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Kehl KL, Lavery JA, Brown S, Fuchs H, Riely G, Schrag D, Newcomb A, Nichols C, Micheel CM, Bedard PL, Sweeney SM, Fiandalo M, Panageas KS. Biomarker Inference and the Timing of Next-Generation Sequencing in a Multi-Institutional, Cross-Cancer Clinicogenomic Data Set. JCO Precis Oncol 2024; 8:e2300489. [PMID: 38484212 PMCID: PMC10954072 DOI: 10.1200/po.23.00489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 12/03/2023] [Accepted: 01/03/2024] [Indexed: 03/19/2024] Open
Abstract
PURPOSE Observational clinicogenomic data sets, consisting of tumor next-generation sequencing (NGS) data linked to clinical records, are commonly used for cancer research. However, in real-world practice, oncologists frequently request NGS in search of treatment options for progressive cancer. The extent and impact of this dynamic on analysis of clinicogenomic research data are not well understood. METHODS We analyzed clinicogenomic data for patients with non-small cell lung, colorectal, breast, prostate, pancreatic, or urothelial cancers in the American Association for Cancer Research Biopharmaceutical Consortium cohort. Associations between baseline and time-varying clinical characteristics and time from diagnosis to NGS were measured. To explore the impact of informative cohort entry on biomarker inference, statistical interactions between selected biomarkers and time to NGS with respect to overall survival were calculated. RESULTS Among 7,182 patients, time from diagnosis to NGS varied significantly by clinical factors, including cancer type, calendar year of sequencing, institution, and age and stage at diagnosis. NGS rates also varied significantly by dynamic clinical status variables; in an adjusted model, compared with patients with stable disease at any given time after diagnosis, patients with progressive disease by imaging or oncologist assessment had higher NGS rates (hazard ratio for NGS, 1.61 [95% CI, 1.45 to 1.78] and 2.32 [95% CI, 2.01 to 2.67], respectively). Statistical interactions between selected biomarkers and time to NGS with respect to survival, potentially indicating biased biomarker inference results, were explored. CONCLUSION To evaluate the appropriateness of a data set for a particular research question, it is crucial to measure associations between dynamic cancer status and the timing of NGS, as well as to evaluate interactions involving biomarkers of interest and NGS timing with respect to survival outcomes.
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Affiliation(s)
- Kenneth L. Kehl
- Division of Population Sciences, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Jessica A. Lavery
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Samantha Brown
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hannah Fuchs
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gregory Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Deborah Schrag
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ashley Newcomb
- Division of Population Sciences, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Chelsea Nichols
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christine M. Micheel
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | | | | | | | - Katherine S. Panageas
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
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2
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Sanz-Garcia E, Brown S, Lavery JA, Weiss J, Fuchs HE, Newcomb A, Postle A, Warner JL, LeNoue-Newton ML, Sweeney SM, Pillai S, Yu C, Nichols C, Mastrogiacomo B, Kundra R, Schultz N, Kehl KL, Riely GJ, Schrag D, Govindarajan A, Panageas KS, Bedard PL. Genomic Characterization and Clinical Outcomes of Patients with Peritoneal Metastases from the AACR GENIE Biopharma Collaborative Colorectal Cancer Registry. Cancer Res Commun 2024; 4:475-486. [PMID: 38329392 PMCID: PMC10876516 DOI: 10.1158/2767-9764.crc-23-0409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/17/2023] [Accepted: 02/06/2024] [Indexed: 02/09/2024]
Abstract
Peritoneal metastases (PM) are common in metastatic colorectal cancer (mCRC). We aimed to characterize patients with mCRC and PM from a clinical and molecular perspective using the American Association of Cancer Research Genomics Evidence Neoplasia Information Exchange (GENIE) Biopharma Collaborative (BPC) registry. Patients' tumor samples underwent targeted next-generation sequencing. Clinical characteristics and treatment outcomes were collected retrospectively. Overall survival (OS) from advanced disease and progression-free survival (PFS) from start of cancer-directed drug regimen were estimated and adjusted for the left truncation bias. A total of 1,281 patients were analyzed, 244 (19%) had PM at time of advanced disease. PM were associated with female sex [OR: 1.67; 95% confidence interval (CI): 1.11-2.54; P = 0.014] and higher histologic grade (OR: 1.72; 95% CI: 1.08-2.71; P = 0.022), while rectal primary tumors were less frequent in patients with PM (OR: 0.51; 95% CI: 0.29-0.88; P < 0.001). APC occurred less frequently in patients with PM (N = 151, 64% vs. N = 788, 79%) while MED12 alterations occurred more frequently in patients with PM (N = 20, 10% vs. N = 32, 4%); differences in MED12 were not significant when restricting to oncogenic and likely oncogenic variants according to OncoKB. Patients with PM had worse OS (HR: 1.45; 95% CI: 1.16-1.81) after adjustment for independently significant clinical and genomic predictors. PFS from initiation of first-line treatment did not differ by presence of PM. In conclusion, PM were more frequent in females and right-sided primary tumors. Differences in frequencies of MED12 and APC alterations were identified between patients with and without PM. PM were associated with shorter OS but not with PFS from first-line treatment. SIGNIFICANCE Utilizing the GENIE BPC registry, this study found that PM in patients with colorectal cancer occur more frequently in females and right-sided primary tumors and are associated with worse OS. In addition, we found a lower frequency of APC alterations and a higher frequency in MED12 alterations in patients with PM.
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Affiliation(s)
- Enrique Sanz-Garcia
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre – University Health Network, Department of Medicine, University of Toronto, Ontario, Canada
| | - Samantha Brown
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jessica Weiss
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre – University Health Network, Department of Medicine, University of Toronto, Ontario, Canada
| | | | | | - Asha Postle
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | - Shawn M. Sweeney
- American Association of Cancer Research, Philadelphia, Pennsylvania
| | - Shirin Pillai
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Celeste Yu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre – University Health Network, Department of Medicine, University of Toronto, Ontario, Canada
| | | | | | - Ritika Kundra
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | - Deborah Schrag
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anand Govindarajan
- Sinai Health System, Toronto, Ontario, Canada
- Department of Surgery, University of Toronto, Ontario, Canada
| | | | - Philippe L. Bedard
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre – University Health Network, Department of Medicine, University of Toronto, Ontario, Canada
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de Bruijn I, Kundra R, Mastrogiacomo B, Tran TN, Sikina L, Mazor T, Li X, Ochoa A, Zhao G, Lai B, Abeshouse A, Baiceanu D, Ciftci E, Dogrusoz U, Dufilie A, Erkoc Z, Garcia Lara E, Fu Z, Gross B, Haynes C, Heath A, Higgins D, Jagannathan P, Kalletla K, Kumari P, Lindsay J, Lisman A, Leenknegt B, Lukasse P, Madela D, Madupuri R, van Nierop P, Plantalech O, Quach J, Resnick AC, Rodenburg SY, Satravada BA, Schaeffer F, Sheridan R, Singh J, Sirohi R, Sumer SO, van Hagen S, Wang A, Wilson M, Zhang H, Zhu K, Rusk N, Brown S, Lavery JA, Panageas KS, Rudolph JE, LeNoue-Newton ML, Warner JL, Guo X, Hunter-Zinck H, Yu TV, Pilai S, Nichols C, Gardos SM, Philip J, Kehl KL, Riely GJ, Schrag D, Lee J, Fiandalo MV, Sweeney SM, Pugh TJ, Sander C, Cerami E, Gao J, Schultz N. Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal. Cancer Res 2023; 83:3861-3867. [PMID: 37668528 PMCID: PMC10690089 DOI: 10.1158/0008-5472.can-23-0816] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/24/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
International cancer registries make real-world genomic and clinical data available, but their joint analysis remains a challenge. AACR Project GENIE, an international cancer registry collecting data from 19 cancer centers, makes data from >130,000 patients publicly available through the cBioPortal for Cancer Genomics (https://genie.cbioportal.org). For 25,000 patients, additional real-world longitudinal clinical data, including treatment and outcome data, are being collected by the AACR Project GENIE Biopharma Collaborative using the PRISSMM data curation model. Several thousand of these cases are now also available in cBioPortal. We have significantly enhanced the functionalities of cBioPortal to support the visualization and analysis of this rich clinico-genomic linked dataset, as well as datasets generated by other centers and consortia. Examples of these enhancements include (i) visualization of the longitudinal clinical and genomic data at the patient level, including timelines for diagnoses, treatments, and outcomes; (ii) the ability to select samples based on treatment status, facilitating a comparison of molecular and clinical attributes between samples before and after a specific treatment; and (iii) survival analysis estimates based on individual treatment regimens received. Together, these features provide cBioPortal users with a toolkit to interactively investigate complex clinico-genomic data to generate hypotheses and make discoveries about the impact of specific genomic variants on prognosis and therapeutic sensitivities in cancer. SIGNIFICANCE Enhanced cBioPortal features allow clinicians and researchers to effectively investigate longitudinal clinico-genomic data from patients with cancer, which will improve exploration of data from the AACR Project GENIE Biopharma Collaborative and similar datasets.
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Affiliation(s)
- Ino de Bruijn
- Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ritika Kundra
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | - Luke Sikina
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tali Mazor
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xiang Li
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Angelica Ochoa
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gaofei Zhao
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bryan Lai
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Adam Abeshouse
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Ersin Ciftci
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | - Ziya Erkoc
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Zhaoyuan Fu
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Benjamin Gross
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles Haynes
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Allison Heath
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - David Higgins
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | | | - Priti Kumari
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Caris Life Sciences, Irving, Texas
| | | | - Aaron Lisman
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | - Divya Madela
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | - Joyce Quach
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Adam C. Resnick
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | | | | | | | | | - Rajat Sirohi
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | - Avery Wang
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Manda Wilson
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hongxin Zhang
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kelsey Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Nicole Rusk
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samantha Brown
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | | | | | - Xindi Guo
- Sage Bionetworks, Seattle, Washington
| | | | | | - Shirin Pilai
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | - John Philip
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | - Deborah Schrag
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jocelyn Lee
- American Association for Cancer Research: Project GENIE, Philadelphia, Pennsylvania
| | - Michael V. Fiandalo
- American Association for Cancer Research: Project GENIE, Philadelphia, Pennsylvania
| | - Shawn M. Sweeney
- American Association for Cancer Research: Project GENIE, Philadelphia, Pennsylvania
| | - Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | - Ethan Cerami
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jianjiong Gao
- Memorial Sloan Kettering Cancer Center, New York, New York
- Caris Life Sciences, Irving, Texas
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Choudhury NJ, Lavery JA, Brown S, de Bruijn I, Jee J, Tran TN, Rizvi H, Arbour KC, Whiting K, Shen R, Hellmann M, Bedard PL, Yu C, Leighl N, LeNoue-Newton M, Micheel C, Warner JL, Ginsberg MS, Plodkowski A, Girshman J, Sawan P, Pillai S, Sweeney SM, Kehl KL, Panageas KS, Schultz N, Schrag D, Riely GJ. The GENIE BPC NSCLC Cohort: A Real-World Repository Integrating Standardized Clinical and Genomic Data for 1,846 Patients with Non-Small Cell Lung Cancer. Clin Cancer Res 2023; 29:3418-3428. [PMID: 37223888 PMCID: PMC10472103 DOI: 10.1158/1078-0432.ccr-23-0580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/08/2023] [Accepted: 05/17/2023] [Indexed: 05/25/2023]
Abstract
PURPOSE We describe the clinical and genomic landscape of the non-small cell lung cancer (NSCLC) cohort of the American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) Biopharma Collaborative (BPC). EXPERIMENTAL DESIGN A total of 1,846 patients with NSCLC whose tumors were sequenced from 2014 to 2018 at four institutions participating in AACR GENIE were randomly chosen for curation using the PRISSMM data model. Progression-free survival (PFS) and overall survival (OS) were estimated for patients treated with standard therapies. RESULTS In this cohort, 44% of tumors harbored a targetable oncogenic alteration, with EGFR (20%), KRAS G12C (13%), and oncogenic fusions (ALK, RET, and ROS1; 5%) as the most frequent. Median OS (mOS) on first-line platinum-based therapy without immunotherapy was 17.4 months [95% confidence interval (CI), 14.9-19.5 months]. For second-line therapies, mOS was 9.2 months (95% CI, 7.5-11.3 months) for immune checkpoint inhibitors (ICI) and 6.4 months (95% CI, 5.1-8.1 months) for docetaxel ± ramucirumab. In a subset of patients treated with ICI in the second-line or later setting, median RECIST PFS (2.5 months; 95% CI, 2.2-2.8) and median real-world PFS based on imaging reports (2.2 months; 95% CI, 1.7-2.6) were similar. In exploratory analysis of the impact of tumor mutational burden (TMB) on survival on ICI treatment in the second-line or higher setting, TMB z-score harmonized across gene panels was associated with improved OS (univariable HR, 0.85; P = 0.03; n = 247 patients). CONCLUSIONS The GENIE BPC cohort provides comprehensive clinicogenomic data for patients with NSCLC, which can improve understanding of real-world patient outcomes.
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Affiliation(s)
- Noura J. Choudhury
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Jessica A. Lavery
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samantha Brown
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ino de Bruijn
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Justin Jee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Thinh Ngoc Tran
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Kathryn C. Arbour
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Karissa Whiting
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Philippe L. Bedard
- Cancer Clinical Research Unit, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Celeste Yu
- Cancer Clinical Research Unit, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Natasha Leighl
- Cancer Clinical Research Unit, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Michele LeNoue-Newton
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Christine Micheel
- Department of Medicine, Vanderbilt Ingram Cancer Center, Nashville, Tennessee
| | - Jeremy L. Warner
- Department of Medicine, Vanderbilt Ingram Cancer Center, Nashville, Tennessee
- Lifespan Cancer Institute, Providence, Rhode Island
- Legorreta Cancer Center at Brown University, Providence, Rhode Island
| | - Michelle S. Ginsberg
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew Plodkowski
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jeffrey Girshman
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Peter Sawan
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shirin Pillai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shawn M. Sweeney
- American Association for Cancer Research, Philadelphia, Pennsylvania
| | - Kenneth L. Kehl
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Katherine S. Panageas
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Deborah Schrag
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Gregory J. Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
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5
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Sweeney SM, Lavery JA, Fuchs HE, Lee JA, Brown S, Panageas KS, Sawyers CL, Bedard PL. Addressing racial and ethnic disparities in AACR project GENIE. NPJ Precis Oncol 2023; 7:81. [PMID: 37653066 PMCID: PMC10471569 DOI: 10.1038/s41698-023-00425-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/26/2023] [Indexed: 09/02/2023] Open
Grants
- Dr. Jocelyn Lee owns stock in Abbott and Gilead Sciences. Dr. Lee is the Associate Director of AACR Project GENIE. AAACR Project GENIE received funding from Amgen, Inc., Bristol-Myers Squibb Company, Bayer HealthCare Pharmaceuticals Inc., Merck Sharp & Dohme Corp., Pfizer, AstraZeneca UK Limited, Genentech, Novartis, Boehringer Ingelheim, and Janssen Pharmaceuticals, Inc.
- Dr. Shawn Sweeney has an immediate family member who works for ConcertAI. He is a science advisor to Bayer Healthcare. Dr. Sweeney is the Senior Director of AACR Project GENIE. AACR Project GENIE received funding from Amgen, Inc., Bristol-Myers Squibb Company, Bayer HealthCare Pharmaceuticals Inc., Merck Sharp & Dohme Corp., Pfizer, AstraZeneca UK Limited, Genentech, Novartis, Boehringer Ingelheim, and Janssen Pharmaceuticals, Inc.
- A portion of Jessica Lavery’s support is paid by AACR Project GENIE. AAAACR Project GENIE received funding from Amgen, Inc., Bristol-Myers Squibb Company, Bayer HealthCare Pharmaceuticals Inc., Merck Sharp & Dohme Corp., Pfizer, AstraZeneca UK Limited, Genentech, Novartis, Boehringer Ingelheim, and Janssen Pharmaceuticals, Inc.
- A portion of Hannah Fuch’s support is paid by AACR Project GENIE. AAAACR Project GENIE received funding from Amgen, Inc., Bristol-Myers Squibb Company, Bayer HealthCare Pharmaceuticals Inc., Merck Sharp & Dohme Corp., Pfizer, AstraZeneca UK Limited, Genentech, Novartis, Boehringer Ingelheim, and Janssen Pharmaceuticals, Inc.
- A portion of Samantha Brown’s support is paid by AACR Project GENIE. AACR Project GENIE received funding from Amgen, Inc., Bristol-Myers Squibb Company, Bayer HealthCare Pharmaceuticals Inc., Merck Sharp & Dohme Corp., Pfizer, AstraZeneca UK Limited, Genentech, Novartis, Boehringer Ingelheim, and Janssen Pharmaceuticals, Inc.
- Dr. Katherine Panageas owns stock in Adicet Bio, Codexis, Chinook Therapeutics, T2 Biosystems, Vincerx Pharma, and 23andMe. A portion of Dr. Panageas’ support is paid by AACR Project GENIE. AACR Project GENIE received funding from Amgen, Inc., Bristol-Myers Squibb Company, Bayer HealthCare Pharmaceuticals Inc., Merck Sharp & Dohme Corp., Pfizer, AstraZeneca UK Limited, Genentech, Novartis, Boehringer Ingelheim, and Janssen Pharmaceuticals, Inc.
- Dr. Charles Sawyers serves on the Board of Directors of Novartis, is a co-founder of ORIC Pharmaceuticals and co-inventor of enzalutamide and apalutamide. He is a science advisor to Arsenal, Beigene, Blueprint, Column Group, Foghorn, Housey Pharma, Nextech, KSQ and PMV.
- Dr. Phillipe Bedard serves as science advisor to Seattle Genetics, Elli Lilly and Co., Amgen, Inc., Gilead Sciences, Bristol-Myers Squibb Company, Pfizer, AstraZeneca UK Limited, Genentech/Roche, GlaxoSmithKline, Novartis, Merck Sharp & Dohme Corp., Bicara, Zymeworks, Medicenna, Bayer HealthCare Pharmaceuticals Inc.
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Affiliation(s)
- Shawn M Sweeney
- AACR Project GENIE, American Association for Cancer Research, Philadelphia, PA, USA
| | - Jessica A Lavery
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hannah E Fuchs
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jocelyn A Lee
- AACR Project GENIE, American Association for Cancer Research, Philadelphia, PA, USA.
| | - Samantha Brown
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katherine S Panageas
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Philippe L Bedard
- Division of Medical Oncology & Hematology, University Health Network - Princess Margaret Cancer Centre, Toronto, ON, Canada
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6
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Sweeney SM, Hamadeh HK, Abrams N, Adam SJ, Brenner S, Connors DE, Davis GJ, Fiore L, Gawel SH, Grossman RL, Hanlon SE, Hsu K, Kelloff GJ, Kirsch IR, Louv B, McGraw D, Meng F, Milgram D, Miller RS, Morgan E, Mukundan L, O'Brien T, Robbins P, Rubin EH, Rubinstein WS, Salmi L, Schaller T, Shi G, Sigman CC, Srivastava S. Challenges to Using Big Data in Cancer. Cancer Res 2023; 83:1175-1182. [PMID: 36625843 PMCID: PMC10102837 DOI: 10.1158/0008-5472.can-22-1274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/29/2022] [Accepted: 12/05/2022] [Indexed: 01/11/2023]
Abstract
Big data in healthcare can enable unprecedented understanding of diseases and their treatment, particularly in oncology. These data may include electronic health records, medical imaging, genomic sequencing, payor records, and data from pharmaceutical research, wearables, and medical devices. The ability to combine datasets and use data across many analyses is critical to the successful use of big data and is a concern for those who generate and use the data. Interoperability and data quality continue to be major challenges when working with different healthcare datasets. Mapping terminology across datasets, missing and incorrect data, and varying data structures make combining data an onerous and largely manual undertaking. Data privacy is another concern addressed by the Health Insurance Portability and Accountability Act, the Common Rule, and the General Data Protection Regulation. The use of big data is now included in the planning and activities of the FDA and the European Medicines Agency. The willingness of organizations to share data in a precompetitive fashion, agreements on data quality standards, and institution of universal and practical tenets on data privacy will be crucial to fully realizing the potential for big data in medicine.
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Affiliation(s)
- Shawn M. Sweeney
- American Association for Cancer Research, Philadelphia, Pennsylvania
| | | | - Natalie Abrams
- Division of Cancer Prevention, Early Detection Research Network, National Cancer Institute, Rockville, Maryland
| | - Stacey J. Adam
- Foundation for the National Institutes of Health, Bethesda, Maryland
| | - Sara Brenner
- Office of In Vitro Diagnostics, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Dana E. Connors
- Foundation for the National Institutes of Health, Bethesda, Maryland
| | - Gerard J. Davis
- Abbott Diagnostics Division, Abbott Laboratories, Lake Forest, Illinois
| | - Louis Fiore
- Boston University School of Medicine, Boston and New England Department of Veterans Affairs, Bedford, Massachusetts
| | - Susan H. Gawel
- Abbott Diagnostics Division, Abbott Laboratories, Lake Forest, Illinois
| | - Robert L. Grossman
- Center for Translational Data Science, The University of Chicago, Chicago, Illinois
| | - Sean E. Hanlon
- Center for Strategic Scientific Initiatives, National Cancer Institute, Bethesda, Maryland
| | | | - Gary J. Kelloff
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland
| | | | - Bill Louv
- Project Data Sphere, Morrisville, North Carolina
| | - Deven McGraw
- Ciitizen Platform at Invitae, San Francisco, California
| | - Frank Meng
- Boston University and Veterans Administration Boston Healthcare System, Boston, Massachusetts
| | | | - Robert S. Miller
- CancerLinQ, American Society of Clinical Oncology, Alexandria, Virginia
| | - Emily Morgan
- Foundation for the National Institutes of Health, Bethesda, Maryland
| | | | | | | | | | - Wendy S. Rubinstein
- Office of In Vitro Diagnostics, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Liz Salmi
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | | | - George Shi
- Abbott Diagnostics Division, Abbott Laboratories, Lake Forest, Illinois
| | - Caroline C. Sigman
- Boston University and Veterans Administration Boston Healthcare System, Boston, Massachusetts
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Rockville, Maryland
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7
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Sweeney SM, Hamadeh HK, Abrams N, Adam SJ, Brenner S, Connors DE, Davis GJ, Fiore LD, Gawel SH, Grossman RL, Hanlon SE, Hsu K, Kelloff GJ, Kirsch IR, Louv B, McGraw D, Meng F, Milgram D, Miller RS, Morgan E, Mukundan L, O'Brien T, Robbins P, Rubin EH, Salmi L, Schaller TH, Shi G, Sigman CC, Srivastava S. Case studies for overcoming challenges in using big data in cancer. Cancer Res 2023; 83:1183-1190. [PMID: 36625851 PMCID: PMC10102839 DOI: 10.1158/0008-5472.can-22-1277] [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] [Received: 04/15/2022] [Revised: 07/29/2022] [Accepted: 12/06/2022] [Indexed: 01/11/2023]
Abstract
The analysis of big healthcare data has enormous potential as a tool for advancing oncology drug development and patient treatment, particularly in the context of precision medicine. However, there are challenges in organizing, sharing, integrating, and making these data readily accessible to the research community. This review presents five case studies illustrating various successful approaches to addressing such challenges. These efforts are CancerLinQ, the American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange, Project Data Sphere, the National Cancer Institute Genomic Data Commons, and the Veterans Health Administration Clinical Data Initiative. Critical factors in the development of these systems include attention to the use of robust pipelines for data aggregation, common data models, data de-identification to enable multiple uses, integration of data collection into physician workflows, terminology standardization and attention to interoperability, extensive quality assurance and quality control activity, incorporation of multiple data types, and understanding how data resources can be best applied. By describing some of the emerging resources, we hope to inspire consideration of the secondary use of such data at the earliest possible step to ensure the proper sharing of data in order to generate insights that advance the understanding and treatment of cancer.
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Affiliation(s)
- Shawn M Sweeney
- American Association For Cancer Research, Philadelphia, United States
| | | | | | - Stacey J Adam
- Foundation for the National Institutes of Health, North Bethesda, MD, United States
| | - Sara Brenner
- United States Food and Drug Administration, United States
| | - Dana E Connors
- Foundation for the National Institutes of Health, North Bethesda, United States
| | | | - Louis D Fiore
- Boston University School of Medicine, Boston, United States
| | - Susan H Gawel
- Abbott Laboratories, Abbott Park City, Illinois, United States
| | | | - Sean E Hanlon
- National Cancer Institute, Bethesda, MD, United States
| | - Karl Hsu
- Sanofi Research and Development, Cambridge, MA, United States
| | - Gary J Kelloff
- National Institutes of Health, Rockville, MD, United States
| | - Ilan R Kirsch
- Adaptive Biotechnologies (United States), Seattle, WA, United States
| | - Bill Louv
- CEO Roundtable on Cancer, Cary, United States
| | | | - Frank Meng
- Boston University School of Medicine, United States
| | | | - Robert S Miller
- American Society of Clinical Oncology, Alexandria, VA, United States
| | - Emily Morgan
- Foundation for the National Institutes of Health, Rockville, United States
| | - Lata Mukundan
- CCS Associates (United States), Fremont, United States
| | | | | | - Eric H Rubin
- Merck Research Laboratories, North Wales, PA, United States
| | - Liz Salmi
- Beth Israel Deaconess Medical Center, Boston, CA, United States
| | | | - George Shi
- Abbott (United States), Lake Forest, United States
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8
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Pugh TJ, Bell JL, Bruce JP, Doherty GJ, Galvin M, Green MF, Hunter-Zinck H, Kumari P, Lenoue-Newton ML, Li MM, Lindsay J, Mazor T, Ovalle A, Sammut SJ, Schultz N, Yu TV, Sweeney SM, Bernard B. AACR Project GENIE: 100,000 Cases and Beyond. Cancer Discov 2022; 12:2044-2057. [PMID: 35819403 PMCID: PMC9437568 DOI: 10.1158/2159-8290.cd-21-1547] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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: 11/22/2021] [Revised: 05/20/2022] [Accepted: 07/07/2022] [Indexed: 01/26/2023]
Abstract
The American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) is an international pan-cancer registry with the goal to inform cancer research and clinical care worldwide. Founded in late 2015, the milestone GENIE 9.1-public release contains data from >110,000 tumors from >100,000 people treated at 19 cancer centers from the United States, Canada, the United Kingdom, France, the Netherlands, and Spain. Here, we demonstrate the use of these real-world data, harmonized through a centralized data resource, to accurately predict enrollment on genome-guided trials, discover driver alterations in rare tumors, and identify cancer types without actionable mutations that could benefit from comprehensive genomic analysis. The extensible data infrastructure and governance framework support additional deep patient phenotyping through biopharmaceutical collaborations and expansion to include new data types such as cell-free DNA sequencing. AACR Project GENIE continues to serve a global precision medicine knowledge base of increasing impact to inform clinical decision-making and bring together cancer researchers internationally. SIGNIFICANCE AACR Project GENIE has now accrued data from >110,000 tumors, placing it among the largest repository of publicly available, clinically annotated genomic data in the world. GENIE has emerged as a powerful resource to evaluate genome-guided clinical trial design, uncover drivers of cancer subtypes, and inform real-world use of genomic data. This article is highlighted in the In This Issue feature, p. 2007.
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Affiliation(s)
- Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,University of Toronto, Toronto, Ontario, Canada.,Corresponding Authors: Trevor J. Pugh, Princess Margaret Cancer Centre, University Health Network, MaRS Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada. Phone: 416-946-2000; E-mail: ; and Brady Bernard, 4805 NE Glisan Street, Suite 2N35, Portland, OR 97213. Phone: 503-215-6588; E-mail:
| | | | - Jeff P. Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Gary J. Doherty
- Cancer Research United Kingdom (CRUK) Cambridge Centre, Cambridge, United Kingdom.,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Matthew Galvin
- Earle A. Chiles Research Institute, Portland, Oregon.,Providence Cancer Institute, Portland, Oregon
| | | | | | - Priti Kumari
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michele L. Lenoue-Newton
- Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Marilyn M. Li
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - Tali Mazor
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Stephen-John Sammut
- Cancer Research United Kingdom (CRUK) Cambridge Centre, Cambridge, United Kingdom.,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | | | | | - Shawn M. Sweeney
- American Association for Cancer Research, Philadelphia, Pennsylvania
| | - Brady Bernard
- Earle A. Chiles Research Institute, Portland, Oregon.,Providence Cancer Institute, Portland, Oregon.,Corresponding Authors: Trevor J. Pugh, Princess Margaret Cancer Centre, University Health Network, MaRS Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada. Phone: 416-946-2000; E-mail: ; and Brady Bernard, 4805 NE Glisan Street, Suite 2N35, Portland, OR 97213. Phone: 503-215-6588; E-mail:
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9
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Brown S, Lavery JA, Shen R, Martin AS, Kehl KL, Sweeney SM, Lepisto EM, Rizvi H, McCarthy CG, Schultz N, Warner JL, Park BH, Bedard PL, Riely GJ, Schrag D, Panageas KS. Implications of Selection Bias Due to Delayed Study Entry in Clinical Genomic Studies. JAMA Oncol 2021; 8:287-291. [PMID: 34734967 DOI: 10.1001/jamaoncol.2021.5153] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Importance Real-world data sets that combine clinical and genomic data may be subject to left truncation (when potential study participants are not included because they have already passed the milestone of interest at the time of study recruitment). The lapse between diagnosis and molecular testing can present analytic challenges and threaten the validity and interpretation of survival analyses. Observations Effects of ignoring left truncation when estimating overall survival are illustrated using data from the American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange Biopharma Collaborative (GENIE BPC), and a straightforward risk-set adjustment approach is described. Ignoring left truncation results in overestimation of overall survival: unadjusted median survival estimates from diagnosis among patients with stage IV non-small cell lung cancer or stage IV colorectal cancer were overestimated by more than 1 year. Conclusions and Relevance Clinicogenomic data are a valuable resource for evaluation of real-world cancer outcomes and should be analyzed using appropriate methods to maximize their potential. Analysts must become adept at application of appropriate statistical methods to ensure valid, meaningful, and generalizable research findings.
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Affiliation(s)
- Samantha Brown
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Ronglai Shen
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Axel S Martin
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenneth L Kehl
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Shawn M Sweeney
- American Association for Cancer Research, Philadelphia, Pennsylvania
| | - Eva M Lepisto
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Hira Rizvi
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | - Ben Ho Park
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | - Deborah Schrag
- Memorial Sloan Kettering Cancer Center, New York, New York.,Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
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10
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Kehl KL, Riely GJ, Lepisto EM, Lavery JA, Warner JL, LeNoue-Newton ML, Sweeney SM, Rudolph JE, Brown S, Yu C, Bedard PL, Schrag D, Panageas KS. Correlation Between Surrogate End Points and Overall Survival in a Multi-institutional Clinicogenomic Cohort of Patients With Non-Small Cell Lung or Colorectal Cancer. JAMA Netw Open 2021; 4:e2117547. [PMID: 34309669 PMCID: PMC8314138 DOI: 10.1001/jamanetworkopen.2021.17547] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
IMPORTANCE Contemporary observational cancer research requires associating genomic biomarkers with reproducible end points; overall survival (OS) is a key end point, but interpretation can be challenging when multiple lines of therapy and prolonged survival are common. Progression-free survival (PFS), time to treatment discontinuation (TTD), and time to next treatment (TTNT) are alternative end points, but their utility as surrogates for OS in real-world clinicogenomic data sets has not been well characterized. OBJECTIVE To measure correlations between candidate surrogate end points and OS in a multi-institutional clinicogenomic data set. DESIGN, SETTING, AND PARTICIPANTS A retrospective cohort study was conducted of patients with non-small cell lung cancer (NSCLC) or colorectal cancer (CRC) whose tumors were genotyped at 4 academic centers from January 1, 2014, to December 31, 2017, and who initiated systemic therapy for advanced disease. Patients were followed up through August 31, 2020 (NSCLC), and October 31, 2020 (CRC). Statistical analyses were conducted on January 5, 2021. EXPOSURES Candidate surrogate end points included TTD; TTNT; PFS based on imaging reports only; PFS based on medical oncologist ascertainment only; PFS based on either imaging or medical oncologist ascertainment, whichever came first; and PFS defined by a requirement that both imaging and medical oncologist ascertainment have indicated progression. MAIN OUTCOMES AND MEASURES The primary outcome was the correlation between candidate surrogate end points and OS. RESULTS There were 1161 patients with NSCLC (648 women [55.8%]; mean [SD] age, 63 [11] years) and 1150 with CRC (647 men [56.3%]; mean [SD] age, 54 [12] years) identified for analysis. Progression-free survival based on both imaging and medical oncologist documentation was most correlated with OS (NSCLC: ρ = 0.76; 95% CI, 0.73-0.79; CRC: ρ = 0.73; 95% CI, 0.69-0.75). Time to treatment discontinuation was least associated with OS (NSCLC: ρ = 0.45; 95% CI, 0.40-0.50; CRC: ρ = 0.13; 95% CI, 0.06-0.19). Time to next treatment was modestly associated with OS (NSCLC: ρ = 0.60; 0.55-0.64; CRC: ρ = 0.39; 95% CI, 0.32-0.46). CONCLUSIONS AND RELEVANCE This cohort study suggests that PFS based on both a radiologist and a treating oncologist determining that a progression event has occurred was the surrogate end point most highly correlated with OS for analysis of observational clinicogenomic data.
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Affiliation(s)
- Kenneth L. Kehl
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Gregory J. Riely
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eva M. Lepisto
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jessica A. Lavery
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jeremy L. Warner
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Informatics, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Shawn M. Sweeney
- American Association for Cancer Research, Philadelphia, Pennsylvania
| | - Julia E. Rudolph
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samantha Brown
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Celeste Yu
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Philippe L. Bedard
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Deborah Schrag
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Associate Editor, JAMA
| | - Katherine S. Panageas
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
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11
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Brown S, Lavery JA, Lepisto EM, McCarthy C, Rizvi H, Yu C, Kehl KL, Sweeney SM, Rudolph JE, Schultz N, Kundra R, Mastrogiacomo B, Bedard P, Warner JL, Riely GJ, Schrag D, Panageas KS. Abstract 2620: Ignoring left truncation in overall survival within real-world genomic-phenomic data leads to inflated survival estimates. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2620] [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
Studies linking genomic and phenomic data are subject to selection biases, including delayed entry or immortal time bias. Delayed entry can be problematic for time-to-event analyses, but utilization of appropriate statistical methods to account for delayed entry are underutilized. Delayed entry commonly occurs when genomic sequencing results are obtained after the start time for survival estimation.
To evaluate the impact of left truncation on overall survival (OS) estimates, we explored outcomes in patients with de novo stage IV non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) from the AACR GENIE Biopharma Collaborative, who had genomic sequencing within a specified timeframe. We analyzed OS from diagnosis and from start of the most common first-line regimen, carboplatin/pemetrexed for NSCLC (N = 212 patients) and FOLFOX for CRC (N = 369 patients). We compared median OS using standard Kaplan-Meier methods to median OS using left truncation methods to account for delayed entry. All NSCLC and CRC patients underwent genomic sequencing after their diagnosis date. Among NSCLC patients on carboplatin/pemetrexed, 41% and among CRC patients on FOLFOX, 14% had sequencing determined after starting first-line regimen. The survfit function in R package survival was used, and the absolute differences and percent differences in median OS estimates were calculated.
Failure to account for delayed entry leads to an overestimation of OS, regardless of cohort and start date. Adjusting survival outcomes using left truncation methods reduces the influence of some aspects of selection bias and results in better estimates of time to event outcomes. Analyses from these cohorts can provide meaningful insights about survival outcomes outside the clinical trial setting and may support trial design and reliable selection of control arms. As such, it is imperative that analytic methods to account for the inflated survival estimates are incorporated.
EstimateCRC Stage IV (N = 658)NSCLC Stage IV (N = 722)Unadjusted Median (IQR) Overall Survival from Diagnosis (Years)3.2 (2.9, 3.4)2.3 (2.0, 2.5)Median (IQR) Overall Survival from Diagnosis in Years, Adjusting for Delayed Entry2.1 (1.9, 2.4)1.3 (1.1, 1.6)Difference in Medians (Years)1.11.0% Difference in Medians34%44%EstimateCRC Stage IV (N = 369)NSCLC Stage IV (N = 212)Unadjusted Median (IQR) Overall Survival from Most Common First-Line Regimen (Years)2.9 (2.6, 3.4)1.3 (1.0, 1.6)Median (IQR) Overall Survival from Most Common First-Line Regimen in Years, Adjusting for Delayed Entry2.1 (1.8, 2.5)0.9 (0.7, 1.2)Difference in Medians (Years)0.80.4% Difference in Medians28%31%
Citation Format: Samantha Brown, Jessica A. Lavery, Eva M. Lepisto, Caroline McCarthy, Hira Rizvi, Celeste Yu, Kenneth L. Kehl, Shawn M. Sweeney, Julia E. Rudolph, Nikolaus Schultz, Ritika Kundra, Brooke Mastrogiacomo, Phillipe Bedard, Jeremy L. Warner, Gregory J. Riely, Deborah Schrag, Katherine S. Panageas, The AACR Project GENIE Consortium. Ignoring left truncation in overall survival within real-world genomic-phenomic data leads to inflated survival estimates [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2620.
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Affiliation(s)
| | | | | | | | - Hira Rizvi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Celeste Yu
- 3Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | | | | | - Ritika Kundra
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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12
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Lavery JA, Brown S, Lepisto E, Lenoue-Newton ML, McCarthy C, Rizvi H, Yu C, Kehl KL, Sweeney SM, Rudolph JE, Schultz N, Mastrogiacomo B, Kundra R, Warner J, Bedard P, Riely GJ, Panageas KS, Schrag D. Abstract 2619: Defining real-world recurrence in the AACR Project GENIE Biopharma Collaborative Data. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2619] [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
Obtaining information regarding cancer recurrence from a retrospective, EHR-based dataset poses several challenges primarily due to the lack of structured data. Patients are at risk for cancer recurrence beginning at a time point at which they are characterized as having no evidence of disease. The absence of cancer may be indicated on a radiology report or a medical oncologist assessment, requiring manual review and interpretation of potentially ambiguous free text. Further, the recurrence event itself can be defined based on several distinct data sources including pathology, imaging, clinician assessments, or tumor markers. The likelihood of ascertaining recurrence is dependent on the frequency and type of surveillance performed and varies based on tumor type and based on clinicians' thresholds for pursuing workup of borderline or suspicious findings; if follow up assessments are infrequent, there are fewer opportunities to detect recurrence. Given these challenges, there is currently no standardized approach to evaluating cancer recurrence in EHR data, impeding analyses of rare molecular tumor subtypes in multi-institutional linked clinico-genomic databases.
For this analysis, we leveraged the AACR Project GENIE Biopharma Collaborative data based on the PRISSMM curation model to develop an algorithm for identifying recurrence among patients diagnosed with stage I-III non-small cell lung cancer or with stage I-III colorectal cancer. This algorithm involves using curated pathology report data to identify a definitive surgery as the time at which patients have completed curative intent treatment. Subsequent imaging reports, pathology reports, medical oncologist assessments and tumor marker data are then evaluated in order to characterize the timing of specific recurrence events.
We will present the real-world recurrence algorithm, its underlying rationale and discuss applications of recurrence endpoints. Beyond enabling estimates of recurrence-free survival, identifying cancer recurrence will allow for estimation of progression-free survival among stage I-III patients in addition to estimation of PFS among de novo stage IV patients. Estimating PFS in a large cohort of patients with linked phenomic and genomic data has historically been a limitation of these types of datasets. Overcoming this limitation will allow for precision medicine advances in oncology by facilitating data pooling across institutions and enabling examination of rare molecular subtypes in relation to clinically meaningful endpoints.
Citation Format: Jessica A. Lavery, Samantha Brown, Eva Lepisto, Michele L. Lenoue-Newton, Caroline McCarthy, Hira Rizvi, Celeste Yu, Kenneth L. Kehl, Shawn M. Sweeney, Julia E. Rudolph, Nikolaus Schultz, Brooke Mastrogiacomo, Ritika Kundra, Jeremy Warner, Philippe Bedard, Gregory J. Riely, Katherine S. Panageas, Deborah Schrag, AACR Project GENIE Consortium. Defining real-world recurrence in the AACR Project GENIE Biopharma Collaborative Data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2619.
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Affiliation(s)
| | | | | | | | | | - Hira Rizvi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Celeste Yu
- 4Princess Margaret - University Health Network, Toronto, Ontario, Canada
| | | | | | | | | | | | - Ritika Kundra
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Philippe Bedard
- 4Princess Margaret - University Health Network, Toronto, Ontario, Canada
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13
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Smyth LM, Zhou Q, Nguyen B, Yu C, Lepisto EM, Arnedos M, Hasset MJ, Lenoue-Newton ML, Blauvelt N, Dogan S, Micheel CM, Wathoo C, Horlings H, Hudecek J, Gross BE, Kundra R, Sweeney SM, Gao J, Schultz N, Zarski A, Gardos SM, Lee J, Sheffler-Collins S, Park BH, Sawyers CL, André F, Levy M, Meric-Bernstam F, Bedard PL, Iasonos A, Schrag D, Hyman DM. Characteristics and Outcome of AKT1 E17K-Mutant Breast Cancer Defined through AACR Project GENIE, a Clinicogenomic Registry. Cancer Discov 2020; 10:526-535. [PMID: 31924700 DOI: 10.1158/2159-8290.cd-19-1209] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/18/2019] [Accepted: 01/10/2020] [Indexed: 01/10/2023]
Abstract
AKT inhibitors have promising activity in AKT1 E17K-mutant estrogen receptor (ER)-positive metastatic breast cancer, but the natural history of this rare genomic subtype remains unknown. Utilizing AACR Project GENIE, an international clinicogenomic data-sharing consortium, we conducted a comparative analysis of clinical outcomes of patients with matched AKT1 E17K-mutant (n = 153) and AKT1-wild-type (n = 302) metastatic breast cancer. AKT1-mutant cases had similar adjusted overall survival (OS) compared with AKT1-wild-type controls (median OS, 24.1 vs. 29.9, respectively; P = 0.98). AKT1-mutant cases enjoyed longer durations on mTOR inhibitor therapy, an observation previously unrecognized in pivotal clinical trials due to the rarity of this alteration. Other baseline clinicopathologic features, as well as durations on other classes of therapy, were broadly similar. In summary, we demonstrate the feasibility of using a novel and publicly accessible clincogenomic registry to define outcomes in a rare genomically defined cancer subtype, an approach with broad applicability to precision oncology. SIGNIFICANCE: We delineate the natural history of a rare genomically distinct cancer, AKT1 E17K-mutant ER-positive breast cancer, using a publicly accessible registry of real-world patient data, thereby illustrating the potential to inform drug registration through synthetic control data.See related commentary by Castellanos and Baxi, p. 490.
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Affiliation(s)
| | - Qin Zhou
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bastien Nguyen
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Celeste Yu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | | | | | | | | | | | - Chetna Wathoo
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hugo Horlings
- Netherlands Cancer Institute (NKI), Amsterdam, the Netherlands
| | - Jan Hudecek
- Netherlands Cancer Institute (NKI), Amsterdam, the Netherlands
| | | | - Ritika Kundra
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shawn M Sweeney
- American Association for Cancer Research, Philadelphia, Pennsylvania
| | - JianJiong Gao
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Andrew Zarski
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jocelyn Lee
- American Association for Cancer Research, Philadelphia, Pennsylvania
| | | | - Ben H Park
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee
| | | | | | - Mia Levy
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee
| | | | | | - Alexia Iasonos
- Memorial Sloan Kettering Cancer Center, New York, New York
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14
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Micheel CM, Sweeney SM, LeNoue-Newton ML, André F, Bedard PL, Guinney J, Meijer GA, Rollins BJ, Sawyers CL, Schultz N, Shaw KRM, Velculescu VE, Levy MA. American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange: From Inception to First Data Release and Beyond-Lessons Learned and Member Institutions' Perspectives. JCO Clin Cancer Inform 2019; 2:1-14. [PMID: 30652542 PMCID: PMC6873906 DOI: 10.1200/cci.17.00083] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 11/20/2022] Open
Abstract
The American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) is an international data-sharing consortium focused on enabling advances in precision oncology through the gathering and sharing of tumor genetic sequencing data linked with clinical data. The project's history, operational structure, lessons learned, and institutional perspectives on participation in the data-sharing consortium are reviewed. Individuals involved with the inception and execution of AACR Project GENIE from each member institution described their experiences and lessons learned. The consortium was conceived in January 2014 and publicly released its first data set in January 2017, which consisted of 18,804 samples from 18,324 patients contributed by the eight founding institutions. Commitment and contributions from many individuals at AACR and the member institutions were crucial to the consortium's success. These individuals filled leadership, project management, informatics, data curation, contracts, ethics, and security roles. Many lessons were learned during the first 3 years of the consortium, including on how to gather, harmonize, and share data; how to make decisions and foster collaboration; and how to set the stage for continued participation and expansion of the consortium. We hope that the lessons shared here will assist new GENIE members as well as others who embark on the journey of forming a genomic data-sharing consortium.
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Affiliation(s)
- Christine M Micheel
- Christine M. Micheel, Michele L. LeNoue-Newton, and Mia A. Levy, Vanderbilt University Medical Center, Nashville, TN; Shawn M. Sweeney, American Association for Cancer Research, Philadelphia, PA; Fabrice André, Institut Gustave Roussy, Villejuif, France; Philippe L. Bedard, University of Toronto, Toronto, Ontario, Canada; Justin Guinney, Sage Bionetworks, Seattle, WA; Gerrit A. Meijer, Netherlands Cancer Institute, Amsterdam, the Netherlands; Barrett J. Rollins, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA; Charles L. Sawyers and Nikolaus Schultz, Memorial Sloan Kettering Cancer Center, New York, NY; Charles L. Sawyers, Howard Hughes Medical Institute, Chevy Chase, MD; Victor E. Velculescu, Johns Hopkins University School of Medicine, Baltimore, MD; and Kenna R. Mills Shaw, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shawn M Sweeney
- Christine M. Micheel, Michele L. LeNoue-Newton, and Mia A. Levy, Vanderbilt University Medical Center, Nashville, TN; Shawn M. Sweeney, American Association for Cancer Research, Philadelphia, PA; Fabrice André, Institut Gustave Roussy, Villejuif, France; Philippe L. Bedard, University of Toronto, Toronto, Ontario, Canada; Justin Guinney, Sage Bionetworks, Seattle, WA; Gerrit A. Meijer, Netherlands Cancer Institute, Amsterdam, the Netherlands; Barrett J. Rollins, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA; Charles L. Sawyers and Nikolaus Schultz, Memorial Sloan Kettering Cancer Center, New York, NY; Charles L. Sawyers, Howard Hughes Medical Institute, Chevy Chase, MD; Victor E. Velculescu, Johns Hopkins University School of Medicine, Baltimore, MD; and Kenna R. Mills Shaw, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michele L LeNoue-Newton
- Christine M. Micheel, Michele L. LeNoue-Newton, and Mia A. Levy, Vanderbilt University Medical Center, Nashville, TN; Shawn M. Sweeney, American Association for Cancer Research, Philadelphia, PA; Fabrice André, Institut Gustave Roussy, Villejuif, France; Philippe L. Bedard, University of Toronto, Toronto, Ontario, Canada; Justin Guinney, Sage Bionetworks, Seattle, WA; Gerrit A. Meijer, Netherlands Cancer Institute, Amsterdam, the Netherlands; Barrett J. Rollins, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA; Charles L. Sawyers and Nikolaus Schultz, Memorial Sloan Kettering Cancer Center, New York, NY; Charles L. Sawyers, Howard Hughes Medical Institute, Chevy Chase, MD; Victor E. Velculescu, Johns Hopkins University School of Medicine, Baltimore, MD; and Kenna R. Mills Shaw, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Fabrice André
- Christine M. Micheel, Michele L. LeNoue-Newton, and Mia A. Levy, Vanderbilt University Medical Center, Nashville, TN; Shawn M. Sweeney, American Association for Cancer Research, Philadelphia, PA; Fabrice André, Institut Gustave Roussy, Villejuif, France; Philippe L. Bedard, University of Toronto, Toronto, Ontario, Canada; Justin Guinney, Sage Bionetworks, Seattle, WA; Gerrit A. Meijer, Netherlands Cancer Institute, Amsterdam, the Netherlands; Barrett J. Rollins, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA; Charles L. Sawyers and Nikolaus Schultz, Memorial Sloan Kettering Cancer Center, New York, NY; Charles L. Sawyers, Howard Hughes Medical Institute, Chevy Chase, MD; Victor E. Velculescu, Johns Hopkins University School of Medicine, Baltimore, MD; and Kenna R. Mills Shaw, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Philippe L Bedard
- Christine M. Micheel, Michele L. LeNoue-Newton, and Mia A. Levy, Vanderbilt University Medical Center, Nashville, TN; Shawn M. Sweeney, American Association for Cancer Research, Philadelphia, PA; Fabrice André, Institut Gustave Roussy, Villejuif, France; Philippe L. Bedard, University of Toronto, Toronto, Ontario, Canada; Justin Guinney, Sage Bionetworks, Seattle, WA; Gerrit A. Meijer, Netherlands Cancer Institute, Amsterdam, the Netherlands; Barrett J. Rollins, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA; Charles L. Sawyers and Nikolaus Schultz, Memorial Sloan Kettering Cancer Center, New York, NY; Charles L. Sawyers, Howard Hughes Medical Institute, Chevy Chase, MD; Victor E. Velculescu, Johns Hopkins University School of Medicine, Baltimore, MD; and Kenna R. Mills Shaw, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Justin Guinney
- Christine M. Micheel, Michele L. LeNoue-Newton, and Mia A. Levy, Vanderbilt University Medical Center, Nashville, TN; Shawn M. Sweeney, American Association for Cancer Research, Philadelphia, PA; Fabrice André, Institut Gustave Roussy, Villejuif, France; Philippe L. Bedard, University of Toronto, Toronto, Ontario, Canada; Justin Guinney, Sage Bionetworks, Seattle, WA; Gerrit A. Meijer, Netherlands Cancer Institute, Amsterdam, the Netherlands; Barrett J. Rollins, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA; Charles L. Sawyers and Nikolaus Schultz, Memorial Sloan Kettering Cancer Center, New York, NY; Charles L. Sawyers, Howard Hughes Medical Institute, Chevy Chase, MD; Victor E. Velculescu, Johns Hopkins University School of Medicine, Baltimore, MD; and Kenna R. Mills Shaw, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gerrit A Meijer
- Christine M. Micheel, Michele L. LeNoue-Newton, and Mia A. Levy, Vanderbilt University Medical Center, Nashville, TN; Shawn M. Sweeney, American Association for Cancer Research, Philadelphia, PA; Fabrice André, Institut Gustave Roussy, Villejuif, France; Philippe L. Bedard, University of Toronto, Toronto, Ontario, Canada; Justin Guinney, Sage Bionetworks, Seattle, WA; Gerrit A. Meijer, Netherlands Cancer Institute, Amsterdam, the Netherlands; Barrett J. Rollins, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA; Charles L. Sawyers and Nikolaus Schultz, Memorial Sloan Kettering Cancer Center, New York, NY; Charles L. Sawyers, Howard Hughes Medical Institute, Chevy Chase, MD; Victor E. Velculescu, Johns Hopkins University School of Medicine, Baltimore, MD; and Kenna R. Mills Shaw, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Barrett J Rollins
- Christine M. Micheel, Michele L. LeNoue-Newton, and Mia A. Levy, Vanderbilt University Medical Center, Nashville, TN; Shawn M. Sweeney, American Association for Cancer Research, Philadelphia, PA; Fabrice André, Institut Gustave Roussy, Villejuif, France; Philippe L. Bedard, University of Toronto, Toronto, Ontario, Canada; Justin Guinney, Sage Bionetworks, Seattle, WA; Gerrit A. Meijer, Netherlands Cancer Institute, Amsterdam, the Netherlands; Barrett J. Rollins, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA; Charles L. Sawyers and Nikolaus Schultz, Memorial Sloan Kettering Cancer Center, New York, NY; Charles L. Sawyers, Howard Hughes Medical Institute, Chevy Chase, MD; Victor E. Velculescu, Johns Hopkins University School of Medicine, Baltimore, MD; and Kenna R. Mills Shaw, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Charles L Sawyers
- Christine M. Micheel, Michele L. LeNoue-Newton, and Mia A. Levy, Vanderbilt University Medical Center, Nashville, TN; Shawn M. Sweeney, American Association for Cancer Research, Philadelphia, PA; Fabrice André, Institut Gustave Roussy, Villejuif, France; Philippe L. Bedard, University of Toronto, Toronto, Ontario, Canada; Justin Guinney, Sage Bionetworks, Seattle, WA; Gerrit A. Meijer, Netherlands Cancer Institute, Amsterdam, the Netherlands; Barrett J. Rollins, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA; Charles L. Sawyers and Nikolaus Schultz, Memorial Sloan Kettering Cancer Center, New York, NY; Charles L. Sawyers, Howard Hughes Medical Institute, Chevy Chase, MD; Victor E. Velculescu, Johns Hopkins University School of Medicine, Baltimore, MD; and Kenna R. Mills Shaw, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nikolaus Schultz
- Christine M. Micheel, Michele L. LeNoue-Newton, and Mia A. Levy, Vanderbilt University Medical Center, Nashville, TN; Shawn M. Sweeney, American Association for Cancer Research, Philadelphia, PA; Fabrice André, Institut Gustave Roussy, Villejuif, France; Philippe L. Bedard, University of Toronto, Toronto, Ontario, Canada; Justin Guinney, Sage Bionetworks, Seattle, WA; Gerrit A. Meijer, Netherlands Cancer Institute, Amsterdam, the Netherlands; Barrett J. Rollins, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA; Charles L. Sawyers and Nikolaus Schultz, Memorial Sloan Kettering Cancer Center, New York, NY; Charles L. Sawyers, Howard Hughes Medical Institute, Chevy Chase, MD; Victor E. Velculescu, Johns Hopkins University School of Medicine, Baltimore, MD; and Kenna R. Mills Shaw, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kenna R Mills Shaw
- Christine M. Micheel, Michele L. LeNoue-Newton, and Mia A. Levy, Vanderbilt University Medical Center, Nashville, TN; Shawn M. Sweeney, American Association for Cancer Research, Philadelphia, PA; Fabrice André, Institut Gustave Roussy, Villejuif, France; Philippe L. Bedard, University of Toronto, Toronto, Ontario, Canada; Justin Guinney, Sage Bionetworks, Seattle, WA; Gerrit A. Meijer, Netherlands Cancer Institute, Amsterdam, the Netherlands; Barrett J. Rollins, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA; Charles L. Sawyers and Nikolaus Schultz, Memorial Sloan Kettering Cancer Center, New York, NY; Charles L. Sawyers, Howard Hughes Medical Institute, Chevy Chase, MD; Victor E. Velculescu, Johns Hopkins University School of Medicine, Baltimore, MD; and Kenna R. Mills Shaw, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Victor E Velculescu
- Christine M. Micheel, Michele L. LeNoue-Newton, and Mia A. Levy, Vanderbilt University Medical Center, Nashville, TN; Shawn M. Sweeney, American Association for Cancer Research, Philadelphia, PA; Fabrice André, Institut Gustave Roussy, Villejuif, France; Philippe L. Bedard, University of Toronto, Toronto, Ontario, Canada; Justin Guinney, Sage Bionetworks, Seattle, WA; Gerrit A. Meijer, Netherlands Cancer Institute, Amsterdam, the Netherlands; Barrett J. Rollins, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA; Charles L. Sawyers and Nikolaus Schultz, Memorial Sloan Kettering Cancer Center, New York, NY; Charles L. Sawyers, Howard Hughes Medical Institute, Chevy Chase, MD; Victor E. Velculescu, Johns Hopkins University School of Medicine, Baltimore, MD; and Kenna R. Mills Shaw, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Mia A Levy
- Christine M. Micheel, Michele L. LeNoue-Newton, and Mia A. Levy, Vanderbilt University Medical Center, Nashville, TN; Shawn M. Sweeney, American Association for Cancer Research, Philadelphia, PA; Fabrice André, Institut Gustave Roussy, Villejuif, France; Philippe L. Bedard, University of Toronto, Toronto, Ontario, Canada; Justin Guinney, Sage Bionetworks, Seattle, WA; Gerrit A. Meijer, Netherlands Cancer Institute, Amsterdam, the Netherlands; Barrett J. Rollins, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA; Charles L. Sawyers and Nikolaus Schultz, Memorial Sloan Kettering Cancer Center, New York, NY; Charles L. Sawyers, Howard Hughes Medical Institute, Chevy Chase, MD; Victor E. Velculescu, Johns Hopkins University School of Medicine, Baltimore, MD; and Kenna R. Mills Shaw, The University of Texas MD Anderson Cancer Center, Houston, TX
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15
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Cerami E, Baras AS, Guinney J, Lepisto E, Pugh TJ, Schultz N, Stricker T, Sweeney SM, Veer LJV, Meijer GA, Andre F, Velculescu VE, Shaw KR, Levy MA, Bedard PL, Rollins BJ, Sawyers CL. Abstract LB-102: Landscape analysis of the initial data release from AACR Project GENIE. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-lb-102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE) is a multi-phase, multi-year, international data-sharing consortium whose goal is to generate an evidence base for precision cancer medicine by integrating and linking clinical-grade cancer genomic data with clinical outcome data for tens of thousands of cancer patients treated at multiple institutions worldwide. The project fulfills an unmet need in oncology by providing the statistical power necessary to identify novel therapeutic targets, to understand genomic determinants of response to therapy, to design new biomarker-driven clinical trials and ultimately, to improve clinical decision-making and the care delivered to patients. Here we describe the goals, structure and data standards of the GENIE consortium and conclusions from a high-level analysis of the first public release of genomic and limited clinical data from approximately 19,000 patients treated at eight cancer centers obtained during this initial phase of the project. We also explore the clinical utility of these genomic data by examining rates of clinical actionability across multiple cancer types and by estimating patient enrollment rates to the NCI MATCH Trial. Based on yearly rates of sequencing at each of the eight founding institutions, together with the planned addition of new members, we estimate the GENIE database could grow to >100,000 samples within five years. Consistent with the goals of the proposed Cancer Moonshot National Cancer Data Ecosystem, GENIE is committed to the principles of generating interoperable, open access data that can be widely shared across the entire scientific community.
Citation Format: Ethan Cerami, Alexander S. Baras, Justin Guinney, Eva Lepisto, Trevor J. Pugh, Nikolaus Schultz, Thomas Stricker, Shawn M. Sweeney, Laura J. van't Veer, Gerrit A. Meijer, Fabrice Andre, Victor E. Velculescu, Kenna R. Shaw, Mia A. Levy, Philippe L. Bedard, Barrett J. Rollins, Charles L. Sawyers, on behalf of the AACR Project GENIE Consortium. Landscape analysis of the initial data release from AACR Project GENIE [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-102. doi:10.1158/1538-7445.AM2017-LB-102
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Affiliation(s)
| | | | | | | | - Trevor J. Pugh
- 4Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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16
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Sweeney SM, Orgel JP, Fertala A, McAuliffe JD, Turner KR, Di Lullo GA, Chen S, Antipova O, Perumal S, Ala-Kokko L, Forlino A, Cabral WA, Barnes AM, Marini JC, Antonio JDS. Candidate cell and matrix interaction domains on the collagen fibril, the predominant protein of vertebrates. J Biol Chem 2008; 283:21187-97. [PMID: 18487200 PMCID: PMC2475701 DOI: 10.1074/jbc.m709319200] [Citation(s) in RCA: 198] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Revised: 04/11/2008] [Indexed: 11/06/2022] Open
Abstract
Type I collagen, the predominant protein of vertebrates, polymerizes with type III and V collagens and non-collagenous molecules into large cable-like fibrils, yet how the fibril interacts with cells and other binding partners remains poorly understood. To help reveal insights into the collagen structure-function relationship, a data base was assembled including hundreds of type I collagen ligand binding sites and mutations on a two-dimensional model of the fibril. Visual examination of the distribution of functional sites, and statistical analysis of mutation distributions on the fibril suggest it is organized into two domains. The "cell interaction domain" is proposed to regulate dynamic aspects of collagen biology, including integrin-mediated cell interactions and fibril remodeling. The "matrix interaction domain" may assume a structural role, mediating collagen cross-linking, proteoglycan interactions, and tissue mineralization. Molecular modeling was used to superimpose the positions of functional sites and mutations from the two-dimensional fibril map onto a three-dimensional x-ray diffraction structure of the collagen microfibril in situ, indicating the existence of domains in the native fibril. Sequence searches revealed that major fibril domain elements are conserved in type I collagens through evolution and in the type II/XI collagen fibril predominant in cartilage. Moreover, the fibril domain model provides potential insights into the genotype-phenotype relationship for several classes of human connective tissue diseases, mechanisms of integrin clustering by fibrils, the polarity of fibril assembly, heterotypic fibril function, and connective tissue pathology in diabetes and aging.
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Affiliation(s)
- Shawn M. Sweeney
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
| | - Joseph P. Orgel
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
| | - Andrzej Fertala
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
| | - Jon D. McAuliffe
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
| | - Kevin R. Turner
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
| | - Gloria A. Di Lullo
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
| | - Steven Chen
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
| | - Olga Antipova
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
| | - Shiamalee Perumal
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
| | - Leena Ala-Kokko
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
| | - Antonella Forlino
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
| | - Wayne A. Cabral
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
| | - Aileen M. Barnes
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
| | - Joan C. Marini
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
| | - James D. San Antonio
- Cardiovascular Institute, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, the
Center for Synchrotron Radiation Research
and Instrumentation, Department of Biological, Chemical, and Physical
Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, the
Department of Dermatology and Cutaneous
Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the
Department of Statistics, Wharton School,
University of Pennsylvania, Philadelphia 19104, Pennsylvania, the
Chicago Medical School, North Chicago,
Illinois 60064, the Collagen Research
Unit, Biocenter and Department of Medical Biochemistry and Molecular Biology,
University of Oulu, Oulu, Finland,
Connective Tissue Gene Tests, Allentown,
Pennsylvania 18103, the Department of
Biochemistry A. Castellani, University of Pavia, Pavia, Italy, the
Bone and Extracellular Matrix Branch,
Eunice Kennedy Shriver National Institute of Child Health and Human
Development, National Institutes of Health, Bethesda, Maryland 20892, and the
Cardeza Foundation for Hematologic
Research and Department of Medicine, Thomas Jefferson University,
Philadelphia, Pennsylvania 19107
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17
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Sweeney SM, DiLullo G, Slater SJ, Martinez J, Iozzo RV, Lauer-Fields JL, Fields GB, San Antonio JD. Angiogenesis in collagen I requires alpha2beta1 ligation of a GFP*GER sequence and possibly p38 MAPK activation and focal adhesion disassembly. J Biol Chem 2003; 278:30516-24. [PMID: 12788934 DOI: 10.1074/jbc.m304237200] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Angiogenesis depends on proper collagen biosynthesis and cross-linking, and type I collagen is an ideal angiogenic scaffold, although its mechanism is unknown. We examined angiogenesis using an assay wherein confluent monolayers of human umbilical vein endothelial cells were overlain with collagen in a serum-free defined medium. Small spaces formed in the cell layer by 2 h, and cells formed net-like arrays by 6-8 h and capillary-like lumens by 24 h. Blocking of alpha2beta1, but not alpha1 or alpha(v)beta3 integrin function halted morphogenesis. We found that a triple-helical, homotrimeric peptide mimetic of a putative alpha2beta1 binding site: alpha1(I)496-507 GARGERGFP*GER (where single-letter amino acid nomenclature is used, P* = hydroxyproline) inhibited tube formation, whereas a peptide carrying another putative site: alpha1(I)127-138 GLP*GERGRP*GAP* or control peptides did not. A chemical inhibitor of p38 mitogen-activated protein kinase (p38 MAPK), SB202190, blocked tube formation, and p38 MAPK activity was increased in collagen-treated cultures, whereas targeting MAPK kinase (MEK), focal adhesion kinase (FAK), or phosphatidylinositol 3-kinase (PI3K) had little effect. Collagen-treated cells had fewer focal adhesions and 3- to 5-fold less activated FAK. Thus capillary morphogenesis requires endothelial alpha2beta1 integrin engagement of a single type I collagen integrin-binding site, possibly signaling via p38 MAPK and focal adhesion disassembly/FAK inactivation.
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Affiliation(s)
- Shawn M Sweeney
- Department of Pathology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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18
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Abstract
Perlecan, a ubiquitous basement membrane heparan sulfate proteoglycan, plays key roles in blood vessel growth and structural integrity. We discovered that the C terminus of perlecan potently inhibited four aspects of angiogenesis: endothelial cell migration, collagen-induced endothelial tube morphogenesis, and blood vessel growth in the chorioallantoic membrane and in Matrigel plug assays. The C terminus of perlecan was active at nanomolar concentrations and blocked endothelial cell adhesion to fibronectin and type I collagen, without directly binding to either protein; henceforth we have named it "endorepellin." We also found that endothelial cells possess a significant number of high affinity (K(d) of 11 nm) binding sites for endorepellin and that endorepellin binds endostatin and counteracts its anti-angiogenic effects. Thus, endorepellin represents a novel anti-angiogenic product, which may retard tumor neovascularization and hence tumor growth in vivo.
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Affiliation(s)
- Maurizio Mongiat
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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19
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Di Lullo GA, Sweeney SM, Korkko J, Ala-Kokko L, San Antonio JD. Mapping the ligand-binding sites and disease-associated mutations on the most abundant protein in the human, type I collagen. J Biol Chem 2002; 277:4223-31. [PMID: 11704682 DOI: 10.1074/jbc.m110709200] [Citation(s) in RCA: 569] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Type I collagen is the most abundant protein in humans, and it helps to maintain the integrity of many tissues via its interactions with cell surfaces, other extracellular matrix molecules, and growth and differentiation factors. Nearly 50 molecules have been found to interact with type I collagen, and for about half of them, binding sites on this collagen have been elucidated. In addition, over 300 mutations in type I collagen associated with human connective tissue disorders have been described. However, the spatial relationships between the known ligand-binding sites and mutation positions have not been examined. To this end, here we have created a map of type I collagen that includes all of its ligand-binding sites and mutations. The map reveals the existence of several hot spots for ligand interactions on type I collagen and that most of the binding sites locate to its C-terminal half. Moreover, on the collagen fibril some potentially relevant relationships between binding sites were observed including the following: fibronectin- and certain integrin-binding regions are near neighbors, which may mechanistically relate to fibronectin-dependent cell-collagen attachment; proteoglycan binding may potentially impact upon collagen fibrillogenesis, cell-collagen attachment, and collagen glycation seen in diabetes and aging; and mutations associated with osteogenesis imperfecta and other disorders show apparently nonrandom distribution patterns within both the monomer and fibril, implying that mutation positions correlate with disease phenotype. These and other observations presented here may provide novel insights into evaluating type I collagen functions and the relationships between its binding partners and mutations.
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Affiliation(s)
- Gloria A Di Lullo
- Department of Medicine and the Cardeza Foundation for Hematologic Research, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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20
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Salomoni P, Condorelli F, Sweeney SM, Calabretta B. Versatility of BCR/ABL-expressing leukemic cells in circumventing proapoptotic BAD effects. Blood 2000; 96:676-84. [PMID: 10887134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
BAD, the proapoptotic member of the "BH3-only" subfamily of BCL-2 proteins, is inactivated by phosphorylation at serines 112 and 136 and by sequestration in the cytoplasm where it interacts with members of the 14-3-3 family. In BCR/ABL-expressing cells, BAD is constitutively phosphorylated and mainly cytoplasmic, whereas in cells expressing BCR/ABL mutants unable to protect from apoptosis, BAD is nonphosphorylated. We show here that both the wild-type (WT) and the S112A/ S136A double mutant (DM) BAD are more potent inducers of apoptosis in parental than in BCR/ABL-expressing 32D myeloid precursor cells. Stable lines of parental cells expressing DM BAD could not be established and most clones from WT BAD retrovirus-infected parental cells lost BAD expression. On IL-3 withdrawal from parental 32D cells, BAD was rapidly dephosphorylated by the serine-threonine phosphatase 1 alpha, and localized in the mitochondria, whereas it remained phosphorylated and did not localize to the mitochondria in the cohort of BCR/ABL-expressing cells escaping apoptosis induced by WT BAD. Moreover, these cells showed high levels of BCL-2 and BCL-X(L) expression. The cohort of BCR/ABL-expressing cells resistant to apoptosis induced by DM BAD showed only high levels of BCL-2 and BCL-X(L). These findings suggest that BCR/ABL-expressing cells are more versatile than normal hematopoietic progenitors in counteracting the apoptotic potential of BAD, and raise the possibility that tumor cells activate multiple antiapoptotic pathways for survival in the face of death-inducing stimuli. (Blood. 2000;96:676-684)
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Affiliation(s)
- P Salomoni
- Department of Microbiology and Immunology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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21
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Sweeney SM, Guy CA, Fields GB, San Antonio JD. Defining the domains of type I collagen involved in heparin- binding and endothelial tube formation. Proc Natl Acad Sci U S A 1998; 95:7275-80. [PMID: 9636139 PMCID: PMC22588 DOI: 10.1073/pnas.95.13.7275] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cell surface heparan sulfate proteoglycan (HSPG) interactions with type I collagen may be a ubiquitous cell adhesion mechanism. However, the HSPG binding sites on type I collagen are unknown. Previously we mapped heparin binding to the vicinity of the type I collagen N terminus by electron microscopy. The present study has identified type I collagen sequences used for heparin binding and endothelial cell-collagen interactions. Using affinity coelectrophoresis, we found heparin to bind as follows: to type I collagen with high affinity (Kd approximately 150 nM); triple-helical peptides (THPs) including the basic N-terminal sequence alpha1(I)87-92, KGHRGF, with intermediate affinities (Kd approximately 2 microM); and THPs including other collagenous sequences, or single-stranded sequences, negligibly (Kd >> 10 microM). Thus, heparin-type I collagen binding likely relies on an N-terminal basic triple-helical domain represented once within each monomer, and at multiple sites within fibrils. We next defined the features of type I collagen necessary for angiogenesis in a system in which type I collagen and heparin rapidly induce endothelial tube formation in vitro. When peptides, denatured or monomeric type I collagen, or type V collagen was substituted for type I collagen, no tubes formed. However, when peptides and type I collagen were tested together, only the most heparin-avid THPs inhibited tube formation, likely by influencing cell interactions with collagen-heparin complexes. Thus, induction of endothelial tube morphogenesis by type I collagen may depend upon its triple-helical and fibrillar conformations and on the N-terminal heparin-binding site identified here.
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Affiliation(s)
- S M Sweeney
- Department of Medicine and the Cardeza Foundation for Hematologic Research, Jefferson Medical College of Thomas Jefferson University, Philadelphia, PA 19107, USA
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22
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Häfeli UO, Sweeney SM, Beresford BA, Humm JL, Macklis RM. Effective targeting of magnetic radioactive 90Y-microspheres to tumor cells by an externally applied magnetic field. Preliminary in vitro and in vivo results. Nucl Med Biol 1995; 22:147-55. [PMID: 7767307 DOI: 10.1016/0969-8051(94)00124-3] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Magnetic biodegradable poly(lactic acid) microspheres that incorporate both magnetite and the beta-emitter 90Y were prepared. By applying a directional external magnetic field gradient in excess of 0.02 Tesla/cm across a 96-well plate containing neuroblastoma cells incubated with the 90Y magnetite loaded microspheres, the radiation dose to the cells could be enhanced or reduced relative to the dose from a uniform loading of the well with 90Y-DTPA. Using the MTT assay, cell survival was measured for the magnetic field directed from above (cell sparing) and from below (cell targeting) the well plate, resulting in 65 +/- 8% or 18 +/- 5% survival respectively. This method was then applied to an in vivo murine tumor model. The biodistribution of intraperitoneally injected magnetic radioactive microspheres, after 24 h in mice, showed that 73 +/- 32% of the radioactivity was found on the subcutaneous tumor that had a rare earth magnet fixed above it. In contrast, the tumor radioactivity with no attached magnet was 6 +/- 4%. Magnetically targeted radiopolymers such as 90Y-microspheres show great promise for regional or intracavitary radiotherapy.
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Affiliation(s)
- U O Häfeli
- Cleveland Clinic Foundation, Radiation Oncology Department, OH 44195, USA
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23
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Häfeli UO, Sweeney SM, Beresford BA, Sim EH, Macklis RM. Magnetically directed poly(lactic acid) 90Y-microspheres: novel agents for targeted intracavitary radiotherapy. J Biomed Mater Res 1994; 28:901-8. [PMID: 7983088 DOI: 10.1002/jbm.820280809] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
High energy beta-emitting radioisotopes like Yttrium-90 have a radiotoxic range of about one centimeter. For cancer treatment they must be brought near the tumor cells and kept there for as long as they are radioactive. We developed as carriers for the ionic form of 90Y a matrix-type polymeric drug delivery system, poly(lactic acid) (PLA) microspheres. This radiopharmaceutical could be selectively delivered to the target site after incorporating 10% Fe3O4 (magnetite) which made the magnetic microspheres (MMS) responsive to an external magnetic field. Furthermore, MMS are biodegradable and slowly hydrolyze into physiologic lactic acid after the radioactivity is completely decayed. Previously prepared 10-40 microns MMS were radiochemically loaded to high specific activity with 90Y at a pH of 5.7. Stability studies showed that approximately 95% of added 90Y is retained within the PLA matrix after 28 days (> 10 half-lives) at 37 degrees C in serum, and electron microscopy showed that the microspheres retained their characteristic morphologic appearance for the same time period. Cytotoxicity studies with SK-N-SH neuroblastoma cells growing in monolayer showed that the radiocytotoxicity of the microspheres could be directed magnetically to either kill or spare specific cell populations, thus making them of great interest for targeted intracavitary tumor therapy. We are currently optimizing this system for use in the treatment of neoplastic meningitis.
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Affiliation(s)
- U O Häfeli
- Joint Center for Radiation Therapy, Harvard Medical School, Boston, Massachusetts
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24
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Abstract
Cerebrospinal fluid formation stems primarily from the transport of Na and Cl in choroid plexus (CP). To characterize properties and modulation of choroidal transporters, we tested diuretics and other agents for ability to alter ion transport in vitro. Adult Sprague-Dawley rats were the source of CPs preincubated with drug for 20 min and then transferred to cerebrospinal fluid (CSF) medium containing 22Na or 36Cl with [3H]mannitol (extracellular correction). Complete base-line curves were established for cellular uptake of Na and Cl at 37 degrees C. The half-maximal uptake occurred at 12 s, so it was used to assess drug effects on rate of transport (nmol Na or Cl/mg CP). Bumetanide (10(-5) and 10(-4) M) decreased uptake of Na and Cl with maximal inhibition (up to 45%) at 10(-5) M. Another cotransport inhibitor, furosemide (10(-4) M), reduced transport of Na by 25% and Cl by 33%. However, acetazolamide (10(-4) M) and atriopeptin III (10(-7) M) significantly lowered uptake of Na (but not Cl), suggesting effect(s) other than on cotransport. The disulfonic stilbene 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid (DIDS; 10(-4) M), known to inhibit Cl-HCO3 exchange, substantially reduced the transport of 36Cl. Bumetanide plus DIDS (both 10(-4) M) caused additive inhibition of 90% of Cl uptake, which provides strong evidence for the existence of both cotransport and antiport Cl carriers. Overall, this in vitro analysis, uncomplicated by variables of blood flow and neural tone, indicates the presence in rat CP of the cotransport of Na and Cl in addition to the established Na-H and Cl-HCO3 exchangers.
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Affiliation(s)
- C E Johanson
- Department of Clinical Neurosciences, Brown University/Rhode Island Hospital, Providence 02902
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