC6859071 DOI: 10.1038/s41591-019-0582-4] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/15/2019] [Indexed: 01/12/2023]
Abstract
Whole-genome sequencing (WGS) brings comprehensive insights to cancer genome interpretation. To explore the clinical value of WGS, we sequenced 254 triple-negative breast cancers (TNBCs) for which associated treatment and outcome data were collected between 2010 and 2015 via the population-based Sweden Cancerome Analysis Network-Breast (SCAN-B) project (ClinicalTrials.gov ID:NCT02306096). Applying the HRDetect mutational-signature-based algorithm to classify tumors, 59% were predicted to have homologous-recombination-repair deficiency (HRDetect-high): 67% explained by germline/somatic mutations of BRCA1/BRCA2, BRCA1 promoter hypermethylation, RAD51C hypermethylation or biallelic loss of PALB2. A novel mechanism of BRCA1 abrogation was discovered via germline SINE-VNTR-Alu retrotransposition. HRDetect provided independent prognostic information, with HRDetect-high patients having better outcome on adjuvant chemotherapy for invasive disease-free survival (hazard ratio (HR) = 0.42; 95% confidence interval (CI) = 0.2-0.87) and distant relapse-free interval (HR = 0.31, CI = 0.13-0.76) compared to HRDetect-low, regardless of whether a genetic/epigenetic cause was identified. HRDetect-intermediate, some possessing potentially targetable biological abnormalities, had the poorest outcomes. HRDetect-low cancers also had inadequate outcomes: ~4.7% were mismatch-repair-deficient (another targetable defect, not typically sought) and they were enriched for (but not restricted to) PIK3CA/AKT1 pathway abnormalities. New treatment options need to be considered for now-discernible HRDetect-intermediate and HRDetect-low categories. This population-based study advocates for WGS of TNBC to better inform trial stratification and improve clinical decision-making.
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Affiliation(s)
- Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden.
| | - Dominik Glodzik
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ana Bosch
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Johan Vallon-Christersson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Christel Reuterswärd
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Jari Häkkinen
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Andrea Degasperi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Tauanne Dias Amarante
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Lao H Saal
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Cecilia Hegardt
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | | | - Anna Ehinger
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Department of Clinical Genetics and Pathology, Department of Laboratory Medicine, Office for Medical Services, Lund, Sweden
| | - Christer Larsson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Lisa Rydén
- Division of Surgery, Department of Clinical Sciences, Lund University, Lund, Sweden
- Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Niklas Loman
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Martin Malmberg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Hans Ehrencrona
- Department of Clinical Genetics and Pathology, Department of Laboratory Medicine, Office for Medical Services, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Helen R Davies
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, Cambridge, UK
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, Cambridge, UK.
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK.
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34
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Vallon-Christersson J, Häkkinen J, Hegardt C, Saal LH, Larsson C, Ehinger A, Lindman H, Olofsson H, Sjöblom T, Wärnberg F, Ryden L, Loman N, Malmberg M, Borg Å, Staaf J. Cross comparison and prognostic assessment of breast cancer multigene signatures in a large population-based contemporary clinical series. Sci Rep 2019; 9:12184. [PMID: 31434940 PMCID: PMC6704148 DOI: 10.1038/s41598-019-48570-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/08/2019] [Indexed: 12/23/2022] Open
Abstract
Multigene expression signatures provide a molecular subdivision of early breast cancer associated with patient outcome. A gap remains in the validation of such signatures in clinical treatment groups of patients within population-based cohorts of unselected primary breast cancer representing contemporary disease stages and current treatments. A cohort of 3520 resectable breast cancers with RNA sequencing data included in the population-based SCAN-B initiative (ClinicalTrials.gov ID NCT02306096) were selected from a healthcare background population of 8587 patients diagnosed within the years 2010-2015. RNA profiles were classified according to 19 reported gene signatures including both gene expression subtypes (e.g. PAM50, IC10, CIT) and risk predictors (e.g. Oncotype DX, 70-gene, ROR). Classifications were analyzed in nine adjuvant clinical assessment groups: TNBC-ACT (adjuvant chemotherapy, n = 239), TNBC-untreated (n = 82), HER2+/ER- with anti-HER2+ ACT treatment (n = 110), HER2+/ER+ with anti-HER2 + ACT + endocrine treatment (n = 239), ER+/HER2-/LN- with endocrine treatment (n = 1113), ER+/HER2-/LN- with endocrine + ACT treatment (n = 243), ER+/HER2-/LN+ with endocrine treatment (n = 423), ER+/HER2-/LN+ with endocrine + ACT treatment (n = 433), and ER+/HER2-/LN- untreated (n = 200). Gene signature classification (e.g., proportion low-, high-risk) was generally well aligned with stratification based on current immunohistochemistry-based clinical practice. Most signatures did not provide any further risk stratification in TNBC and HER2+/ER- disease. Risk classifier agreement (low-, medium/intermediate-, high-risk groups) in ER+ assessment groups was on average 50-60% with occasional pair-wise comparisons having <30% agreement. Disregarding the intermediate-risk groups, the exact agreement between low- and high-risk groups was on average ~80-95%, for risk prediction signatures across all assessment groups. Outcome analyses were restricted to assessment groups of TNBC-ACT and endocrine treated ER+/HER2-/LN- and ER+/HER2-/LN+ cases. For ER+/HER2- disease, gene signatures appear to contribute additional prognostic value even at a relatively short follow-up time. Less apparent prognostic value was observed in the other groups for the tested signatures. The current study supports the usage of gene expression signatures in specific clinical treatment groups within population-based breast cancer. It also stresses the need of further development to reach higher consensus in individual patient classifications, especially for intermediate-risk patients, and the targeting of patients where current gene signatures and prognostic variables provide little support in clinical decision-making.
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Affiliation(s)
- Johan Vallon-Christersson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Jari Häkkinen
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Cecilia Hegardt
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Lao H Saal
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Christer Larsson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, SE 22381, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
- Division of Clinical Genetics and Pathology, Department of Laboratory Medicine, SE 22185, Lund, Sweden
| | - Henrik Lindman
- Department of Immunology, Genetics and Pathology, Uppsala University, SE 75185, Uppsala, Sweden
| | - Helena Olofsson
- Department of Immunology, Genetics and Pathology, Uppsala University, SE 75185, Uppsala, Sweden
- Department of Clinical Pathology, Uppsala University Hospital, SE 75185, Uppsala, Sweden
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Uppsala University, SE 75185, Uppsala, Sweden
| | - Fredrik Wärnberg
- Department of Surgical Sciences, Uppsala University, SE 75185, Uppsala, Sweden
| | - Lisa Ryden
- Division of Surgery, Department of Clinical Sciences, Lund University, SE 22185, Lund, Sweden
| | - Niklas Loman
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
- Department of Hematology, Oncology and Radiation physics, Skåne University Hospital, SE 22185, Lund, Sweden
| | - Martin Malmberg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
- Department of Hematology, Oncology and Radiation physics, Skåne University Hospital, SE 22185, Lund, Sweden
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden.
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35
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Dihge L, Vallon-Christersson J, Hegardt C, Saal LH, Häkkinen J, Larsson C, Ehinger A, Loman N, Malmberg M, Bendahl PO, Borg Å, Staaf J, Rydén L. Prediction of Lymph Node Metastasis in Breast Cancer by Gene Expression and Clinicopathological Models: Development and Validation within a Population-Based Cohort. Clin Cancer Res 2019; 25:6368-6381. [PMID: 31340938 DOI: 10.1158/1078-0432.ccr-19-0075] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 05/24/2019] [Accepted: 07/22/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE More than 70% of patients with breast cancer present with node-negative disease, yet all undergo surgical axillary staging. We aimed to define predictors of nodal metastasis using clinicopathological characteristics (CLINICAL), gene expression data (GEX), and mixed features (MIXED) and to identify patients at low risk of metastasis who might be spared sentinel lymph node biopsy (SLNB).Experimental Design: Breast tumors (n = 3,023) from the population-based Sweden Cancerome Analysis Network-Breast initiative were profiled by RNA sequencing and linked to clinicopathologic characteristics. Seven machine-learning models present the discriminative ability of N0/N+ in development (n = 2,278) and independent validation cohorts (n = 745) stratified as ER+HER2-, HER2+, and TNBC. Possible SLNB reduction rates are proposed by applying CLINICAL and MIXED predictors. RESULTS In the validation cohort, the MIXED predictor showed the highest area under ROC curves to assess nodal metastasis; AUC = 0.72. For the subgroups, the AUCs for MIXED, CLINICAL, and GEX predictors ranged from 0.66 to 0.72, 0.65 to 0.73, and 0.58 to 0.67, respectively. Enriched proliferation metagene and luminal B features were noticed in node-positive ER+HER2- and HER2+ tumors, while upregulated basal-like features were observed in node-negative TNBC tumors. The SLNB reduction rates in patients with ER+HER2- tumors were 6% to 7% higher for the MIXED predictor compared with the CLINICAL predictor accepting false negative rates of 5% to 10%. CONCLUSIONS Although CLINICAL and MIXED predictors of nodal metastasis had comparable accuracy, the MIXED predictor identified more node-negative patients. This translational approach holds promise for development of classifiers to reduce the rates of SLNB for patients at low risk of nodal involvement.
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Affiliation(s)
- Looket Dihge
- Department of Clinical Sciences Lund, Division of Surgery, Lund University, Lund, Sweden. .,Department of Plastic and Reconstructive Surgery, Skåne University Hospital, Malmö, Sweden
| | - Johan Vallon-Christersson
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Cecilia Hegardt
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Lao H Saal
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Jari Häkkinen
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Christer Larsson
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, Lund, Sweden
| | - Anna Ehinger
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Niklas Loman
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Martin Malmberg
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Pär-Ola Bendahl
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Åke Borg
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Johan Staaf
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Lisa Rydén
- Department of Clinical Sciences Lund, Division of Surgery, Lund University, Lund, Sweden.,Department of Surgery, Skåne University Hospital, Lund, Sweden
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36
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Leung SCY, Nielsen TO, Zabaglo LA, Arun I, Badve SS, Bane AL, Bartlett JMS, Borgquist S, Chang MC, Dodson A, Ehinger A, Fineberg S, Focke CM, Gao D, Gown AM, Gutierrez C, Hugh JC, Kos Z, Laenkholm AV, Mastropasqua MG, Moriya T, Nofech-Mozes S, Osborne CK, Penault-Llorca FM, Piper T, Sakatani T, Salgado R, Starczynski J, Sugie T, van der Vegt B, Viale G, Hayes DF, McShane LM, Dowsett M. Analytical validation of a standardised scoring protocol for Ki67 immunohistochemistry on breast cancer excision whole sections: an international multicentre collaboration. Histopathology 2019; 75:225-235. [PMID: 31017314 DOI: 10.1111/his.13880] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/19/2019] [Indexed: 01/12/2023]
Abstract
AIMS The nuclear proliferation marker Ki67 assayed by immunohistochemistry has multiple potential uses in breast cancer, but an unacceptable level of interlaboratory variability has hampered its clinical utility. The International Ki67 in Breast Cancer Working Group has undertaken a systematic programme to determine whether Ki67 measurement can be analytically validated and standardised among laboratories. This study addresses whether acceptable scoring reproducibility can be achieved on excision whole sections. METHODS AND RESULTS Adjacent sections from 30 primary ER+ breast cancers were centrally stained for Ki67 and sections were circulated among 23 pathologists in 12 countries. All pathologists scored Ki67 by two methods: (i) global: four fields of 100 tumour cells each were selected to reflect observed heterogeneity in nuclear staining; (ii) hot-spot: the field with highest apparent Ki67 index was selected and up to 500 cells scored. The intraclass correlation coefficient (ICC) for the global method [confidence interval (CI) = 0.87; 95% CI = 0.799-0.93] marginally met the prespecified success criterion (lower 95% CI ≥ 0.8), while the ICC for the hot-spot method (0.83; 95% CI = 0.74-0.90) did not. Visually, interobserver concordance in location of selected hot-spots varies between cases. The median times for scoring were 9 and 6 min for global and hot-spot methods, respectively. CONCLUSIONS The global scoring method demonstrates adequate reproducibility to warrant next steps towards evaluation for technical and clinical validity in appropriate cohorts of cases. The time taken for scoring by either method is practical using counting software we are making publicly available. Establishment of external quality assessment schemes is likely to improve the reproducibility between laboratories further.
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Affiliation(s)
| | | | | | | | - Sunil S Badve
- Indiana University Simon Cancer Center, Indianapolis, IN, USA
| | - Anita L Bane
- Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada
| | - John M S Bartlett
- Ontario Institute for Cancer Research, Toronto, ON, Canada.,Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, UK
| | - Signe Borgquist
- Division of Oncology and Pathology, Department of Clinical Science, Lund University, Lund, Sweden
| | - Martin C Chang
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, USA
| | - Andrew Dodson
- Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, UK
| | - Anna Ehinger
- Department of Clinical Genetics and Pathology, Skane University Hospital, Lund University, Lund, Sweden
| | - Susan Fineberg
- Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Dongxia Gao
- University of British Columbia, Vancouver, BC, Canada
| | | | - Carolina Gutierrez
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Zuzana Kos
- University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada
| | | | | | | | - Sharon Nofech-Mozes
- University of Toronto Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - C Kent Osborne
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Tammy Piper
- Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, UK
| | | | - Roberto Salgado
- Department of Pathology, GZA-ZNA, Antwerp, Belgium.,Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Jane Starczynski
- Birmingham Heart of England, National Health Service, Birmingham, UK
| | | | | | - Giuseppe Viale
- European Institute of Oncology, Milan, Italy.,University of Milan, Milan, Italy
| | - Daniel F Hayes
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
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37
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Søkilde R, Persson H, Ehinger A, Pirona AC, Fernö M, Hegardt C, Larsson C, Loman N, Malmberg M, Rydén L, Saal L, Borg Å, Vallon-Christerson J, Rovira C. Refinement of breast cancer molecular classification by miRNA expression profiles. BMC Genomics 2019; 20:503. [PMID: 31208318 PMCID: PMC6580620 DOI: 10.1186/s12864-019-5887-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/06/2019] [Indexed: 02/06/2023] Open
Abstract
Background Accurate classification of breast cancer using gene expression profiles has contributed to a better understanding of the biological mechanisms behind the disease and has paved the way for better prognostication and treatment prediction. Results We found that miRNA profiles largely recapitulate intrinsic subtypes. In the case of HER2-enriched tumors a small set of miRNAs including the HER2-encoded mir-4728 identifies the group with very high specificity. We also identified differential expression of the miR-99a/let-7c/miR-125b miRNA cluster as a marker for separation of the Luminal A and B subtypes. High expression of this miRNA cluster is linked to better overall survival among patients with Luminal A tumors. Correlation between the miRNA cluster and their precursor LINC00478 is highly significant suggesting that its expression could help improve the accuracy of present day’s signatures. Conclusions We show here that miRNA expression can be translated into mRNA profiles and that the inclusion of miRNA information facilitates the molecular diagnosis of specific subtypes, in particular the clinically relevant sub-classification of luminal tumors. Electronic supplementary material The online version of this article (10.1186/s12864-019-5887-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rolf Søkilde
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden
| | - Helena Persson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden
| | - Anna Ehinger
- Clinical Pathology, Laboratory Medicine, Skåne University Hospital, Lund, Sweden
| | - Anna Chiara Pirona
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden.,German Cancer Research Center DKFZ, Division of Functional Genome Analysis, Heidelberg, Germany
| | - Mårten Fernö
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden
| | - Cecilia Hegardt
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden
| | - Christer Larsson
- Division of Translational Cancer Research, Lund University, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden
| | - Niklas Loman
- Division of Oncology, Skåne University Hospital, Lund, Sweden
| | - Martin Malmberg
- Division of Oncology, Skåne University Hospital, Lund, Sweden
| | - Lisa Rydén
- Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Lao Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden
| | - Johan Vallon-Christerson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden
| | - Carlos Rovira
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Scheelevägen 2, 223 81, Lund, Sweden. .,BioCARE, Strategic Cancer Research Program, Lund, Sweden.
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Rydén L, Loman N, Larsson C, Hegardt C, Vallon-Christersson J, Malmberg M, Lindman H, Ehinger A, Saal LH, Borg Å. Minimizing inequality in access to precision medicine in breast cancer by real-time population-based molecular analysis in the SCAN-B initiative. Br J Surg 2018; 105:e158-e168. [PMID: 29341157 PMCID: PMC5817401 DOI: 10.1002/bjs.10741] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 09/30/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND Selection of systemic therapy for primary breast cancer is currently based on clinical biomarkers along with stage. Novel genomic tests are continuously being introduced as more precise tools for guidance of therapy, although they are often developed for specific patient subgroups. The Sweden Cancerome Analysis Network - Breast (SCAN-B) initiative aims to include all patients with breast cancer for tumour genomic analysis, and to deliver molecular subtype and mutational data back to the treating physician. METHODS An infrastructure for collection of blood and fresh tumour tissue from all patients newly diagnosed with breast cancer was set up in 2010, initially including seven hospitals within the southern Sweden regional catchment area, which has 1.8 million inhabitants. Inclusion of patients was implemented into routine clinical care, with collection of tumour tissue at local pathology departments for transport to the central laboratory, where routines for rapid sample processing, RNA sequencing and biomarker reporting were developed. RESULTS More than 10 000 patients from nine hospitals have currently consented to inclusion in SCAN-B with high (90 per cent) inclusion rates from both university and secondary hospitals. Tumour samples and successful RNA sequencing are being obtained from more than 70 per cent of patients, showing excellent representation compared with the national quality registry as a truly population-based cohort. Molecular biomarker reports can be delivered to multidisciplinary conferences within 1 week. CONCLUSION Population-based collection of fresh tumour tissue is feasible given a decisive joint effort between academia and collaborative healthcare groups, and with governmental support. An infrastructure for genomic analysis and prompt data output paves the way for novel systemic therapy for patients from all hospitals, irrespective of size and location.
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Affiliation(s)
- L Rydén
- Department of Clinical Sciences Lund, Surgery, Lund University, Lund, Sweden.,Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - N Loman
- Department of Clinical Sciences Lund, Oncology and Pathology, Lund University, Lund, Sweden.,Department of Haematology, Oncology and Radiotherapy, Skåne University Hospital, Lund, Sweden
| | - C Larsson
- Department of Laboratory Medicine Lund, Translational Cancer Research, Lund University, Lund, Sweden
| | - C Hegardt
- Department of Clinical Sciences Lund, Oncology and Pathology, Lund University, Lund, Sweden
| | - J Vallon-Christersson
- Department of Clinical Sciences Lund, Oncology and Pathology, Lund University, Lund, Sweden
| | - M Malmberg
- Department of Clinical Sciences Lund, Oncology and Pathology, Lund University, Lund, Sweden.,Department of Haematology, Oncology and Radiotherapy, Skåne University Hospital, Lund, Sweden
| | - H Lindman
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - A Ehinger
- Department of Clinical Sciences Lund, Oncology and Pathology, Lund University, Lund, Sweden.,Department of Pathology and Cytology, Medicinsk Service, Skåne University Hospital, Lund, Sweden
| | - L H Saal
- Department of Clinical Sciences Lund, Oncology and Pathology, Lund University, Lund, Sweden
| | - Å Borg
- Department of Clinical Sciences Lund, Oncology and Pathology, Lund University, Lund, Sweden
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Ehinger A, Bendahl PO, Rydén L, Fernö M, Alkner S. Stability of oestrogen and progesterone receptor antigenicity in formalin-fixed paraffin-embedded breast cancer tissue over time. APMIS 2018; 126:746-754. [PMID: 30160021 DOI: 10.1111/apm.12884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/05/2018] [Indexed: 01/02/2023]
Abstract
Use of archived formalin-fixed paraffin-embedded (FFPE) tissue is a standard method for evaluation of proposed prognostic and predictive tumour markers. However, little is known of the preservation of biomarker expression in old FFPE tumour blocks. We investigate the quality of immunohistochemical (IHC) oestrogen (ER) and progesterone receptor (PR) evaluation in FFPE tissue over time (1978-2000) using a large breast cancer tissue microarray (N = 573) with access to receptor analyses in cytosol (CYT) at diagnosis, coexpression of other biomarkers and follow-up data. We found a good correlation between ER analysed with CYT at diagnosis and ER analysed with IHC in archived FFPE tissue from the same tumour. ER evaluation did not seem to be affected by tissue storage time. Nor was there any time-dependent difference in ERIHC correlation with other biomarkers (HER2, Ki67) or survival. Discordant cases were more often classified as ER-positive with IHC than with CYT. For PR, however, we found an increased correlation between methods in more recent time periods. This may possibly be explained by more reliable PRIHC results in newer samples, although other explanations may also contribute. Our results indicate stable ER expression in FFPE tissue archived for up to 40 years.
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Affiliation(s)
- Anna Ehinger
- Faculty of Medicine, Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Pär-Ola Bendahl
- Faculty of Medicine, Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Lisa Rydén
- Division of Surgery, Department of Clinical Sciences Lund, Skane University Hospital, Lund University, Lund, Sweden
| | - Mårten Fernö
- Faculty of Medicine, Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Sara Alkner
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Skane University Hospital, Lund University, Lund, Sweden
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Brueffer C, Vallon-Christersson J, Grabau D, Ehinger A, Häkkinen J, Hegardt C, Malina J, Chen Y, Bendahl PO, Manjer J, Malmberg M, Larsson C, Loman N, Rydén L, Borg Å, Saal LH. Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network-Breast Initiative. JCO Precis Oncol 2018; 2:1700135. [PMID: 32913985 PMCID: PMC7446376 DOI: 10.1200/po.17.00135] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Purpose In early breast cancer (BC), five conventional biomarkers-estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG)-are used to determine prognosis and treatment. We aimed to develop classifiers for these biomarkers that were based on tumor mRNA sequencing (RNA-seq), compare classification performance, and test whether such predictors could add value for risk stratification. Methods In total, 3,678 patients with BC were studied. For 405 tumors, a comprehensive multi-rater histopathologic evaluation was performed. Using RNA-seq data, single-gene classifiers and multigene classifiers (MGCs) were trained on consensus histopathology labels. Trained classifiers were tested on a prospective population-based series of 3,273 BCs that included a median follow-up of 52 months (Sweden Cancerome Analysis Network-Breast [SCAN-B], ClinicalTrials.gov identifier: NCT02306096), and results were evaluated by agreement statistics and Kaplan-Meier and Cox survival analyses. Results Pathologist concordance was high for ER, PgR, and HER2 (average κ, 0.920, 0.891, and 0.899, respectively) but moderate for Ki67 and NHG (average κ, 0.734 and 0.581). Concordance between RNA-seq classifiers and histopathology for the independent cohort of 3,273 was similar to interpathologist concordance. Patients with discordant classifications, predicted as hormone responsive by histopathology but non-hormone responsive by MGC, had significantly inferior overall survival compared with patients who had concordant results. This extended to patients who received no adjuvant therapy (hazard ratio [HR], 3.19; 95% CI, 1.19 to 8.57), or endocrine therapy alone (HR, 2.64; 95% CI, 1.55 to 4.51). For cases identified as hormone responsive by histopathology and who received endocrine therapy alone, the MGC hormone-responsive classifier remained significant after multivariable adjustment (HR, 2.45; 95% CI, 1.39 to 4.34). Conclusion Classification error rates for RNA-seq-based classifiers for the five key BC biomarkers generally were equivalent to conventional histopathology. However, RNA-seq classifiers provided added clinical value in particular for tumors determined by histopathology to be hormone responsive but by RNA-seq to be hormone insensitive.
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Affiliation(s)
- Christian Brueffer
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Johan Vallon-Christersson
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Dorthe Grabau
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Anna Ehinger
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Jari Häkkinen
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Cecilia Hegardt
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Janne Malina
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Yilun Chen
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Pär-Ola Bendahl
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Jonas Manjer
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Martin Malmberg
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Christer Larsson
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Niklas Loman
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Lisa Rydén
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Åke Borg
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
| | - Lao H Saal
- , , , , , , , , , , , and , Lund University, Lund; , , , , and , Skåne University Hospital Lund, Lund; , Blekinge County Hospital, Karlskrona; and and , Skåne University Hospital Malmö, Malmö, Sweden
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Morgan G, Larsson C, Tahin B, Vallon-Christersson J, Häkkinen J, Ehinger A, Malmberg M, Hegardt C, Borg Å, Rydén L, Saal LH, Hedenfalk I, Loman N. Abstract P3-02-02: Concordance between immunohistochemical and gene-expression based subtyping of early breast cancer using core needle biopsies and surgical specimens - experices from SCAN-B. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p3-02-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Preoperative chemotherapy in early breast cancer increases the rate of breast preservation and provides prognostic information. Treatment decisions in these cases rely on biomarker assessments and subtyping from tissue acquired through core needle biopsies. Tumor heterogeneity and representativity are pit-falls when limited tissue is available. Biomarker expression may change considerably as a result of preoperative chemotherapy, and in a subset of cases a complete pathological response at time of surgery may even preclude any further assessment. Therefore, the reliability and reproducibility of biomarkers in base-line core biopsies are of utmost importance for patients treated with preoperative chemotherapy.
Material and Methods: In an ongoing population-based study of early breast cancer, the SCAN-B (NCT02306096), patients were identified for whom an ultra-sound guided core needle biopsy was analyzed for biomarkers during primary clinical work-up and the patient was offered primary surgery as initial treatment. Clinical biomarker profiles including immunohistochemical (IHC) determinations of ER, PgR, HER2 and Ki67 were translated to subtypes according to modified St Gallen criteria (2013) and compared with paired samples from surgical specimens. In addition, tumor specimens for biomolecule extraction and RNA sequencing were collected fresh in RNAlater.
Results: IHC data was available from 51 paired samples. The subtype distribution in core needle biopsies was DCIS in 1 case (2 %), LCIS in 1 case (2 %) Luminal A-like in 16 cases (31 %), Luminal B-like (HER2 negative) in 26 cases (51 %), Luminal B-HER2-like (HER2 positive) in 4 cases (8 %), HER2-positive (non-luminal) in 1 case (2 %) and triple negative (ductal) breast cancer in 2 cases (4 %). The subtype distribution in surgical specimens was DCIS in 0 case (0 %), LCIS in 1 case (2 %) Luminal A-like in 18 cases (35 %), Luminal B-like (HER2negative) in 23 cases (45 %), Luminal B--like (HER2 positive) in 6 cases (12 %), HER2-positive (non-luminal) in 1 case (2 %) and triple negative (ductal) breast cancer in 2 cases (4 %). Notably, 5/16 cases classified as Luminal A-like in the core needle biopsy were reclassified as Luminal B-like (HER2-negative) in the surgical specimen, whereas 9/26 cases classified as Luminal B-like (HER2-negative) in the core needle biopsy were reclassified as either Luminal A-like (7 cases) or Luminal B-like (HER2 positive) (2 cases) in the surgical specimen. In all instances, except one, transition between Luminal A-like and Luminal B-like was due to recorded Ki67 expression. One case that was classified as a DCIS in the core needle was reclassified as Luminal B-like (HER2 negative) at time of surgery.
Discussion: In this limited material, discordance between evaluations regarding Luminal A-like and Luminal B-like was considerable. Especially the misclassification of primary HER2-positive breast cancer needs further evaluation. These findings may be caused by tumor heterogeneity, and highlight the risk of both over- and under-treatment upon biomarker assessment from core needle biopsies. Data from gene expression based subtype classifications will be presented during the meeting.
Citation Format: Morgan G, Larsson C, Tahin B, Vallon-Christersson J, Häkkinen J, Ehinger A, Malmberg M, Hegardt C, Borg Å, Rydén L, Saal LH, Hedenfalk I, Loman N. Concordance between immunohistochemical and gene-expression based subtyping of early breast cancer using core needle biopsies and surgical specimens - experices from SCAN-B [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-02-02.
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Affiliation(s)
- G Morgan
- Skåne University Hospital, Lund, Sweden; Lund University, Lund, Sweden; Lund University Cancer Centre, Medicon Village, Lund, Sweden; Skåne Univerisity Hospital, Lund, Sweden; Skåne University Hopsital, Malmö, Sweden
| | - C Larsson
- Skåne University Hospital, Lund, Sweden; Lund University, Lund, Sweden; Lund University Cancer Centre, Medicon Village, Lund, Sweden; Skåne Univerisity Hospital, Lund, Sweden; Skåne University Hopsital, Malmö, Sweden
| | - B Tahin
- Skåne University Hospital, Lund, Sweden; Lund University, Lund, Sweden; Lund University Cancer Centre, Medicon Village, Lund, Sweden; Skåne Univerisity Hospital, Lund, Sweden; Skåne University Hopsital, Malmö, Sweden
| | - J Vallon-Christersson
- Skåne University Hospital, Lund, Sweden; Lund University, Lund, Sweden; Lund University Cancer Centre, Medicon Village, Lund, Sweden; Skåne Univerisity Hospital, Lund, Sweden; Skåne University Hopsital, Malmö, Sweden
| | - J Häkkinen
- Skåne University Hospital, Lund, Sweden; Lund University, Lund, Sweden; Lund University Cancer Centre, Medicon Village, Lund, Sweden; Skåne Univerisity Hospital, Lund, Sweden; Skåne University Hopsital, Malmö, Sweden
| | - A Ehinger
- Skåne University Hospital, Lund, Sweden; Lund University, Lund, Sweden; Lund University Cancer Centre, Medicon Village, Lund, Sweden; Skåne Univerisity Hospital, Lund, Sweden; Skåne University Hopsital, Malmö, Sweden
| | - M Malmberg
- Skåne University Hospital, Lund, Sweden; Lund University, Lund, Sweden; Lund University Cancer Centre, Medicon Village, Lund, Sweden; Skåne Univerisity Hospital, Lund, Sweden; Skåne University Hopsital, Malmö, Sweden
| | - C Hegardt
- Skåne University Hospital, Lund, Sweden; Lund University, Lund, Sweden; Lund University Cancer Centre, Medicon Village, Lund, Sweden; Skåne Univerisity Hospital, Lund, Sweden; Skåne University Hopsital, Malmö, Sweden
| | - Å Borg
- Skåne University Hospital, Lund, Sweden; Lund University, Lund, Sweden; Lund University Cancer Centre, Medicon Village, Lund, Sweden; Skåne Univerisity Hospital, Lund, Sweden; Skåne University Hopsital, Malmö, Sweden
| | - L Rydén
- Skåne University Hospital, Lund, Sweden; Lund University, Lund, Sweden; Lund University Cancer Centre, Medicon Village, Lund, Sweden; Skåne Univerisity Hospital, Lund, Sweden; Skåne University Hopsital, Malmö, Sweden
| | - LH Saal
- Skåne University Hospital, Lund, Sweden; Lund University, Lund, Sweden; Lund University Cancer Centre, Medicon Village, Lund, Sweden; Skåne Univerisity Hospital, Lund, Sweden; Skåne University Hopsital, Malmö, Sweden
| | - I Hedenfalk
- Skåne University Hospital, Lund, Sweden; Lund University, Lund, Sweden; Lund University Cancer Centre, Medicon Village, Lund, Sweden; Skåne Univerisity Hospital, Lund, Sweden; Skåne University Hopsital, Malmö, Sweden
| | - N Loman
- Skåne University Hospital, Lund, Sweden; Lund University, Lund, Sweden; Lund University Cancer Centre, Medicon Village, Lund, Sweden; Skåne Univerisity Hospital, Lund, Sweden; Skåne University Hopsital, Malmö, Sweden
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Nielsen TO, Leung SCY, Zabaglo LA, Arun I, Badve SS, Bane AL, Bartlet JMS, Borgquist S, Chang MC, Dodson A, Ehinger A, Fineberg S, Focke CM, Gao D, Gown AM, Gutierrez C, Hugh JC, Kos Z, Lænkholm AV, Mastropasqua MG, Moriya T, Nofech-Mozes S, Osborne CK, Penault-Llorca FM, Piper T, Sakatani T, Salgado R, Starczynski J, Sugie T, van der Vegt B, Viale G, Hayes DF, McShane LM, Dowsett M. Abstract P2-03-01: Analytical validation of a standardized scoring protocol for Ki67 assessed on breast excision whole sections: An international multicenter collaboration. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-03-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Aims: (i) Determine whether between-observer reproducibility for Ki67 when assessed on whole sections according to a standardized scoring protocol is adequate for clinical application. (ii) Compare between-observer reproducibility of Ki67 scores assessed on hot-spots to scores using a global method that averages across a tissue section.
Background: The nuclear proliferation biomarker Ki67 has multiple potential roles in breast cancer, including aiding decisions based on prognosis, but unacceptable levels of between-laboratory variability have been observed. The International Ki67 in Breast Cancer Working Group has undertaken a systematic program to determine whether Ki67 measurement can be analytically validated and standardized across labs. In phase 1, variability in visual interpretation was identified as an important source of variability. Phases 2 and 3a showed that adherence to defined scoring methods substantially improved reproducibility in scoring tissue microarrays and core-cut biopsies. We now assess whether acceptable reproducibility can be achieved on whole sections.
Methods: Adjacent sections from 30 primary ER+ breast cancers were centrally stained for Ki67 to assemble 4 sets of 30 stained tumor sections, circulated around 23 labs in 12 countries. Ki67 was scored by 2 methods by all labs: (a) global: 4 fields of 100 tumor cells each were selected to reflect observed heterogeneity in nuclear staining (b) hot-spot: the field with highest Ki67 percentage of tumor cells with nuclear staining was selected and up to 500 cells scored. Ki67 scores were log2-transformed for statistical analyses and back-transformed for presentation. The primary objective was to assess whether either method could achieve an intraclass correlation coefficient (ICC) significantly greater than 0.8, considered substantial to almost-perfect reproducibility. Secondary objectives were to assess which method had highest observed ICC and to assess whether observers identified the same “hot-spots”.
Results: ICC for the global method was 0.87 (95%CI: 0.799-0.93), marginally meeting the prespecified success criterion. The ICC for the hot-spot method was 0.83 (95%CI: 0.74-0.90) and had a CI extending below the success criterion. Across the 23 labs, geometric mean value of the 30 scores ranged from 8.5 to 19.6 for the global method and from 12.8 to 30.3 for the hot-spot method. The overall mean (95% CI) of these values was 12.9 (11.9-14.0) and 20.9 (19.1-22.8), respectively. Visually, between-laboratory agreement in location of selected hot-spot varies between cases. The median times for scoring were 9 and 6 minutes for global and hot-spot methods respectively.
Conclusions: The global method marginally met the prespecified criterion of success; it should now be evaluated for clinical validity in appropriate cohorts of cases. The hot-spot method was observed to have slightly less reproducibility between labs. The time taken for scoring by either method is practical using counting software we are making publicly available. Establishment of external quality assessment schemes is likely to improve the reproducibility between labs further.
(Supported by a grant from the Breast Cancer Research Foundation)
Citation Format: Nielsen TO, Leung SCY, Zabaglo LA, Arun I, Badve SS, Bane AL, Bartlet JMS, Borgquist S, Chang MC, Dodson A, Ehinger A, Fineberg S, Focke CM, Gao D, Gown AM, Gutierrez C, Hugh JC, Kos Z, Lænkholm A-V, Mastropasqua MG, Moriya T, Nofech-Mozes S, Osborne CK, Penault-Llorca FM, Piper T, Sakatani T, Salgado R, Starczynski J, Sugie T, van der Vegt B, Viale G, Hayes DF, McShane LM, Dowsett M. Analytical validation of a standardized scoring protocol for Ki67 assessed on breast excision whole sections: An international multicenter collaboration [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-03-01.
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Affiliation(s)
- TO Nielsen
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - SCY Leung
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - LA Zabaglo
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - I Arun
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - SS Badve
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - AL Bane
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - JMS Bartlet
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - S Borgquist
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - MC Chang
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - A Dodson
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - A Ehinger
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - S Fineberg
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - CM Focke
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - D Gao
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - AM Gown
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - C Gutierrez
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - JC Hugh
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - Z Kos
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - A-V Lænkholm
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - MG Mastropasqua
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - T Moriya
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - S Nofech-Mozes
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - CK Osborne
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - FM Penault-Llorca
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - T Piper
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - T Sakatani
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - R Salgado
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - J Starczynski
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - T Sugie
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - B van der Vegt
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - G Viale
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - DF Hayes
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - LM McShane
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
| | - M Dowsett
- University of British Columbia, Vancouver, BC, Canada; The Institute of Cancer Research, London, United Kingdom; Tata Medical Center, Kolkata, West Bengal, India; Indiana University Simon Cancer Center, Indianapolis, IN; Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Lund University, Lund, Sweden; Sinai Health System and University of Toronto, Toronto, ON, Canada; Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden Hospital, London, United Kingdom; Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY; Dietrich-Bonhoeffer Medical Center, Neubrandenburg, Mecklenburg-Vorpommern, Germany; PhenoPath Laboratories, Seattle, WA; Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; University of Alberta, Edmonton, AB, Canada; University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada; Zealand University Hosp
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Staaf J, Vallon-Christersson J, Häkkinen J, Saal LH, Hegardt C, Larsson C, Ehinger A, Ryden L, Loman N, Malmberg M, Borg Å. Abstract P1-06-01: Putting multigene signatures to the test: Prognostic assessment in population-based contemporary clinical breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p1-06-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
Gene expression signatures hold promise for a molecularly driven division of primary breast cancer with clinical implications. A gap still remains in the application/validation of such signatures in actual clinical treatment groups from unselected, population-based, primary breast cancer receiving current standard of care therapy. We analyzed classification proportions and overall survival (OS) of 14 reported gene expression phenotypes (GEPs) and risk predictors (RPs) in seven clinical treatments groups from an 3273-sample breast cancer cohort representative of population-based disease in the South Swedish healthcare region.
Patients and methods
Between 2010-09-01 to 2015-03-31, 5101 (87%) of 5892 patients with invasive primary disease in the healthcare region were included in the SCAN-B study (ClinicalTrials.gov ID: NCT02306096). Inclusion criteria included no generalized/prior contralateral disease and known surgery/treatment status (neo- or adjuvant). 3273 tumors were profiled by RNA sequencing and matched to clinicopathological patient data from the National Breast Cancer Register, with distribution of clinicopathological characteristics reflecting proportions in the catchment region. RNA profiles were classified according to 14 reported gene signatures featuring both GEPs (PAM50, IC10, CIT, TNBCtype) and specific risk predictors (e.g. Oncotype Dx, 70-gene, 76-gene, ROR-variants, genomic grade index). Classifications were investigated for association with patient OS by univariate and multivariate analyses in seven adjuvant clinical treatment groups: TNBC-ACT (adjuvant chemotherapy, n=228), TNBC-untreated (n=83), HER2+/ER- with trastuzumab + ACT treatment (n=101), HER2+/ER+ with trastuzumab + ACT + endocrine treatment (n=210), ER+/HER2- with endocrine treatment (n=1477), ER+/HER2- with endocrine + ACT treatment (n=637), and ER+/HER2- untreated (n=216).
Results
For the majority of signatures, analysis of classification demonstrated prognostic value limited to ER+/HER2- tumors given follow-up time. Several signatures (including Oncotype Dx, 70-gene, ROR-variants) showed strong predictive value in identifying a subset of ER+/HER2- patients receiving a combination of endocrine and ACT therapy with excellent overall survival (>96%), indicating appropriate therapy selection. In addition, for both ER+/HER2- treatment groups signature analysis identified high-risk groups of patients in clear need of additional treatment beyond standard therapeutic regimes, even with less than 5-years of follow-up.
Conclusions
Our results support the prognostic association of gene expression signatures in large unselected population-based primary breast cancer cohorts even with a short follow-up of OS.Importantly, prognostic associations are limited to specific subgroups for different classifiers and in population-based breast cancer some clinically important subgroups constitute a small proportion of cases. In this context, continued population-based inclusion and broad transcriptional profiling of breast cancer patients provides an opportunity for application to broader patient groups (e.g. TNBC and HER2+), and for consensus classification of individual risk assessments that could potentially provide more stable predictions.
Citation Format: Staaf J, Vallon-Christersson J, Häkkinen J, Saal LH, Hegardt C, Larsson C, Ehinger A, Ryden L, Loman N, Malmberg M, Borg Å. Putting multigene signatures to the test: Prognostic assessment in population-based contemporary clinical breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-06-01.
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Affiliation(s)
- J Staaf
- Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden
| | | | - J Häkkinen
- Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden
| | - LH Saal
- Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden
| | - C Hegardt
- Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden
| | - C Larsson
- Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden
| | - A Ehinger
- Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden
| | - L Ryden
- Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden
| | - N Loman
- Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden
| | - M Malmberg
- Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden
| | - Å Borg
- Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden
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Loman N, Chen Y, Aaltonen K, Brueffer C, George AM, Zander L, Vallon-Christersson J, Häkkinen J, Förnvik D, Rigo R, Ehinger A, Malmberg M, Larsson C, Hegardt C, Borg Å, Rydén L, Saal LH. Abstract P2-02-09: Breast cancer subtype distribution and circulating tumor DNA in response to neoadjuvant chemotherapy: Experiences from a preoperative cohort within SCAN-B. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-02-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Preoperative chemotherapy in early breast cancer increases the rate of breast preservation and provides prognostic information. In the case of residual disease, a change in subtypes may be observed. Sensitive and reproducible biomarkers predicting treatment response early during the treatment course are needed in order to better exploit the potential benefit of an individualized preoperative treatment.
Material and Methods: In an ongoing prospective study within the population-based SCAN-B project (NCT02306096), patients undergoing preoperative chemotherapy for early or locally recurrent breast cancer have been treated with iv Epirubicin and Cyclophosphamide q3w x 3 in sequence with either Docetaxel q3w x 3 or Paclitaxel q1w x 9 with a preoperative intent. HER2-positive cases also received HER2-directed treatment. At baseline, patients were staged using sentinel node biopsy for clinically node-negative patients and CT scan for cytologically confirmed node-positive cases. A clinical core needle biopsy as well as tissue from the surgical specimen was collected for determination of conventional biomarkers including ER, PgR, HER2 and Ki67. Tumor biopsies for biomolecule-extraction and RNA-sequencing were taken using ultrasound guidance and collected fresh in RNAlater at baseline, after 2 treatment cycles, as well as at surgery. Blood plasma samples were collected at baseline, after one-, three-, and six- 3w treatment cycles, and post-surgery. Using RNA-sequencing data, somatic mutations were identified in the tumor biopsies and personalized analyses for circulating tumor DNA (ctDNA) were performed. A pathological complete remission (pCR) was defined as the complete disappearance of invasive breast cancer in the breast and axilla at time of definitive surgery. Subtyping was performed using modified St Gallen criteria (2013).
Results: Thus far, 45 patients aged 24-74 years have been included, of which 34 (76 %) were clinical stage 2 and 11 (24%) were stage 3. The subtype distribution at baseline was five Luminal A-like (11 %), 21 Luminal B-like (HER2 negative) (47 %), 8 HER2-positive (18 %) and 11 Triple-negative (ductal) (24 %). The rates of pCR in 38 operated cases to date were 0/3 Luminal A-like, 3/19 Luminal B-like (HER2 negative), 2/8 HER2-positive, and 4/7 Triple-negative (overall 24 % pCR rate). One patient did not undergo surgery due to clinically progressive disease. In 25 cases with evaluable residual disease at surgery, there was a shift in the subtype in 13 (52 %), the majority of which represented a transition from Luminal B to Luminal A. No Triple-negative cases underwent a change in subtype during treatment. Results of the ctDNA analyses will be presented at the meeting.
Discussion: We have established an infrastructure allowing for an extensive evaluation of preoperative chemotherapy in early breast cancer. The goal is to develop methods to refine response-guided treatment in early breast cancer using molecular responses in the tumor as well as in the blood circulation. The patients continue to be prospectively monitored with iterative ctDNA analyses during follow-up.
Citation Format: Loman N, Chen Y, Aaltonen K, Brueffer C, George AM, Zander L, Vallon-Christersson J, Häkkinen J, Förnvik D, Rigo R, Ehinger A, Malmberg M, Larsson C, Hegardt C, Borg Å, Rydén L, Saal LH. Breast cancer subtype distribution and circulating tumor DNA in response to neoadjuvant chemotherapy: Experiences from a preoperative cohort within SCAN-B [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-02-09.
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Affiliation(s)
- N Loman
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - Y Chen
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - K Aaltonen
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - C Brueffer
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - AM George
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - L Zander
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - J Vallon-Christersson
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - J Häkkinen
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - D Förnvik
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - R Rigo
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - A Ehinger
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - M Malmberg
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - C Larsson
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - C Hegardt
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - Å Borg
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - L Rydén
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
| | - LH Saal
- Deartment och Oncology, Skåne University Hospital, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Division of Molecular Pathology, Department of Laboratory Medicine, Lund, Sweden
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Brueffer C, Vallon-Christersson J, Grabau D, Ehinger A, Häkkinen J, Hegardt C, Malina J, Chen Y, Bendahl PO, Manjer J, Malmberg M, Larsson C, Loman N, Ryden L, Borg Å, Saal LH. Abstract P4-09-03: On the development and clinical value of RNA-sequencing-based classifiers for prediction of the five conventional breast cancer biomarkers: A report from the population-based multicenter SCAN-B study. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p4-09-03] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background:
In early breast cancer, five histopathological biomarkers are part of current clinical routines and used for determining prognosis and treatment: estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (ERBB2/HER2), Ki67, and Nottingham histological grade (NHG). We aimed to develop classifiers for these biomarkers based on tumor mRNA-sequencing (RNA-seq), compare classification performance to conventional histopathology, and test whether RNA-seq-based predictors could add value for patient risk-stratification.
Patients and Methods:
In total, 3678 breast tumors were studied. For 405 breast tumors in the training cohort, a comprehensive histopathological biomarker evaluation was performed by three pathology readings to estimate inter-pathologist variability on the original diagnostic slides as well as on repeat immunostains for this study, and the consensus biomarker status for all five conventional biomarkers was determined. Whole transcriptome gene expression profiling was performed by RNA-sequencing on the Illumina platform. Using RNA-seq-derived tumor gene expression data as input, single-gene classifiers (SGC) and multi-gene classifiers (MGC) were trained on the consensus pathology biomarker labels. The trained classifiers were tested on an independent prospective population-based series of 3273 primary breast cancer cases from the multicenter SCAN-B study with median 41 months follow-up (ClinicalTrials.gov identifier NCT02306096), and classifications were evaluated by agreement statistics and by Kaplan-Meier and Cox regression survival analyses.
Results:
For the histopathological evaluation, pathologist evaluation concordance was high for ER, PgR, and HER2 (average kappa values of .920, .891, and .899, respectively), but moderate for Ki67 and NHG (.734 and .581). Classification concordance between RNA-seq classifiers and histopathology for the independent 3273-cohort was similar to that within histopathology assessments, with SGCs slightly outperforming MGCs. Importantly, patients with discordant results, classified as hormone responsive (HoR+) by histopathology but non-hormone responsive by MGC, presented with significantly inferior overall survival compared to patients with concordant results. These results extended to patients with no adjuvant systemic therapy (hazard ratio, HR, 4.54; 95% confidence interval, CI, 1.42-14.5), endocrine therapy alone (HR 3.46; 95% CI, 2.01-5.95), or receiving chemotherapy (HR 2.57; 95% CI 1.13-5.86). For HoR+ cases receiving endocrine therapy alone, the MGC HoR classifier remained significant after multivariable adjustment (HR 3.14; 95% CI, 1.75-5.65).
Conclusions:
RNA-seq-based classifiers for the five key early breast cancer biomarkers were generally equivalent to conventional histopathology with regards to classification error rate. However, when benchmarked using overall survival, our RNA-seq classifiers provided added clinical value in particular for cases that are determined by histopathology to be hormone-responsive but by RNA-seq appear hormone-insensitive and have a significantly poorer outcome when treated with endocrine therapy alone.
Citation Format: Brueffer C, Vallon-Christersson J, Grabau D, Ehinger A, Häkkinen J, Hegardt C, Malina J, Chen Y, Bendahl P-O, Manjer J, Malmberg M, Larsson C, Loman N, Ryden L, Borg Å, Saal LH. On the development and clinical value of RNA-sequencing-based classifiers for prediction of the five conventional breast cancer biomarkers: A report from the population-based multicenter SCAN-B study [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-09-03.
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Affiliation(s)
- C Brueffer
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - J Vallon-Christersson
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - D Grabau
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - A Ehinger
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - J Häkkinen
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - C Hegardt
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - J Malina
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - Y Chen
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - P-O Bendahl
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - J Manjer
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - M Malmberg
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - C Larsson
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - N Loman
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - L Ryden
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - Å Borg
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
| | - LH Saal
- Lund University, Lund, Sweden; Lund University Cancer Center, Medicon Village, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Blekinge County Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden
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Saal LH, Hegardt C, Vallon-Christersson J, Häkkinen J, Ehinger A, Manjer J, Larsson C, Loman N, Rydén L, Malmberg M, Borg Å. Abstract P1-07-17: The SCAN-B study: 5-year summary of a large-scale population-based prospective breast cancer translational genomics platform covering a wide geography of Sweden (NCT02306096). Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p1-07-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background:
Breast cancer exhibits significant molecular, pathological, and clinical heterogeneity. Current clinicopathological evaluation is imperfect for predicting outcome, which results in overtreatment for many patients, and for others, leads to death from recurrent disease. Therefore, additional criteria are needed to better personalize care and maximize treatment effectiveness and survival. To address these challenges, large-scale population-based studies are needed to develop and evaluate new predictive biomarker tests under real-world conditions.
Methods:
In 2010 we initiated the Sweden Cancerome Analysis Network - Breast (SCAN-B) multicenter prospective study (ClinicalTrials.gov identifier NCT02306096) with longsighted aims to 1) analyze breast cancers with next-generation genomic technologies for translational research in a population-based manner and integrated with healthcare; 2) decipher fundamental tumor biology from these analyses; 3) utilize genomic data to develop and validate new clinically-actionable biomarker assays; and 4) establish real-time clinical implementation of molecular diagnostic and treatment-predictive tests. Eligibility criteria are suspicion or confirmed diagnosis of primary breast cancer. Eligibility will be extended to recurrent breast cancer in late 2016. For all patients, tumor biopsy and/or surgical tumor specimen and baseline blood samples are collected, as well as follow-up blood samples at defined intervals, and clinical data are obtained from regional and national databases. From all samples, DNA, RNA, and protein fractions are isolated, and tissue arrays are constructed. In the first phase, we focus on molecular profiling of tumor tissue by next-generation RNA-sequencing.
Results:
From August 2010 through May 2016, we have consented and enrolled 8,669 patients with primary breast cancer at 9 hospital sites in Sweden, representing approximately 85% of eligible patients in the catchment area. Preoperative blood samples have been collected for 8,288 (96%) patients and primary fresh-frozen tumor specimens collected for 6,129 (71%) patients. All tumors have been RNA-sequenced, and newly enrolled cases are analyzed in “real-time” within an average of 7 days after biopsy/surgery. Herein we describe the study infrastructure and protocols and present initial proof of concept results from prospective RNA-sequencing including tumor molecular subtyping, detection of driver gene mutations, and determination of ER, PgR, HER2, Ki67, and tumor grade from RNA-seq data. Prospective patient enrollment is ongoing and pilot clinical reports are being evaluated at multidisciplinary breast cancer conferences.
Conclusions:
We demonstrate that population-based collection and real-time RNA-sequencing analysis of breast cancer is feasible at large-scale. The SCAN-B Study should significantly reduce the time to discovery, validation, and clinical implementation of novel molecular diagnostic and predictive tests. We welcome the participation of additional comprehensive cancer treatment centers.
Citation Format: Saal LH, Hegardt C, Vallon-Christersson J, Häkkinen J, Ehinger A, Manjer J, Larsson C, Loman N, Rydén L, Malmberg M, Borg Å. The SCAN-B study: 5-year summary of a large-scale population-based prospective breast cancer translational genomics platform covering a wide geography of Sweden (NCT02306096) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-07-17.
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Affiliation(s)
- LH Saal
- Lund University, Lund, Sweden; Blekinge Country Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden; Skåne University Hospital, Lund, Sweden
| | - C Hegardt
- Lund University, Lund, Sweden; Blekinge Country Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden; Skåne University Hospital, Lund, Sweden
| | - J Vallon-Christersson
- Lund University, Lund, Sweden; Blekinge Country Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden; Skåne University Hospital, Lund, Sweden
| | - J Häkkinen
- Lund University, Lund, Sweden; Blekinge Country Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden; Skåne University Hospital, Lund, Sweden
| | - A Ehinger
- Lund University, Lund, Sweden; Blekinge Country Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden; Skåne University Hospital, Lund, Sweden
| | - J Manjer
- Lund University, Lund, Sweden; Blekinge Country Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden; Skåne University Hospital, Lund, Sweden
| | - C Larsson
- Lund University, Lund, Sweden; Blekinge Country Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden; Skåne University Hospital, Lund, Sweden
| | - N Loman
- Lund University, Lund, Sweden; Blekinge Country Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden; Skåne University Hospital, Lund, Sweden
| | - L Rydén
- Lund University, Lund, Sweden; Blekinge Country Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden; Skåne University Hospital, Lund, Sweden
| | - M Malmberg
- Lund University, Lund, Sweden; Blekinge Country Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden; Skåne University Hospital, Lund, Sweden
| | - Å Borg
- Lund University, Lund, Sweden; Blekinge Country Hospital, Karlskrona, Sweden; Skåne University Hospital, Malmö, Sweden; Skåne University Hospital, Lund, Sweden
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Ehinger A, Malmström P, Bendahl PO, Elston CW, Falck AK, Forsare C, Grabau D, Rydén L, Stål O, Fernö M. Histological grade provides significant prognostic information in addition to breast cancer subtypes defined according to St Gallen 2013. Acta Oncol 2017; 56:68-74. [PMID: 27762648 DOI: 10.1080/0284186x.2016.1237778] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The St Gallen surrogate definition of the intrinsic subtypes of breast cancer consist of five subgroups based on estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor type 2 (HER2), and Ki-67. PgR and Ki-67 are used for discriminating between the 'Luminal A-like' and 'Luminal B-like (HER2-negative)' subtypes. Histological grade (G) has prognostic value in breast cancer; however, its relationship to the St Gallen subtypes is not clear. Based on a previous pilot study, we hypothesized that G could be a primary discriminator for ER-positive/HER2-negative breast cancers that were G1 or G3, whereas Ki-67 and PgR could provide additional prognostic information specifically for patients with G2 tumors. To test this hypothesis, a larger patient cohort was examined. PATIENTS AND METHODS Six hundred seventy-one patients (≥35 years of age, pT1-2, pN0-1) with ER-positive/HER2-negative breast cancer and complete data for PgR, Ki-67, G, lymph node status, tumor size, age, and distant disease-free survival (DDFS; median follow-up 9.2 years) were included. RESULTS 'Luminal A-like' tumors were mostly G1 or G2 (90%) whereas 'Luminal B-like' tumors were mostly G2 or G3 (87%) and corresponded with good and poor DDFS, respectively. In 'Luminal B-like' tumors that were G1 (n = 23), no metastasis occurred, whereas 14 of 40 'Luminal A-like' tumors that were G3 metastasized. In the G2 subgroup, low PgR and high Ki-67 were associated with an increased risk of distant metastases, hazard ratio (HR) and 95% confidence interval (CI) 1.8 (0.95-3.4) and 1.5 (0.80-2.8), respectively. CONCLUSIONS Patients with ER-positive/HER2-negative/G1 breast cancer have a good prognosis, similar to that of 'Luminal A-like', while those with ER-positive/HER2-negative/G3 breast cancer have a worse prognosis, similar to that of 'Luminal B-like', when assessed independently of PgR and Ki-67. Therapy decisions based on Ki-67 and PgR might thus be restricted to the subgroup G2.
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Affiliation(s)
- Anna Ehinger
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund Cancer Center at Medicon Village, Lund University, Lund, Sweden
- Department of Pathology and Cytology, Blekinge County Hospital, Karlskrona, Sweden
| | - Per Malmström
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund Cancer Center at Medicon Village, Lund University, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Pär-Ola Bendahl
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | - Christopher W. Elston
- Department of Histopathology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Anna-Karin Falck
- Department of Surgery, Helsingborg Hospital, Helsingborg, Sweden
| | - Carina Forsare
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | - Dorthe Grabau
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund Cancer Center at Medicon Village, Lund University, Lund, Sweden
- Department of Pathology, Skåne University Hospital, Lund, Sweden
| | - Lisa Rydén
- Division of Surgery, Department of Clinical Sciences, Lund Cancer Center at Medicon Village, Lund University, Lund, Sweden
- Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Olle Stål
- Division of Oncology, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden
| | - Mårten Fernö
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund Cancer Center at Medicon Village, Lund University, Lund, Sweden
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Alkner S, Bendahl PO, Ehinger A, Lövgren K, Rydén L, Fernö M. Prior Adjuvant Tamoxifen Treatment in Breast Cancer Is Linked to Increased AIB1 and HER2 Expression in Metachronous Contralateral Breast Cancer. PLoS One 2016; 11:e0150977. [PMID: 26959415 PMCID: PMC4784945 DOI: 10.1371/journal.pone.0150977] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/22/2016] [Indexed: 01/22/2023] Open
Abstract
Aim The estrogen receptor coactivator Amplified in Breast Cancer 1 (AIB1) has been associated with an improved response to adjuvant tamoxifen in breast cancer, but also with endocrine treatment resistance. We hereby use metachronous contralateral breast cancer (CBC) developed despite prior adjuvant tamoxifen for the first tumor as an “in vivo”-model for tamoxifen resistance. AIB1-expression in the presumable resistant (CBC after prior tamoxifen) and naïve setting (CBC without prior tamoxifen) is compared and correlated to prognosis after CBC. Methods From a well-defined population-based cohort of CBC-patients we have constructed a unique tissue-microarray including >700 patients. Results CBC developed after adjuvant tamoxifen more often had a HER2-positive/triple negative-subtype and a high AIB1-expression (37% vs. 23%, p = 0.009), than if no prior endocrine treatment had been administered. In patients with an estrogen receptor (ER) positive CBC, a high AIB1-expression correlated to an inferior prognosis. However, these patients seemed to respond to tamoxifen, but only if endocrine therapy had not been administered for BC1. Conclusions Metachronous CBC developed after prior endocrine treatment has a decreased ER-expression and an increased HER2-expression. This is consistent with endocrine treatment escape mechanisms previously suggested, and indicates metachronous CBC to be a putative model for studies of treatment resistance “in vivo”. The increased AIB1-expression in CBC developed after prior tamoxifen suggests a role of AIB1 in endocrine treatment resistance. In addition, we found indications that the response to tamoxifen in CBC with a high AIB1-expression seem to differ depending on previous exposure to this drug. A different function for AIB1 in the tamoxifen treatment naïve vs. resistant setting is suggested, and may explain previously conflicting results where a high AIB1-expression has been correlated to both a good response to adjuvant tamoxifen and tamoxifen resistance.
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Affiliation(s)
- Sara Alkner
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Medicon Village, SE-223 63, Lund, Sweden
- Skåne Clinic of Oncology, Skåne University Hospital Lund, SE-222 41, Lund, Sweden
- * E-mail:
| | - Pär-Ola Bendahl
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Medicon Village, SE-223 63, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Medicon Village, SE-223 63, Lund, Sweden
- Department of Pathology and Cytology, Blekinge County Hospital, SE-371 85, Karlskrona, Sweden
| | - Kristina Lövgren
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Medicon Village, SE-223 63, Lund, Sweden
| | - Lisa Rydén
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Medicon Village, SE-223 63, Lund, Sweden
- Clinic of Surgery, Skåne University Hospital Lund, SE-222 41, Lund, Sweden
| | - Mårten Fernö
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Medicon Village, SE-223 63, Lund, Sweden
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Alkner S, Ehinger A, Bendahl PO, Rydén L, Fernö M. Prognosis, stage and oestrogen receptor status of contralateral breast cancer in relation to characteristics of the first tumour, prior endocrine treatment and radiotherapy. Eur J Cancer 2015; 51:2304-13. [DOI: 10.1016/j.ejca.2015.07.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 05/15/2015] [Accepted: 07/16/2015] [Indexed: 11/30/2022]
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Alkner S, Tang MHE, Brueffer C, Dahlgren M, Chen Y, Olsson E, Winter C, Baker S, Ehinger A, Rydén L, Saal LH, Fernö M, Gruvberger-Saal SK. Contralateral breast cancer can represent a metastatic spread of the first primary tumor: determination of clonal relationship between contralateral breast cancers using next-generation whole genome sequencing. Breast Cancer Res 2015; 17:102. [PMID: 26242876 PMCID: PMC4531539 DOI: 10.1186/s13058-015-0608-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 07/01/2015] [Indexed: 12/26/2022] Open
Abstract
Introduction By convention, a contralateral breast cancer (CBC) is treated as a new primary tumor, independent of the first cancer (BC1). Although there have been indications that the second tumor (BC2) sometimes may represent a metastatic spread of BC1, this has never been conclusively shown. We sought to apply next-generation sequencing to determine a “genetic barcode” for each tumor and reveal the clonal relationship of CBCs. Methods Ten CBC patients with detailed clinical information and available fresh frozen tumor tissue were studied. Using low-coverage whole genome DNA-sequencing data for each tumor, chromosomal rearrangements were enumerated and copy number profiles were generated. Comparisons between tumors provided an estimate of clonal relatedness for tumor pairs within individual patients. Results Between 15–256 rearrangements were detected in each tumor (median 87). For one patient, 76 % (68 out of 90) of the rearrangements were shared between BC1 and BC2, highly consistent with what has been seen for true primary-metastasis pairs (>50 %) and thus confirming a common clonal origin of the two tumors. For most of the remaining cases, BC1 and BC2 had similarly low overlap as unmatched randomized pairs of tumors from different individuals, suggesting the CBC to represent a new independent primary tumor. Conclusion Using rearrangement fingerprinting, we show for the first time with certainty that a contralateral BC2 can represent a metastatic spread of BC1. Given the poor prognosis of a generalized disease compared to a new primary tumor, these women need to be identified at diagnosis of CBC for appropriate determination of treatment. Our approach generates a promising new method to assess clonal relationship between tumors. Additional studies are required to confirm the frequency of CBCs representing metastatic events. Electronic supplementary material The online version of this article (doi:10.1186/s13058-015-0608-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Alkner
- Division of Oncology and Pathology, Clinical Sciences Lund, Lund University, MV 404-B2, Lund, SE-22381, Sweden. .,Skåne Clinic of Oncology, Skåne University Hospital Lund, Lund, SE-22241, Sweden.
| | - Man-Hung Eric Tang
- Division of Oncology and Pathology, Clinical Sciences Lund, Lund University, MV 404-B2, Lund, SE-22381, Sweden.
| | - Christian Brueffer
- Division of Oncology and Pathology, Clinical Sciences Lund, Lund University, MV 404-B2, Lund, SE-22381, Sweden.
| | - Malin Dahlgren
- Division of Oncology and Pathology, Clinical Sciences Lund, Lund University, MV 404-B2, Lund, SE-22381, Sweden.
| | - Yilun Chen
- Division of Oncology and Pathology, Clinical Sciences Lund, Lund University, MV 404-B2, Lund, SE-22381, Sweden.
| | - Eleonor Olsson
- Division of Oncology and Pathology, Clinical Sciences Lund, Lund University, MV 404-B2, Lund, SE-22381, Sweden.
| | - Christof Winter
- Division of Oncology and Pathology, Clinical Sciences Lund, Lund University, MV 404-B2, Lund, SE-22381, Sweden.
| | - Sara Baker
- Division of Oncology and Pathology, Clinical Sciences Lund, Lund University, MV 404-B2, Lund, SE-22381, Sweden.
| | - Anna Ehinger
- Division of Oncology and Pathology, Clinical Sciences Lund, Lund University, MV 404-B2, Lund, SE-22381, Sweden. .,Department of Pathology and Cytology, Blekinge County Hospital, Karlskrona, SE-37185, Sweden.
| | - Lisa Rydén
- Division of Oncology and Pathology, Clinical Sciences Lund, Lund University, MV 404-B2, Lund, SE-22381, Sweden. .,Clinic of Surgery, Skåne University Hospital Lund, Lund, SE-22241, Sweden.
| | - Lao H Saal
- Division of Oncology and Pathology, Clinical Sciences Lund, Lund University, MV 404-B2, Lund, SE-22381, Sweden.
| | - Mårten Fernö
- Division of Oncology and Pathology, Clinical Sciences Lund, Lund University, MV 404-B2, Lund, SE-22381, Sweden.
| | - Sofia K Gruvberger-Saal
- Division of Oncology and Pathology, Clinical Sciences Lund, Lund University, MV 404-B2, Lund, SE-22381, Sweden.
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