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Nowlen CJ, Daniels M, Uzunparmak B, Ileana Dumbrava EE, Yuan Y, Patel KP, Rayes N, Harkenrider J, Wathoo C, Veazie J, Luna KA, Wang W, Horombe C, Javle M, Ahnert JR, Yap TA, Arun B, Lu KH, Meric-Bernstam F. Limited Independent Follow-Up with Germline Testing of Variants Detected in BRCA1 and BRCA2 by Tumor-Only Sequencing. J Immunother Precis Oncol 2024; 7:7-17. [PMID: 38327755 PMCID: PMC10846638 DOI: 10.36401/jipo-23-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 08/28/2023] [Accepted: 10/10/2023] [Indexed: 02/09/2024]
Abstract
Introduction Genomic profiling is performed in patients with advanced or metastatic cancer, in order to direct cancer treatment, often sequencing tumor-only, without a matched germline comparator. However, because many of the genes analyzed on tumor profiling overlap with those known to be associated with hereditary cancer predisposition syndromes (HCPS), tumor-only profiling can unknowingly uncover germline pathogenic (P) and likely pathogenic variants (LPV). In this study, we evaluated the number of patients with P/LPVs identified in BRCA1 and BRCA2 (BRCA1/2) via tumor-only profiling, then determined the germline testing outcomes for those patients. Methods A retrospective chart review was performed to identify patients with BRCA1/2 variants on tumor-only genomic profiling, and whether they had germline testing. Results This study found that of 2923 patients with 36 tumor types who underwent tumor-only testing, 554 had a variant in BRCA1/2 (19.0%); 119 of the 554 patients (21.5%) had a P/LP BRCA1/2 variant, representing 4.1% of the overall population who underwent genomic profiling. Seventy-three (61.3%) of 119 patients with BRCA1/2 P/LPV on tumor-only testing did not undergo germline testing, 34 (28.6%) had already had germline testing before tumor-only testing, and 12 (10.1%) underwent germline testing after tumor-only testing. Twenty-eight germline BRCA1/2 P/LPVs were detected, 24 in those who had prior germline testing, and 4 among the 12 patients who had germline testing after tumor-only testing. Conclusion Tumor-only testing is likely to identify P/LPVs in BRCA1/2. Efforts to improve follow-up germline testing is needed to improve identification of germline BRCA1/2 alterations.
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Affiliation(s)
- Carol J. Nowlen
- The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Molly Daniels
- Department of Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Burak Uzunparmak
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ecaterina E. Ileana Dumbrava
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ying Yuan
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keyur P. Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nadine Rayes
- Department of Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jacqueline Harkenrider
- Department of Obstetrics, Gynecology, and Reproductive Sciences, The University of Texas Health Science Center at Houston John P. and Katherine G. McGovern Medical School, Houston, TX, USA
| | - Chetna Wathoo
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer Veazie
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krystle A. Luna
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wanlin Wang
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chacha Horombe
- Department of Enterprise Development & Integration, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jordi Rodon Ahnert
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy A. Yap
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Banu Arun
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Karen H. Lu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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LeNoue-Newton ML, Chen SC, Stricker T, Hyman DM, Blauvelt N, Bedard PL, Meric-Bernstam F, Punglia RS, Schrag D, Lepisto EM, Andre F, Smyth L, Dogan S, Yu C, Wathoo C, Levy M, Eli LD, Xu F, Mann G, Lalani AS, Ye F, Micheel CM, Arnedos M. Natural History and Characteristics of ERBB2-mutated Hormone Receptor-positive Metastatic Breast Cancer: A Multi-institutional Retrospective Case-control Study from AACR Project GENIE. Clin Cancer Res 2022; 28:2118-2130. [PMID: 35190802 DOI: 10.1158/1078-0432.ccr-21-0885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/29/2021] [Revised: 06/21/2021] [Accepted: 02/16/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE We wanted to determine the prognosis and the phenotypic characteristics of hormone receptor-positive advanced breast cancer tumors harboring an ERBB2 mutation in the absence of a HER2 amplification. EXPERIMENTAL DESIGN We retrospectively collected information from the American Association of Cancer Research-Genomics Evidence Neoplasia Information Exchange registry database from patients with hormone receptor-positive, HER2-negative, ERBB2-mutated advanced breast cancer. Phenotypic and co-mutational features, as well as response to treatment and outcome were compared with matched control cases ERBB2 wild type. RESULTS A total of 45 ERBB2-mutant cases were identified for 90 matched controls. The presence of an ERBB2 mutation was not associated with worse outcome determined by overall survival (OS) from first metastatic relapse. No significant differences were observed in phenotypic characteristics apart from higher lobular infiltrating subtype in the ERBB2-mutated group. ERBB2 mutation did not seem to have an impact in response to treatment or time-to-progression (TTP) to endocrine therapy compared with ERBB2 wild type. In the co-mutational analyses, CDH1 mutation was more frequent in the ERBB2-mutated group (FDR < 1). Although not significant, fewer co-occurring ESR1 mutations and more KRAS mutations were identified in the ERBB2-mutated group. CONCLUSIONS ERBB2-activating mutation was not associated with a worse OS from time of first metastatic relapse, or differences in TTP on treatment as compared with a series of matched controls. Although not significant, differences in coexisting mutations (CDH1, ESR1, and KRAS) were noted between the ERBB2-mutated and the control group.
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Affiliation(s)
| | - Sheau-Chiann Chen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Thomas Stricker
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David M Hyman
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Philippe L Bedard
- Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, Texas
| | - Rinaa S Punglia
- Department of Radiation Oncology, DFCI, Harvard Medical School, Boston, Massachusetts
| | - Deborah Schrag
- Division of Population Sciences and the Department of Medical Oncology, Dana-Farber/Harvard Cancer Center, Boston, Massachusetts
| | - Eva M Lepisto
- Division of Population Sciences and the Department of Medical Oncology, Dana-Farber/Harvard Cancer Center, Boston, Massachusetts
| | - Fabrice Andre
- Department of Medical Oncology, Gustave Roussy Cancer Campus, Villejuif, France
- INSERM Unit, U981, Gustave Roussy Cancer Campus, Villejuif, France
| | - Lillian Smyth
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Semih Dogan
- Department of Medical Oncology, Gustave Roussy Cancer Campus, Villejuif, France
- INSERM Unit, U981, Gustave Roussy Cancer Campus, Villejuif, France
| | - Celeste Yu
- Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Chetna Wathoo
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, Texas
| | - Mia Levy
- Departments of Biomedical Informatics and Medicine, Division of Hematology/Oncology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lisa D Eli
- PUMA Biotechnology, Los Angeles, California
| | - Feng Xu
- PUMA Biotechnology, Los Angeles, California
| | - Grace Mann
- PUMA Biotechnology, Los Angeles, California
| | | | - Fei Ye
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Christine M Micheel
- Department of Medicine, Division of Hematology/Oncology and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Monica Arnedos
- Department of Medical Oncology, Gustave Roussy Cancer Campus, Villejuif, France
- INSERM Unit, U981, Gustave Roussy Cancer Campus, Villejuif, France
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DiPeri TP, Evans KW, Tzeng CWD, Kwong L, Kahle MP, Zheng X, Li D, Cao HST, Vu T, Kim S, Su F, Kirby B, Wathoo C, Raso G, Rizvi Y, Wang H, Janku F, Shaw K, Yap T, Javle M, Rodon J, Meric-Bernstam F. Abstract 2710: The MD Anderson patient-derived xenograft series for modeling precision oncology in biliary tract cancers. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose: Biliary tract cancers (BTCs), including intrahepatic cholangiocarcinoma (ICC), extrahepatic cholangiocarcinoma (ECC), and gallbladder cancer (GBC), are rare malignancies which frequently present at advanced stage and have a poor survival. Incorporation of next-generation sequencing into clinical care has provided an avenue for the development of targeted therapies in BTCs which are rich in actionable mutations. However, clinically relevant models for BTC are limited, representing a major challenge in the field. We sought to develop a catalog of BTC patient-derived xenograft (PDX) models and representing diverse molecular profiles to create a resource for the modeling of precision oncology.
Methods: Tumor tissue from surgical specimens or image-guided biopsies was collected from consenting patients at MD Anderson Cancer Center with histologically-confirmed BTCs for PDX development. Tumor fragments were implanted in the flank of NSG mice and passaged into nude mice. Whole-exome sequencing (WES) was performed on tumors from early-passage (P1-P2) PDXs and matching patient blood to determine somatic mutations/indels and copy number variations. Functional alterations in cancer-related genes that are targetable directly or indirectly with approved or investigational agents were considered “actionable”.
Results: Samples were obtained from 97 patients undergoing image-guided biopsy (86/97, 89%) or surgical resection (11/97, 11%). Out of 97 tumors implanted, 33 (34%) PDXs from 30 patients were successfully established: 74% (24/33) ICC, 15% (5/33) ECC, and 12% (4/33) GBC. Relative take rates for PDX development were 34% (29/86) for those developed from biopsy samples and 36% (4/11) for those developed from surgical samples. In two patients, multiple PDXs were developed from biopsies at different time points during their care. WES demonstrated that the PDXs captured several key actionable alterations including alterations in ERRB2, FGFR2, IDH1, ATM, PIK3CA, PTEN and KRAS.
Conclusion: Here, we describe a unique collection of clinically and molecularly annotated BTC PDX models which reflect the genomic heterogeneity present in ICC, ECC, and GBC. WES of early-passage PDXs provides evidence that these models capture the variety of actionable alterations harbored in the parental tumor and may enable the development of novel, biomarker-driven treatment strategies and rational combination therapies. To date, this is one of the largest collections of BTC PDX models available and will serve as an invaluable resource to guide the development of personalized treatments for patients with these aggressive malignancies.
Citation Format: Timothy Philip DiPeri, Kurt W. Evans, Ching-Wei D. Tzeng, Lawrence Kwong, Michael P. Kahle, Xiaofeng Zheng, Dali Li, Hop S. Tran Cao, Thuy Vu, Sunhee Kim, Fei Su, Bryce Kirby, Chetna Wathoo, Gabriela Raso, Yasmin Rizvi, Huamin Wang, Filip Janku, Kenna Shaw, Timothy Yap, Milind Javle, Jordi Rodon, Funda Meric-Bernstam. The MD Anderson patient-derived xenograft series for modeling precision oncology in biliary tract cancers [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 2710.
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Affiliation(s)
| | | | | | | | | | | | - Dali Li
- MD Anderson Cancer Center, Houston, TX
| | | | - Thuy Vu
- MD Anderson Cancer Center, Houston, TX
| | | | - Fei Su
- MD Anderson Cancer Center, Houston, TX
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Avila M, Wathoo C, Zeng J, Andersen C, Yuan Y, Yap TA, Rodon Ahnert J, Meric-Bernstam F. Variety of clinical trial enrollment by actionable tumor suppressor genotype. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e15674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e15674 Background: In the last decade, genomics has been increasingly used for therapeutic management of cancer. In precision oncology, genes that can be directly or indirectly targeted with therapeutic agents are considered “actionable”. However, not all alterations affect gene function and alterations in tumor suppressor genes are especially challenging to interpret. The objective of this study was to determine frequency of trial enrollment in patients with “actionable” tumor suppressor alterations and determine whether this varied by genotype and tumor type. Methods: A single-institution retrospective review was performed on patients with metastatic, advanced, or recurrent solid tumors perceived to likely benefit from genomic profiling. Between 1/2015 and 1/2020, the top 5 tumor suppressor alterations CDKN2A, BRCA1/2, PTEN, ATM and NF1 were considered most common “actionable” tumor suppressor genes among patients reviewed by MD Anderson Precision Oncology Decision Support system. Once literature-based or inferred actionability of the tumor-suppressor alteration was determined, a clinical record review was performed to assess an institution-specific annotation detailing trial availability. This annotation matches somatic genomic alteration based on therapeutic significance and availability of matched investigative therapy based on available literature at the time. From here, patient demographics and trial enrollment was extracted from the electronic medical record. Results: 424 patients were categorized as having actionable alterations that had a trial available for enrollment based on genomic characteristics. Of these, 61 patients (14%) enrolled in a matched trial. Primary reasons for non-enrollment for a specific alteration were: enrollment in non-targeted therapeutic trial (39%), treatment with another stand of care therapy (32%), or enrollment in another genomically matched trial targeting another genomic alteration (14%). There was variability in enrollment by disease type approaching statistical significance (p = 0.073). CDKN2A alterations were the most common while BRCA1/2 had the highest rate of matched enrollment (39.5%). Conclusions: In this cohort of patients, the presence of an actionable tumor-suppressor alteration was associated with trial enrollment varying by genotype. Further work is needed to determine the impact of decision support on trial enrollment as well as strategies to increase actionability by building genomically-driven combination therapy trials.
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Affiliation(s)
- Monica Avila
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chetna Wathoo
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jia Zeng
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Clark Andersen
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ying Yuan
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Timothy A Yap
- The University of Texas MD Anderson Cancer Center, Houston, TX
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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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Sánchez NS, Kahle MP, Bailey AM, Wathoo C, Balaji K, Demirhan ME, Yang D, Javle M, Kaseb A, Eng C, Subbiah V, Janku F, Raymond VM, Lanman RB, Mills Shaw KR, Meric-Bernstam F. Identification of Actionable Genomic Alterations Using Circulating Cell-Free DNA. JCO Precis Oncol 2019; 3:PO.19.00017. [PMID: 32923868 PMCID: PMC7448805 DOI: 10.1200/po.19.00017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2019] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Cell-free DNA (cfDNA) next-generation sequencing is a noninvasive approach for genomic testing. We report the frequency of identifying alterations and their clinical actionability in patients with advanced/metastatic cancer. PATIENTS AND METHODS Prospectively consented patients had cfDNA testing performed. Alterations were assessed for therapeutic implications. RESULTS We enrolled 575 patients with 37 tumor types. Of these patients, 438 (76.2%) had at least one alteration detected, and 205 (35.7%) had one or more alterations of high potential for clinical action. In diseases with 10 or more patients enrolled, 50% or more had at least one alteration deemed of high potential for clinical action. Trials were identified in 80% of patients (286 of 357) with any alteration and in 92% of patients (188 of 205) with one or more alterations of high potential for clinical action of whom 57.6% (118 of 205) had 6 or more months of follow-up available. Of these patients, 10% (12 of 118) had received genomically matched therapy through enrollment in clinical trials (n = 8), off-label drug use (n = 3), or standard of care (n = 1). Although 88.6% of all patients had a performance status of 0 or 1 upon enrollment, the primary reason for not acting on alterations was poor performance status at next treatment change (28.1%; 27 of 96). CONCLUSION cfDNA testing represents a readily accessible method for genomic testing and allows for detection of genomic alterations in most patients with advanced disease. Utility may be higher in patients interested in investigational therapeutics with adequate performance status. Additional study is needed to determine whether utility is enhanced by testing earlier in the treatment course.
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Affiliation(s)
- Nora S. Sánchez
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Chetna Wathoo
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kavitha Balaji
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Dong Yang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Milind Javle
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ahmed Kaseb
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Cathy Eng
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vivek Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Filip Janku
- The University of Texas MD Anderson Cancer Center, Houston, TX
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7
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Ileana Dumbrava E, Brusco L, Daniels MS, Wathoo C, Shaw KR, Lu KH, Zheng X, Strong LC, Litton J, Arun BK, Eterovic AK, Routbort MJ, Patel KP, Qi Y, Piha-Paul SA, Subbiah V, Hong DS, Rodon J, Kopetz S, Mendelsohn J, Mills GB, Chen K, Meric-Bernstam F. Expanded analysis of secondary germline findings from matched tumor/normal sequencing identifies additional clinically significant mutations. JCO Precis Oncol 2019; 3:PO.18.00143. [PMID: 31517177 PMCID: PMC6741435 DOI: 10.1200/po.18.00143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) for tumor molecular profiling can reveal secondary germline pathogenic and likely pathogenic variants (LPV/PV). The American College of Medical Genetics (ACMG) recommends return of secondary results for a subset of 59 genes, but other genes with evidence of clinical utility are emerging. We previously reported that 4.3% of patients who underwent NGS of a targeted panel of 201 genes had LPV/PV based on the ACMG list. Here we report the frequency of additional germline cancer-related gene variants and discuss their clinical utility. PATIENTS AND METHODS Matched tumor and germline DNA NGS of a targeted panel of 201 genes was performed in a research laboratory on samples from 1000 patients with advanced or metastatic solid tumors enrolled in a molecular testing protocol (NCT01772771). The frequency of germline LPV/PV in 54 cancer-related genes, beyond the genes in ACMG list, were analyzed. RESULTS Among 1000 patients who underwent tumor/normal DNA sequencing, 46 (4.6%) were found to have a germline LPV/PV in the following genes: AR-(5), ATM-(4), BAP1-(1), CDH1-(1), CDKN2A-(1), CHEK1-(2), CHEK2-(10), EGFR-(1), ERCC3-(4), ERCC5-(1), HNF1B-(1), HRAS-(1), MITF-(4), MLL3-(1), NF1-(3), PKHD1-(4), PTCH1-(1), and SMARCA4-(1). Thus, a total 8.7% of patients had an LPV/PV with 2 patients having 2 concomitant germline LPV/PV. Five mutations in high-penetrance hereditary cancer predisposition genes were selected to be returned to patients or their representatives: BAP1, CDH1, CDKN2A, EGFR, and SMARCA4. CONCLUSIONS Broader genomic testing is likely to identify additional secondary pathogenic germline alterations, some with potential clinical utility for return to patients and their relatives. The recommended genes for which germline results should be returned are continually changing, warranting continued study.
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Affiliation(s)
| | - Lauren Brusco
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Chetna Wathoo
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kenna R. Shaw
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Karen H. Lu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xiaofeng Zheng
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jennifer Litton
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Banu K. Arun
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Keyur P. Patel
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yuan Qi
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Vivek Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David S. Hong
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jordi Rodon
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John Mendelsohn
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gordon B. Mills
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ken Chen
- The University of Texas MD Anderson Cancer Center, Houston, TX
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8
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Kono M, Fujii T, Matsuda N, Harano K, Chen H, Wathoo C, Joon AY, Tripathy D, Meric-Bernstam F, Ueno NT. Somatic mutations, clinicopathologic characteristics, and survival in patients with untreated breast cancer with bone-only and non-bone sites of first metastasis. J Cancer 2018; 9:3640-3646. [PMID: 30310523 PMCID: PMC6171013 DOI: 10.7150/jca.26825] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 07/07/2018] [Indexed: 02/01/2023] Open
Abstract
Background: Bone is the most common site of metastasis of breast cancer. Biological mechanisms of metastasis to bone may be different from mechanisms of metastasis to non-bone sites, and identification of distinct signaling pathways and somatic mutations may provide insights on biology and rational targets for treatment and prevention of bone metastasis. The aims of this study were to compare and contrast somatic mutations, clinicopathologic characteristics, and survival in breast cancer patients with bone-only versus non-bone sites of first metastasis. Methods: Primary tumor samples were collected before treatment from 389 patients with untreated primary breast cancer and distant metastasis at diagnosis. In each sample, 46 or 50 cancer-related genes were analyzed for mutations by AmpliSeq Ion Torrent next-generation sequencing. Fisher's exact test was used to identify somatic mutations associated with bone-only first metastasis. Logistic regression models were used to identify differences in detected somatic mutations, clinicopathologic characteristics, and survival between patients with bone-only first metastasis and patients with first metastasis in non-bone sites only (“other-only first metastasis”). Results: Among the 389 patients, 72 (18.5%) had bone-only first metastasis, 223 (57.3%) had other-only first metastasis, and 94 (24.2%) had first metastasis in both bone and non-bone sites. The most commonly mutated genes were TP53 (N=103), PIK3CA (N=79), AKT (N=13), and PTEN (N=2). Compared to patients with other-only first metastasis, patients with bone-only first metastasis had higher rates of hormone-receptor-positive disease, non-triple-negative subtype, and lower grade (grade 1 or 2; Nottingham grading system) (all three comparisons, p<0.001); had a lower ratio of cases of invasive ductal carcinoma to cases of invasive lobular carcinoma (p=0.002); and tended to have a higher 5-year overall survival (OS) rate (78.2% [95% confidence interval (CI), 68.6%-89.0%] vs 55.0% [95% CI, 48.1%-62.9%]; p=0.051). However, in the subgroup of patients with TP53 mutation and in the subgroup of patients with PIK3CA mutation, OS did not differ between patients with bone-only and other-only first metastasis (p=0.49 and p=0.68, respectively). In univariate analysis, the rate of TP53 mutation tended to be lower in patients with bone-only first metastasis than in those with other-only first metastasis (15.3% vs 29.1%; p=0.051). In multivariate analysis, TP53 mutation was not significantly associated with site of first metastasis (p=0.54) but was significantly associated with hormone-receptor-negative disease (p<0.001). Conclusions: We did not find associations between somatic mutations and bone-only first metastasis in patients with untreated breast cancer. Patients with bone-only first metastasis tend to have longer OS than patients with other-only first metastasis. More comprehensive molecular analysis may be needed to further understand the factors associated with bone-only metastatic disease in breast cancer.
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Affiliation(s)
- Miho Kono
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Takeo Fujii
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Naoko Matsuda
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenichi Harano
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huiqin Chen
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chetna Wathoo
- Sheikh Khalifa Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Aron Y Joon
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Debu Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Funda Meric-Bernstam
- Sheikh Khalifa Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Investigational Cancer Therapeutics (Phase I Trials Department), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Naoto T Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Sanchez NS, Bailey AM, Wathoo C, Balaji K, Demirhan ME, Yang D, Kahle M, Kaseb AO, Javle MM, Eng C, Subbiah V, Janku F, Raymond VM, Lanman RB, Shaw KR, Meric-Bernstam F. Identification of actionable genomic alterations utilizing cfDNA. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.12110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Nora Sylvia Sanchez
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy/ University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ann Marie Bailey
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chetna Wathoo
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Dong Yang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michael Kahle
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Cathy Eng
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vivek Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Filip Janku
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Kenna Rael Shaw
- University of Texas MD Anderson Cancer Center Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, Houston, TX
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10
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Meric-Bernstam F, Zheng X, Shariati M, Damodaran S, Wathoo C, Brusco L, Demirhan ME, Tapia C, Eterovic AK, Basho RK, Ueno NT, Janku F, Sahin A, Rodon J, Broaddus R, Kim TB, Mendelsohn J, Mills Shaw KR, Tripathy D, Mills GB, Chen K. Survival Outcomes by TP53 Mutation Status in Metastatic Breast Cancer. JCO Precis Oncol 2018; 2018. [PMID: 30035249 DOI: 10.1200/po.17.00245] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Purpose We sought to determine the significant genomic alterations in patients with metastatic breast cancer (MBC), and survival outcomes in common genotypes. Patients and Methods High-depth next generation sequencing was performed for 202 genes in tumor and normal DNA from 257 patients with MBC, including 165 patients with ER/PR+ HER2- (hormone receptor positive, HR+ positive), 32 patients with HER2+ and 60 patients with triple negative (ER/PR/HER2-) cancer. Kaplan Meier survival analysis was performed in our discovery set, in breast cancer patients analyzed in The Cancer Genome Atlas, and in a separate cohort of 98 patients with MBC who underwent clinical genomic testing. Results Significantly mutated genes (SMGs) varied by histology and tumor subtype, but TP53 was a SMG in all three subtypes. The most SMGs in HR+ patients included PIK3CA (32%), TP53 (29%), GATA3 (15%), CDH1 (8%), MAP3K1 (8%), PTEN (5%), TGFBR2 (4%), AKT1 (4%), and MAP2K4 (4%). TP53 mutations were associated with shorter recurrence-free survival (P=0.004), progression-free survival (P=0.00057) and overall survival (P=0.003). Further, TP53 status was prognostic among HR+ patients with PIK3CA mutations. TP53 mutations were also associated with poorer overall survival in the 442 HR+ breast cancer patients in the TCGA (P=0.042) and in an independent set of 96 HR+ MBC who underwent clinical sequencing (P=0.0004). Conclusions SMGs differ by tumor subtype but TP53 is significantly mutated in all three breast cancer subtypes. TP53 mutations are associated with poor prognosis in HR+ breast cancer. TP53 mutations should be considered in the design and interpretation of precision oncology trials.
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Affiliation(s)
- Funda Meric-Bernstam
- The Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030.,Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030.,Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Xiaofeng Zheng
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Maryam Shariati
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Senthil Damodaran
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030.,Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Chetna Wathoo
- The Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Lauren Brusco
- The Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030.,Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Mehmet Esat Demirhan
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Coya Tapia
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030.,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Agda Karina Eterovic
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Reva K Basho
- Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030.,current address: Cedars-Sinai, Los Angeles, CA 90048
| | - Naoto T Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Filip Janku
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Aysegul Sahin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Jordi Rodon
- The Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030.,Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Russell Broaddus
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Tae-Beom Kim
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - John Mendelsohn
- The Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Kenna R Mills Shaw
- The Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Debu Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Gordon B Mills
- The Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Ken Chen
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
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Kono M, Fujii T, Matsuda N, Harano K, Chen H, Wathoo C, Aron JY, Tripathy D, Meric-Bernstam F, Ueno NT. Abstract P1-16-04: Somatic mutations, clinicopathologic characteristics, and survival in patients with untreated breast cancer with bone-only and non-bone sites of first metastasis. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p1-16-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Bone is the most common site of metastasis of breast cancer, and bone metastasis is associated with a high rate of skeletal-related events, all of which contribute to decreased quality of life and poor outcomes. Biological mechanisms of metastasis to bone may be unique, and identification of distinct signaling pathways and somatic mutations may provide biological insight into or rational targets for treatment of and prevention of bone metastasis. The aims of this study were to compare and contrast somatic mutations, clinicopathologic characteristics, and survival in breast cancer patients with bone only versus non-bone as first metastatic site.
Methods: Tumor samples were collected from 389 patients who had metastasis and untreated primary breast cancer. In each sample, 46 or 50 cancer-related genes were selectively amplified and analyzed for mutations by AmpliSeq Ion Torrent next-generation sequencing. We used Fisher's exact test to identify somatic mutations associated with bone-only first metastasis and logistic regression models to identify differences in clinicopathologic characteristics, survival, and somatic mutations between patients with bone-only first metastasis and patients with first metastasis in non-bone sites only (“other-only first metastasis”).
Results: Among the 389 patients, the first metastasis was located in bone only in 72 patients (18.5%), non-bone sites only in 223 patients (57.3%), and both in 94 patients (24.2%). Of the cancer-related genes analyzed, the most commonly mutated were TP53 (N=103), PIK3CA (N=79), AKT (N=13), and PTEN (N=2). Compared to patients with other-only first metastasis, patients with bone-only first metastasis had higher rates of hormone-receptor-positive disease, non-triple-negative subtype, and low nuclear grade (grade 1 or 2) (all 3 comparisons, p<0.001); had a lower ratio of cases of invasive ductal carcinoma to cases of invasive lobular carcinoma (p=0.002); and tended to have a higher 5-year overall survival (OS) rate (78.2% [95% confidence interval (CI), 68.6%-89.0%] vs 55.0% [95% CI, 48.1%-62.9%]; p=0.051). However, in the subgroup of patients with TP53 mutation and in the subgroup of patients with PIK3CA mutation, OS did not differ between patients with bone-only and other-only first metastasis (p=0.49 and p=0.68; respectively). In univariate analysis, the rate of TP53 mutation tended to be lower in patients with bone-only first metastasis than in those with other-only first metastasis (15.3% vs 29.1%; p=0.051). In multivariate analysis, TP53 mutation was not significantly associated with site of first metastasis (p=0.54) but was significantly associated with hormone-receptor-negative disease (p<0.001).
Conclusions: We did not find associations between somatic mutations and bone-only first metastasis in patients with untreated breast cancer. Patients with bone-only first metastasis have longer OS than patients with other-only first metastasis. More comprehensive molecular analysis may be needed to further understand the factors associated with bone-only metastatic disease in breast cancer.
Citation Format: Kono M, Fujii T, Matsuda N, Harano K, Chen H, Wathoo C, Aron JY, Tripathy D, Meric-Bernstam F, Ueno NT. Somatic mutations, clinicopathologic characteristics, and survival in patients with untreated breast cancer with bone-only and non-bone sites of first metastasis [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-16-04.
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Affiliation(s)
- M Kono
- Section of Translational Breast Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Biostatistics, Houston, TX; Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Houston, TX
| | - T Fujii
- Section of Translational Breast Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Biostatistics, Houston, TX; Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Houston, TX
| | - N Matsuda
- Section of Translational Breast Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Biostatistics, Houston, TX; Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Houston, TX
| | - K Harano
- Section of Translational Breast Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Biostatistics, Houston, TX; Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Houston, TX
| | - H Chen
- Section of Translational Breast Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Biostatistics, Houston, TX; Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Houston, TX
| | - C Wathoo
- Section of Translational Breast Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Biostatistics, Houston, TX; Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Houston, TX
| | - JY Aron
- Section of Translational Breast Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Biostatistics, Houston, TX; Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Houston, TX
| | - D Tripathy
- Section of Translational Breast Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Biostatistics, Houston, TX; Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Houston, TX
| | - F Meric-Bernstam
- Section of Translational Breast Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Biostatistics, Houston, TX; Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Houston, TX
| | - NT Ueno
- Section of Translational Breast Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Biostatistics, Houston, TX; Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Houston, TX
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Fujii T, Matsuda N, Kono M, Harano K, Chen H, Luthra R, Roy-Chowdhuri S, Sahin AA, Wathoo C, Joon AY, Tripathy D, Meric-Bernstam F, Ueno NT. Prior systemic treatment increased the incidence of somatic mutations in metastatic breast cancer. Eur J Cancer 2017; 89:64-71. [PMID: 29232568 DOI: 10.1016/j.ejca.2017.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 11/01/2017] [Accepted: 11/10/2017] [Indexed: 01/10/2023]
Abstract
BACKGROUND Understanding the biology of breast cancer is important for guiding treatment strategies and revealing resistance mechanisms. Our objectives were to investigate the relationship between previous systemic therapy exposure and mutational spectrum in metastatic breast cancer and to identify clinicopathological factors associated with identified frequent somatic mutations. METHODS Archival tissues of patients with metastatic breast cancer were subjected to hotspot molecular testing by next-generation sequencing. The variables that significantly differed (P < 0.05) in univariate analysis were selected to fit multivariate models. Logistic models were fit to estimate the association between mutation status and clinical variables of interest. Five-fold cross-validation was performed to estimate the prediction error of each model. RESULTS A total of 922 patients were included in the analysis. In multivariate analysis, previous systemic treatment before molecular testing (N = 186) was associated with a significantly higher rate of TP53 and PIK3CA mutations compared with the lack of systemic treatment (P < 0.001 for both). CONCLUSION Systemic treatment exposure is an independent risk factor for high rates of TP53 and PIK3CA mutation, which suggests the importance of testing samples after systemic therapy to accurately assess mutations. It is worth testing the gene profile when tumours become resistant to systemic treatments.
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Affiliation(s)
- Takeo Fujii
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Naoko Matsuda
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Miho Kono
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Kenichi Harano
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Huiqin Chen
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rajyalakshmi Luthra
- Molecular Diagnostic Laboratory, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Aysegul A Sahin
- Department of Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Chetna Wathoo
- Sheikh Khalifa Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Aron Y Joon
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Debu Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Funda Meric-Bernstam
- Sheikh Khalifa Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Investigational Cancer Therapeutics (Phase I Trials Department), The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Naoto T Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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13
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Brusco LL, Wathoo C, Mills Shaw KR, Holla VR, Bailey AM, Johnson AM, Khotskaya YB, Litzenburger BC, Sanchez NS, Zeng J, Bernstam EV, Eng C, Kee BK, Amaria RN, Routbort MJ, Mills GB, Mendelsohn J, Meric-Bernstam F. Physician interpretation of genomic test results and treatment selection. Cancer 2017; 124:966-972. [PMID: 29165790 DOI: 10.1002/cncr.31112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND Genomic testing is increasingly performed in oncology, but concerns remain regarding the clinician's ability to interpret results. In the current study, the authors sought to determine the agreement between physicians and genomic annotators from the Precision Oncology Decision Support (PODS) team at The University of Texas MD Anderson Cancer Center in Houston regarding actionability and the clinical use of test results. METHODS On a prospective protocol, patients underwent clinical genomic testing for hotspot mutations in 46 or 50 genes. Six months after sequencing, physicians received questionnaires for patients who demonstrated a variant in an actionable gene, investigating their perceptions regarding the actionability of alterations and clinical use of these findings. Genomic annotators independently classified these variants as actionable, potentially actionable, unknown, or not actionable. RESULTS Physicians completed 250 of 288 questionnaires (87% response rate). Physicians considered 168 of 250 patients (67%) as having an actionable alteration; of these, 165 patients (98%) were considered to have an actionable alteration by the PODS team and 3 were of unknown significance. Physicians were aware of genotype-matched therapy available for 119 patients (71%) and 48 of these 119 patients (40%) received matched therapy. Approximately 46% of patients in whom physicians regarded alterations as not actionable (36 of 79 patients) were classified as having an actionable/potentially actionable mutation by the PODS team. However, many of these were only theoretically actionable due to limited trials and/or therapies (eg, KRAS). CONCLUSIONS Physicians are aware of recurrent mutations in actionable genes on "hotspot" panels. As larger genomic panels are used, there may be a growing need for annotation of actionability. Decision support to increase awareness of genomically relevant trials and novel treatment options for recurrent mutations (eg, KRAS) also are needed. Cancer 2018;124:966-72. © 2017 American Cancer Society.
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Affiliation(s)
- Lauren L Brusco
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chetna Wathoo
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kenna R Mills Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vijaykumar R Holla
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ann M Bailey
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Amber M Johnson
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yekaterina B Khotskaya
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Beate C Litzenburger
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nora S Sanchez
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jia Zeng
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elmer V Bernstam
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas.,Division of General Internal Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Cathy Eng
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bryan K Kee
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark J Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gordon B Mills
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John Mendelsohn
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Funda Meric-Bernstam
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Ileana Dumbrava EE, Brusco L, Daniels MS, Wathoo C, Shaw KR, Lu KH, Zheng X, Strong LC, Litton JK, Arun B, Eterovic AK, Routbort M, Piha-Paul SA, Subbiah V, Hong DS, Kopetz S, Mendelsohn J, Mills GB, Chen K, Meric-Bernstam F. Prevalence of incidental germline pathogenic (PV) and likely pathogenic (LPV) variants in hereditary cancer-related genes identified in matched tumor/normal sequencing of advanced solid tumors. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.1524] [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: 11/20/2022] Open
Abstract
1524 Background: Next-generation sequencing (NGS) for tumor molecular profiling can reveal germline incidental mutations in hereditary cancer-related genes. The American College of Medical Genetics and Genomics (ACMG) has recommended that laboratories performing clinical sequencing seek and report PV and LPV in 56 genes. We assessed the prevalence of incidental germline LPV and PV in other cancer-related genes among patients undergoing hybrid capture sequencing of 201 cancer-related genes. Methods: Matched tumor and germline DNA NGS of a targeted panel of 201 genes was performed in 1000 patients (pts) with advanced or metastatic solid tumors enrolled in a molecular testing protocol (NCT01772771) in a research laboratory. We previously reported germline alterations in the putative most actionable genes as designated by ACMG (PMID: 26787237). We assessed the germline LPV and PV in 54 additional cancer-related genes. Results: Among the 1000 patients who underwent tumor and normal DNA sequencing, 37 patients (3.7%) were found to have a germline PV or LPV in the following genes: ATM (4); BAP1 (1); CDH1 (1); CDKN2A (1); CHEK1 (2); CHEK2 (10); EGFR (1); ERCC3 (4); ERCC5 (1); HNF1B (1); HRAS (1); MLL3 (1); NF1 (3); PKHD1 (4); PTCH1 (1) and SMARCA4 (1). Eight pts (22%) had previous genetic counseling and testing for various reasons, but only 3 pts (8%) had previously identified alterations (all with NF1 mutations). After discussion in our return of germline results board, it was decided to return the findings in established hereditary cancer predisposition genes with high penetrance: BAP1 (p.Y401X), CDH1 (p.C688X), CDKN2A (p.G101W), EGFR (p.T790M) and SMARCA4 (p.S332FfsX55) after validation in a CLIA laboratory. Conclusions: Return of the previously unrecognized germline LPV or PV in patients with advanced or metastatic cancers who undergo somatic profiling is of great interest. The exact genes for which the germline results should be returned is controversial. Broader genomic testing is likely to identify additional incidental germline alterations with potential clinical utility to patients and their relatives.
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Affiliation(s)
| | - Lauren Brusco
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Molly S Daniels
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chetna Wathoo
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kenna Rael Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Karen H. Lu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Banu Arun
- MD Anderson Cancer Center, Houston, TX
| | | | - Mark Routbort
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Vivek Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David S. Hong
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John Mendelsohn
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gordon B. Mills
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ken Chen
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Program), The University of Texas MD Anderson Cancer Center, Houston, TX
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Ileana Dumbrava EE, Brusco L, Daniels MS, Wathoo C, Shaw KR, Lu KH, Zheng X, Strong LC, Litton JK, Arun B, Eterovic AK, Piha-Paul SA, Subbiah V, Hong DS, Woodman SE, Mendelsohn J, Yap TA, Mills GB, Chen K, Meric-Bernstam F. Pathogenic variants in DNA damage response (DDR) genes in patients with advanced solid tumors. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.11567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
11567 Background: Deleterious mutations in DDR genes are frequently associated with response to poly(ADP-ribose) polymerase (PARP) inhibitors and platinum chemotherapy. However, much remains unknown about their association with specific molecular signaling pathways. We report the prevalence of pathogenic variants in DDR genes and their co-alteration with other somatic variants. Methods: Targeted exome sequencing of 201 genes was performed in 1,189 patients (pts) with advanced solid tumors enrolled in a molecular testing protocol (NCT01772771), using matched normal and tumor DNA. We assessed germline and somatic alterations in 15 cancer-related DDR genes, their co-occuring genomic alterations and the tumor mutation burden (TMB), defined as number of somatic non-synonymous mutations. Results: A total of 124 pathogenic or likely pathogenic variants in DDR genes were identified in 111/1189 (9%) pts with 57% of these alterations being somatic. These variants were found in the following genes: ATM 17 pts (1.4%); BAP1 5 pts (0.4%); BRCA1 18 pts (1.5%); BRCA2 17pts (1.4%); CHEK1 8 pts (0.7%); CHEK2 16 pts (1.3%); ERCC3 4 pts (0.3%); ERCC4 2 pts (0.2%); ERCC5 3 pts (0.2%); MLH1 4pts (0.3%); MSH2 8 pts (0.7%); MSH6 6 pts (0.5%); PALB2 3 pts (0.2%) and RAD51 1pt (0.1%). DDR alterations were found more frequently in the following tumor types tested: breast 14%, colorectal 12%, melanoma 8%, glioblastoma 6% and ovarian 6%. The most relevant somatic co-alterations with DDR mutations were activation of the PI3K/AKT/mTOR pathway through mutations or copy-number variations in AKT1, MTOR, NF1, PIK3CA, PIK3R1, PTEN, TSC1 and TSC2 (p = 0.008). Patients with deleterious variants in mismatch excision repair genes (MLH1, MSH2 or MSH6) had a significantly higher TMB than all other patients enrolled (median TMB = 62 vs 5, p = 0.002). Patients with somatic pathogenic DDR variants had a significantly higher TMB (median = 13) compared to patients with germline DDR variants (median = 5) (p = 0.004). Conclusions: The association of DNA repair mutations with alterations in signaling pathways provide rationale for novel therapeutic combinations. Variations in TMB based on distinct types of DDR gene alterations may have implications for immunotherapy.
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Affiliation(s)
| | - Lauren Brusco
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Molly S Daniels
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chetna Wathoo
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kenna Rael Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Karen H. Lu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Banu Arun
- MD Anderson Cancer Center, Houston, TX
| | | | | | - Vivek Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David S. Hong
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - John Mendelsohn
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Gordon B. Mills
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ken Chen
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Program), The University of Texas MD Anderson Cancer Center, Houston, TX
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16
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Daniels M, Wathoo C, Brusco L, Lu KH, Shaw K, Dumbrava EEI, Arun B, Strong L, Litton JK, Eterovic K, Aytac U, Mendelsohn J, Mills GB, Chen K, Meric-Bernstam F. Active Disclosure of Secondary Germline Findings to Deceased Research Participants' Personal Representatives: Process and Outcomes. JCO Precis Oncol 2017; 1. [PMID: 31552380 DOI: 10.1200/po.17.00074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Molly Daniels
- Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chetna Wathoo
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren Brusco
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Karen H Lu
- Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kenna Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ecaterina E Ileana Dumbrava
- Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Banu Arun
- Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Louise Strong
- Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer K Litton
- Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Karina Eterovic
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ugur Aytac
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Mendelsohn
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gordon B Mills
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ken Chen
- Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Funda Meric-Bernstam
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Investigational Cancer Therapeutics (Phase I Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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17
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Meric-Bernstam F, Brusco L, Daniels M, Wathoo C, Bailey AM, Strong L, Shaw K, Lu K, Qi Y, Zhao H, Lara-Guerra H, Litton J, Arun B, Eterovic AK, Aytac U, Routbort M, Subbiah V, Janku F, Davies MA, Kopetz S, Mendelsohn J, Mills GB, Chen K. Incidental germline variants in 1000 advanced cancers on a prospective somatic genomic profiling protocol. Ann Oncol 2016; 27:795-800. [PMID: 26787237 DOI: 10.1093/annonc/mdw018] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/08/2016] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Next-generation sequencing in cancer research may reveal germline variants of clinical significance. We report patient preferences for return of results and the prevalence of incidental pathogenic germline variants (PGVs). PATIENTS AND METHODS Targeted exome sequencing of 202 genes was carried out in 1000 advanced cancers using tumor and normal DNA in a research laboratory. Pathogenic variants in 18 genes, recommended for return by The American College of Medical Genetics and Genomics, as well as PALB2, were considered actionable. Patient preferences of return of incidental germline results were collected. Return of results was initiated with genetic counseling and repeat CLIA testing. RESULTS Of the 1000 patients who underwent sequencing, 43 had likely PGVs: APC (1), BRCA1 (11), BRCA2 (10), TP53 (10), MSH2 (1), MSH6 (4), PALB2 (2), PTEN (2), TSC2 (1), and RB1 (1). Twenty (47%) of 43 variants were previously known based on clinical genetic testing. Of the 1167 patients who consented for a germline testing protocol, 1157 (99%) desired to be informed of incidental results. Twenty-three previously unrecognized mutations identified in the research environment were confirmed with an orthogonal CLIA platform. All patients approached decided to proceed with formal genetic counseling; in all cases where formal genetic testing was carried out, the germline variant of concern validated with clinical genetic testing. CONCLUSIONS In this series, 2.3% patients had previously unrecognized pathogenic germline mutations in 19 cancer-related genes. Thus, genomic sequencing must be accompanied by a plan for return of germline results, in partnership with genetic counseling.
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Affiliation(s)
- F Meric-Bernstam
- Department of Investigational Cancer Therapeutics Department of Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy Department of Surgical Oncology
| | - L Brusco
- Department of Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy
| | - M Daniels
- Department of Gynecologic Oncology and Reproductive Medicine Program of Clinical Cancer Genetics
| | - C Wathoo
- Department of Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy
| | - A M Bailey
- Department of Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy
| | - L Strong
- Program of Clinical Cancer Genetics
| | - K Shaw
- Department of Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy
| | - K Lu
- Department of Gynecologic Oncology and Reproductive Medicine Program of Clinical Cancer Genetics
| | - Y Qi
- Department of Bioinformatics and Computational Biology
| | - H Zhao
- Department of Bioinformatics and Computational Biology
| | - H Lara-Guerra
- Department of Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy Department of RedSky/Biomedical Institute of the Americas, El Paso, USA
| | - J Litton
- Department of Breast Medical Oncology
| | - B Arun
- Department of Breast Medical Oncology Program of Clinical Cancer Genetics
| | | | - U Aytac
- Department of Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy
| | | | - V Subbiah
- Department of Investigational Cancer Therapeutics
| | - F Janku
- Department of Investigational Cancer Therapeutics
| | - M A Davies
- Department of Systems Biology Department of Melanoma Medical Oncology
| | - S Kopetz
- Department of Gastrointestinal (GI) Medical Oncology, MD Anderson Cancer Center, Houston
| | - J Mendelsohn
- Department of Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy Department of Genomic Medicine
| | - G B Mills
- Department of Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy Department of Systems Biology
| | - K Chen
- Department of Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy Department of Bioinformatics and Computational Biology
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18
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Basho RK, Gagliato DDM, Ueno NT, Alvarez RH, Wathoo C, Chen H, Wei C, Sahin AA, Roy-Chowdhuri S, Moulder SL, Chavez-Mac Gregor M, Litton JK, Valero V, Luthra R, Shaw KR, Mendelsohn J, Mills GB, Tripathy D, Meric-Bernstam F. Clinical outcomes based on multigene profiling in metastatic breast cancer patients. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.1524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Naoto T. Ueno
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Chetna Wathoo
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Huiqin Chen
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Caimiao Wei
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | - Vicente Valero
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Kenna Rael Shaw
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John Mendelsohn
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gordon B. Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Debu Tripathy
- The University of Texas MD Anderson Cancer Center, Houston, TX
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