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Boruah N, Hoyos D, Moses R, Hausler R, Desai H, Le AN, Good M, Kelly G, Raghavakaimal A, Tayeb M, Narasimhamurthy M, Doucette A, Gabriel P, Feldman MJ, Park J, de Rodas ML, Schalper KA, Goldfarb SB, Nayak A, Levine AJ, Greenbaum BD, Maxwell KN. Distinct genomic and immunologic tumor evolution in germline TP53-driven breast cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.588009. [PMID: 38617260 PMCID: PMC11014613 DOI: 10.1101/2024.04.03.588009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Pathogenic germline TP53 alterations cause Li-Fraumeni Syndrome (LFS), and breast cancer is the most common cancer in LFS females. We performed first of its kind multimodal analysis of LFS breast cancer (LFS-BC) compared to sporadic premenopausal BC. Nearly all LFS-BC underwent biallelic loss of TP53 with no recurrent oncogenic variants except ERBB2 (HER2) amplification. Compared to sporadic BC, in situ and invasive LFS-BC exhibited a high burden of short amplified aneuploid segments (SAAS). Pro-apoptotic p53 target genes BAX and TP53I3 failed to be up-regulated in LFS-BC as was seen in sporadic BC compared to normal breast tissue. LFS-BC had lower CD8+ T-cell infiltration compared to sporadic BC yet higher levels of proliferating cytotoxic T-cells. Within LFS-BC, progression from in situ to invasive BC was marked by an increase in chromosomal instability with a decrease in proliferating cytotoxic T-cells. Our study uncovers critical events in mutant p53-driven tumorigenesis in breast tissue.
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Affiliation(s)
- Nabamita Boruah
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - David Hoyos
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Renyta Moses
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ryan Hausler
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Heena Desai
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Anh N Le
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Madeline Good
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gregory Kelly
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ashvathi Raghavakaimal
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Maliha Tayeb
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Mohana Narasimhamurthy
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA
| | - Abigail Doucette
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Peter Gabriel
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Michael J. Feldman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA
| | - Jinae Park
- Departments of Medicine and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Shari B. Goldfarb
- Departments of Medicine and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical Center, New York, NY
| | - Anupma Nayak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA
| | | | - Benjamin D. Greenbaum
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Physiology, Biophysics & Systems Biology, Weill Cornell Medical Center, New York, NY:
| | - Kara N. Maxwell
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Corporal Michael Crescenz Veterans Affairs Medical Center, Philadelphia, PA
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2
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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. JOURNAL OF IMMUNOTHERAPY AND PRECISION ONCOLOGY 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] [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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Montgomery B, Wang S, Rettig M, Lee B, Bates J, Pritchard C. Ordering and Interpreting Precision Oncology Studies for Adults With Advanced Solid Tumors: A Primer. Fed Pract 2022; 39:S16-S24. [PMID: 35929009 PMCID: PMC9346578 DOI: 10.12788/fp.0270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND The promise of precision oncology can only be realized when genetic alterations are identified that can be leveraged to improve response and minimize toxicity. Identifying those alterations requires the knowledge to order the right test and to interpret the results correctly. This primer is designed to help clinicians order the appropriate testing for patients with specific malignancies and to give them an informed approach to interpretation. OBSERVATIONS Germline DNA is usually acquired from peripheral blood, buccal swab, or saliva collection in patients with a metastatic malignancy and can provide treatment options otherwise not available. However, germline testing does not indicate alterations that arise solely in tumor tissue. Somatic testing may be performed on primary tumor, metastatic biopsy, or circulating tumor DNA when the alteration is present at the time that the tumor developed and expected to be carried through the evolution of the tumor. CONCLUSIONS The rapid growth in technology and ability to enhance understanding of relevant tumor biology continues to improve the therapeutic landscape for individuals dealing with malignancy as does our ability to find targetable genetic alterations with the potential for meaningful clinical benefit.
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Affiliation(s)
- Bruce Montgomery
- Veterans Affairs Puget Sound Health Care System, Seattle, Washington
- University of Washington, Seattle
| | - Sunny Wang
- San Francisco Veterans Affairs Health Care System, California
- University of California San Francisco
| | - Matthew Rettig
- Greater Los Angeles Health Care System, California
- University of California, Los Angeles
| | - Benson Lee
- Greater Los Angeles Health Care System, California
| | - Jill Bates
- Durham Veterans Affairs Medical Center, North Carolina
- University of North Carolina, Chapel Hill
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Huang CC, Tsai YF, Liu CY, Lien PJ, Lin YS, Chao TC, Feng CJ, Chen YJ, Lai JI, Phan NN, Hsu CY, Chiu JH, Tseng LM. Prevalence of Tumor Genomic Alterations in Homologous Recombination Repair Genes Among Taiwanese Breast Cancers. Ann Surg Oncol 2022; 29:3578-3590. [PMID: 35226219 DOI: 10.1245/s10434-022-11347-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/03/2022] [Indexed: 11/18/2022]
Abstract
PURPOSE Deleterious germline BRCA1/2 mutations are among the most highly pathogenic variants in hereditary breast and ovarian cancer syndrome. Recently, genes implicated in homologous recombination repair (HRR) pathways have been investigated extensively. Defective HRR genes may indicate potential clinical benefits from PARP (poly ADP ribose polymerase) inhibitors beyond BRCA1/2 mutations. METHODS We evaluated the prevalence of BRCA1/2 mutations as well as alterations in HRR genes with targeted sequencing. A total of 648 consecutive breast cancer samples were assayed, and HRR genes were evaluated for prevalence in breast cancer tissues. RESULTS Among 648 breast cancers, there were 17 truncating and 2 missense mutations in BRCA1 and 45 truncating and 1 missense mutation in BRCA2, impacting 3% and 5% of the study population (collectively altered in 6%) with cooccurrence of BRCA1/2 in 7 breast cancers. On the other hand, HRR genes were altered in 122 (19%) breast cancers, while TBB (Talazoparib Beyond BRCA) trial-interrogated genes (excluding BRCA1/2) were mutated in 107 (17%) patients. Beyond BRCA1/2, the most prevalent HRR mutant genes came from ARID1A (7%), PALB2 (7%), and PTEN (6%). Collectively, 164 (25%) of the 648 Taiwanese breast cancer samples harbored at least one mutation among HRR genes. CONCLUSIONS The prevalence of BRCA1/2 mutations was far below one tenth, while the prevalence of HRR mutations was much higher and approached one-fourth among Taiwanese breast cancers. Further opportunities to take advantage of defective HRR genes for breast cancer treatment should be sought for the realization of precision medicine.
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Affiliation(s)
- Chi-Cheng Huang
- Comprehensive Breast Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Yi-Fang Tsai
- Comprehensive Breast Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, College of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan
| | - Chun-Yu Liu
- Comprehensive Breast Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, College of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan.,Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Pei-Ju Lien
- Comprehensive Breast Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yen-Shu Lin
- Comprehensive Breast Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ta-Chung Chao
- Comprehensive Breast Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, College of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan.,Division of Chemotherapy, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chin-Jung Feng
- Comprehensive Breast Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yen-Jen Chen
- Comprehensive Breast Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jiun-I Lai
- Comprehensive Breast Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Clinical Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Nam Nhut Phan
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Biomedical Electronics and Bioinformatics, Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan.,Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
| | - Chih-Yi Hsu
- School of Medicine, College of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan.,Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jen-Hwey Chiu
- Comprehensive Breast Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Traditional Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Ling-Ming Tseng
- Comprehensive Breast Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan. .,Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan. .,School of Medicine, College of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan.
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5
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Mahon SM. Tumor Genomic Testing: Identifying Characteristics Associated With Germline Risk for Developing Malignancy. Clin J Oncol Nurs 2020; 24:623-626. [PMID: 33216058 DOI: 10.1188/20.cjon.623-626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Tumor genomic testing is used primarily to facilitate the selection of the best possible treatment for a malignancy based on the genomic characteristics of the tumor. Germline genomic testing has implications for care and recommendations for cancer prevention and early detection for the patient and their family. Careful review of specific components of tumor genomic testing reports and of the family history of malignancy can help ensure that families with potential germline risk are identified and referred for genetic counseling and genetic testing.
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6
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Establishment of a Molecular Tumor Board (MTB) and Uptake of Recommendations in a Community Setting. J Pers Med 2020; 10:jpm10040252. [PMID: 33260805 PMCID: PMC7711773 DOI: 10.3390/jpm10040252] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 01/02/2023] Open
Abstract
In the precision medicine era, molecular testing in advanced cancer is foundational to patient management. Molecular tumor boards (MTBs) can be effective in processing comprehensive genomic profiling (CGP) results and providing expert recommendations. We assessed an MTB and its role in a community setting. This retrospective analysis included patients with MTB recommendations at a community-based oncology practice January 2015 to December 2018; exclusions were death within 60 days of the MTB and/or no metastatic disease. Potentially actionable genomic alterations from CGP (immunohistochemistry, in-situ hybridization, next-generation sequencing) were reviewed bi-weekly by MTB practice experts, pathologists, genetic counselors, and other support staff, and clinical care recommendations were provided. Subsequent chart reviews determined implementation rates of recommendations. In 613 patients, the most common cancers were lung (23%), breast (19%), and colorectal (17%); others included ovarian, endometrial, bladder, and melanoma. Patients received 837 actionable recommendations: standard therapy (37%), clinical trial (31%), germline testing and genetic counseling (17%), off-label therapy (10%), subspecialty multidisciplinary tumor board review (2%), and advice for classifying tumor of unknown origin (2%). Of these recommendations, 36% to 78% were followed by the treating physician. For clinical trial recommendations (n = 262), 13% of patients enrolled in a clinical trial. The median time between CPG result availability and MTB presentation was 12 days. A community oncology-based comprehensive and high-throughput MTB provided useful clinical guidance in various treatment domains within an acceptable timeframe for patients with cancer in a large community setting.
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Lincoln SE, Nussbaum RL, Kurian AW, Nielsen SM, Das K, Michalski S, Yang S, Ngo N, Blanco A, Esplin ED. Yield and Utility of Germline Testing Following Tumor Sequencing in Patients With Cancer. JAMA Netw Open 2020; 3:e2019452. [PMID: 33026450 PMCID: PMC7542302 DOI: 10.1001/jamanetworkopen.2020.19452] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
IMPORTANCE Both germline genetic testing and tumor DNA sequencing are increasingly used in cancer care. The indications for testing and utility of these 2 tests differ, and guidelines recommend that germline analysis follow tumor sequencing in certain patients to determine whether particular variants are of somatic or germline origin. Broad clinical experience with such follow-up testing has not yet been thoroughly described. OBJECTIVE To examine the yield and utility of germline testing following tumor DNA sequencing in a large, diverse patient population. DESIGN, SETTING, AND PARTICIPANTS A retrospective cohort study examined germline testing through a laboratory supporting multiple academic and community clinics. Participants included 2023 patients with cancer who received germline testing and previously underwent tumor DNA sequencing. These patients received germline testing between January 5, 2015, and January 31, 2020, although most (81% of patients) received testing between January 2, 2018, and January 31, 2020. MAIN OUTCOMES AND MEASURES The prevalence of pathogenic germline variants (PGVs) was calculated by gene, cancer type, and age at diagnosis. Potential actionability of these findings was determined based on current management guidelines, precision therapy labels, and clinical trial eligibility criteria. Patient records were reviewed to determine whether germline follow-up testing would have been recommended by current guidelines. RESULTS Among 2023 eligible patients, 1085 were female (53.6%), and the median age at cancer diagnosis was 56 (range, 0-92) years. Pathogenic germline variants were detected in 617 patients (30.5%; 95% CI, 28.5%-32.6%) and were prevalent across patient ages (1-85 years) and cancer types, including cancers known to be strongly associated with germline variance (eg, breast, colorectal) as well as others (eg, renal, lung, and bladder). Many patients (78%-82%) with PGVs met criteria for germline follow-up testing, and 8.1% of PGVs were missed by tumor sequencing. Among those with germline-positive findings, 69 patients (11.2%) had PGVs identified only after presenting with a second primary cancer that possibly could have been detected earlier or prevented given current gene-specific surveillance and risk-reduction recommendations. CONCLUSIONS AND RELEVANCE The findings of this study suggest that germline analysis following tumor sequencing often produces findings that may impact patient care by influencing systemic therapy choices, surgical decisions, additional cancer screening, and genetic counseling in families. Current guidelines and tumor testing approaches appear to capture many, but not all, of these germline findings, reinforcing the utility of both expanded germline follow-up testing as well as germline analysis independent of tumor sequencing in appropriate patients.
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Affiliation(s)
| | | | | | | | | | | | - Shan Yang
- Invitae Corp, San Francisco, California
| | - Nhu Ngo
- Invitae Corp, San Francisco, California
| | - Amie Blanco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco
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Poduval DB, Ognedal E, Sichmanova Z, Valen E, Iversen GT, Minsaas L, Lønning PE, Knappskog S. Assessment of tumor suppressor promoter methylation in healthy individuals. Clin Epigenetics 2020; 12:131. [PMID: 32859265 PMCID: PMC7455917 DOI: 10.1186/s13148-020-00920-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022] Open
Abstract
Background The number of tumor suppressor genes for which germline mutations have been linked to cancer risk is steadily increasing. However, while recent reports have linked constitutional normal tissue promoter methylation of BRCA1 and MLH1 to ovarian and colon cancer risk, the role of epigenetic alterations as cancer risk factors remains largely unknown, presenting an important area for future research. Currently, we lack fast and sensitive methods for assessment of promoter methylation status across known tumor suppressor genes. Results In this paper, we present a novel NGS-based approach assessing promoter methylation status across a large panel of defined tumor suppressor genes to base-pair resolution. The method omits the limitations related to commonly used array-approaches. Our panel includes 565 target regions covering the promoters of 283 defined tumor suppressors, selected by pre-specified criteria, and was applied for rapid targeted methylation-specific NGS. The feasibility of the method was assessed by analyzing normal tissue DNA (white blood cells, WBC) samples from 34 healthy postmenopausal women and by performing preliminary assessment of the methylation landscape of tumor suppressors in these individuals. The mean target coverage was 189.6x providing a sensitivity of 0.53%, sufficient for promoter methylation assessment of low-level methylated genes like BRCA1. Within this limited test-set, we detected 206 regions located in the promoters of 149 genes to be differentially methylated (hyper- or hypo-) at > 99% confidence level. Seven target regions in gene promoters (CIITA, RASSF1, CHN1, PDCD1LG2, GSTP1, XPA, and ZNF668) were found to be hyper-methylated in a minority of individuals, with a > 20 percent point difference in mean methylation across the region between individuals. In an exploratory hierarchical clustering analysis, we found that the individuals analyzed may be grouped into two main groups based on their WBC methylation profile across the 283 tumor suppressor gene promoters. Conclusions Methylation-specific NGS of our tumor suppressor panel, with detailed assessment of differential methylation in healthy individuals, presents a feasible method for identification of novel epigenetic risk factors for cancer.
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Affiliation(s)
- Deepak B Poduval
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Elisabet Ognedal
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, Bergen, Norway.,Present address: Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Zuzana Sichmanova
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Gjertrud T Iversen
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Laura Minsaas
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Per E Lønning
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Stian Knappskog
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway. .,Department of Oncology, Haukeland University Hospital, Bergen, Norway.
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9
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Melas M, Subbiah S, Saadat S, Rajurkar S, McDonnell KJ. The Community Oncology and Academic Medical Center Alliance in the Age of Precision Medicine: Cancer Genetics and Genomics Considerations. J Clin Med 2020; 9:E2125. [PMID: 32640668 PMCID: PMC7408957 DOI: 10.3390/jcm9072125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 06/28/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022] Open
Abstract
Recent public policy, governmental regulatory and economic trends have motivated the establishment and deepening of community health and academic medical center alliances. Accordingly, community oncology practices now deliver a significant portion of their oncology care in association with academic cancer centers. In the age of precision medicine, this alliance has acquired critical importance; novel advances in nucleic acid sequencing, the generation and analysis of immense data sets, the changing clinical landscape of hereditary cancer predisposition and ongoing discovery of novel, targeted therapies challenge community-based oncologists to deliver molecularly-informed health care. The active engagement of community oncology practices with academic partners helps with meeting these challenges; community/academic alliances result in improved cancer patient care and provider efficacy. Here, we review the community oncology and academic medical center alliance. We examine how practitioners may leverage academic center precision medicine-based cancer genetics and genomics programs to advance their patients' needs. We highlight a number of project initiatives at the City of Hope Comprehensive Cancer Center that seek to optimize community oncology and academic cancer center precision medicine interactions.
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Affiliation(s)
- Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA;
| | - Shanmuga Subbiah
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Glendora, CA 91741, USA;
| | - Siamak Saadat
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Colton, CA 92324, USA;
| | - Swapnil Rajurkar
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Upland, CA 91786, USA;
| | - Kevin J. McDonnell
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA 91010, USA
- Center for Precision Medicine, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
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Ceyhan-Birsoy, PhD O, Misyura M, Mandelker D. A Clinical Approach to Detecting Germline Pathogenic Variants From Tumor-Only Sequencing. JNCI Cancer Spectr 2020; 4:pkaa019. [PMID: 32596634 PMCID: PMC7306191 DOI: 10.1093/jncics/pkaa019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/28/2020] [Indexed: 11/17/2022] Open
Affiliation(s)
| | - Maksym Misyura
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Klek S, Heald B, Milinovich A, Ni Y, Abraham J, Mahdi H, Estfan B, Khorana AA, Bolwell BJ, Grivas P, Sohal DPS, Funchain P. Genetic Counseling and Germline Testing in the Era of Tumor Sequencing: A Cohort Study. JNCI Cancer Spectr 2020; 4:pkaa018. [PMID: 32596633 PMCID: PMC7306190 DOI: 10.1093/jncics/pkaa018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/10/2019] [Accepted: 02/19/2020] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The clinical impact of addressing potential germline alterations from tumor-only next-generation sequencing (NGS) is not well characterized. Current guidelines for cancer genetic testing may miss clinically actionable germline changes, which may have important implications for cancer screening, treatment, and prevention. We examined whether increasing involvement of the clinical genetics service during somatic tumor-only NGS review at Molecular Tumor Board (MTB) increases the detection of germline findings. METHODS In a retrospective evaluation of patients who underwent tumor-only NGS and were reviewed at MTB, we quantified genetic counseling (GC) referrals as well as germline testing uptake and results across three cohorts: before (C1) and after (C2) the addition of tumor-only NGS review and after (C3) instituting a formal process to coordinate NGS-based genetics referrals to preexisting oncology appointments. All statistical tests were two-sided. RESULTS From 2013 to 2017, 907 tumor-only NGS reports were reviewed at MTB (nC1 = 281, nC2 = 493, nC3 = 133); gastrointestinal (22.5%), lung (19.7%), genitourinary (14.8%), and breast (14.1%) were the most common index cancers. GC visits due to MTB increased with each successive cohort (C1 = 1.1%, C2 = 6.9%, C3 = 13.5%; P for trend [P trend] < .001), as did germline testing (C1 = 0.7%, C2 = 3.2%, C3 = 11.3%; P trend < .001). Diagnosis of germline pathogenic variants increased with each successive cohort (C1 = 1.4%, C2 = 2.0%, C3 = 7.5%; P trend = .003) and with germline pathogenic variants found by MTB review (C1 = 0.4%, C2 = 0.4%, C3 = 2.3%; P trend = .12). CONCLUSIONS Both review of tumor-only NGS by genetics and the institution of a process coordinating GC with oncology appointments increased the discovery of germline pathogenic variants from tumor-only NGS testing. Furthermore, this process identified germline pathogenic variant carriers who would not have otherwise met standard criteria for germline testing.
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Affiliation(s)
- Stefan Klek
- Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Brandie Heald
- Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Alex Milinovich
- Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Ying Ni
- Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Jame Abraham
- Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Haider Mahdi
- Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Bassam Estfan
- Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Alok A Khorana
- Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Brian J Bolwell
- Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Petros Grivas
- University of Washington, Seattle Cancer Care Alliance, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Pauline Funchain
- Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
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