1
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Ryu KH, Park S, Chun JW, Cho E, Choi J, Lee DE, Shim H, Kim YH, Han SS, Park SJ, Woo SM, Kong SY. Prevalence and Risk Factors of Germline Pathogenic Variants in Pancreatic Ductal Adenocarcinoma. Cancer Res Treat 2023; 55:1303-1312. [PMID: 37024097 PMCID: PMC10582541 DOI: 10.4143/crt.2023.291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
PURPOSE The genetic attribution for pancreatic ductal adenocarcinoma (PDAC) has been reported as 5%-10%. However, the incidence of germline pathogenic variants (PVs) in Korean PDAC patients has not been thoroughly investigated. Therefore, we studied to identify the risk factors and prevalence of PV for future treatment strategies in PDAC. MATERIALS AND METHODS Total of 300 (155 male) patients with a median age of 65 years (range, 33 to 90 years) were enrolled in National Cancer Center in Korea. Cancer predisposition genes, clinicopathologic characteristics, and family history of cancer were analyzed. RESULTS PVs were detected in 20 patients (6.7%, median age 65) in ATM (n=7, 31.8%), BRCA1 (n=3, 13.6%), BRCA2 (n=3), and RAD51D (n=3). Each one patient showed TP53, PALB2, PMS2, RAD50, MSH3, and SPINK1 PV. Among them, two likely PVs were in ATM and RAD51D, respectively. Family history of various types of cancer including pancreatic cancer (n=4) were found in 12 patients. Three patients with ATM PVs and a patient with three germline PVs (BRCA2, MSH3, and RAD51D) had first-degree relatives with pancreatic cancer. Familial pancreatic cancer history and PVs detection had a significant association (4/20, 20% vs. 16/264, 5.7%; p=0.035). CONCLUSION Our study demonstrated that germline PVs in ATM, BRCA1, BRCA2, and RAD51D are most frequent in Korean PDAC patients and it is comparable to those of different ethnic groups. Although this study did not show guidelines for germline predisposition gene testing in patients with PDAC in Korea, it would be emphasized the need for germline testing for all PDAC patients.
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Affiliation(s)
- Kum Hei Ryu
- Center for Cancer Prevention and Detection, National Cancer Center, Goyang, Korea
| | - Sunhwa Park
- Targeted Therapy Branch, Center for Rare Cancers, National Cancer Center, Goyang, Korea
| | - Jung Won Chun
- Center for Liver and Pancreatobiliary Cancer, National Cancer Center, Goyang, Korea
| | - Eunhae Cho
- GC Genome, Green Cross Laboratories, Yongin, Korea
| | - Jongmun Choi
- GC Genome, Green Cross Laboratories, Yongin, Korea
| | - Dong-Eun Lee
- Biostatics Collaboration Team, Research Institute, National Cancer Center, Goyang, Korea
| | - Hyoeun Shim
- Department of Laboratory Medicine, Hospital, National Cancer Center, Goyang, Korea
| | - Yun-Hee Kim
- Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Korea
- Division of Convergence Technology, Research Institute, National Cancer Center, Goyang, Korea
| | - Sung-Sik Han
- Center for Liver and Pancreatobiliary Cancer, National Cancer Center, Goyang, Korea
| | - Sang-Jae Park
- Center for Liver and Pancreatobiliary Cancer, National Cancer Center, Goyang, Korea
| | - Sang Myung Woo
- Center for Liver and Pancreatobiliary Cancer, National Cancer Center, Goyang, Korea
- Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Korea
| | - Sun-Young Kong
- Targeted Therapy Branch, Center for Rare Cancers, National Cancer Center, Goyang, Korea
- Department of Laboratory Medicine, Hospital, National Cancer Center, Goyang, Korea
- Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Korea
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2
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Mohindroo C, De Jesus-Acosta A, Yurgelun MB, Maitra A, Mork M, McAllister F. The Evolving Paradigm of Germline Testing in Pancreatic Ductal Adenocarcinoma and Implications for Clinical Practice. Surg Pathol Clin 2022; 15:491-502. [PMID: 36049831 DOI: 10.1016/j.path.2022.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Identification of deleterious germline mutations in pancreatic ductal adenocarcinoma (PDAC) patients can have therapeutic implications for the patients and result in cascade testing and prevention in their relatives. Universal testing for germline mutations is now considered standard of care in patients with PDAC, regardless of family history, personal history, or age. Here, we highlight the commonly identified germline mutations in PDAC patients as well as the impact of multigene panel testing. We further discuss therapeutic implications of germline testing on the index cases, and the impact of cascade testing on cancer early detection and prevention in relatives.
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Affiliation(s)
- Chirayu Mohindroo
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Unit 1360, Houston, TX 77030, USA; Department of Internal Medicine, Sinai Hospital of Baltimore, 2435 W. Belvedere Ave, Ste 56, Baltimore, MD 21215, USA
| | - Ana De Jesus-Acosta
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, 401 North Broadway, Baltimore, MD 21231, USA
| | - Matthew B Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Anirban Maitra
- Department of Translational Molecular Pathology, Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, 2130 West Holcombe Boulevard, Houston, TX 77030, USA
| | - Maureen Mork
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Florencia McAllister
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Unit 1360, Houston, TX 77030, USA; Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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3
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Goebel EA, Kerkhof J, Dzyubak O, McLachlin CM, McGee J, Sadikovic B. Examining the Diagnostic Yield of Tumour Testing and Qualifying Germline Concordance for Hereditary Cancer Variants in Patients with High-Grade Serous Carcinoma. Genes (Basel) 2022; 13:genes13081398. [PMID: 36011309 PMCID: PMC9407448 DOI: 10.3390/genes13081398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/16/2022] Open
Abstract
Despite advances in treatment, prognosis for most patients with high-grade serous carcinoma (HGSC) remains poor. Genomic alterations in the homologous recombination (HR) pathway are used for cancer risk assessment and render tumours sensitive to platinum-based chemotherapy and poly (ADP-ribose) polymerase inhibitors (PARPi), which can be associated with more favourable outcomes. In addition to patients with tumours containing BRCA1 or BRCA2 pathologic variants, there is emerging evidence that patients with tumours harbouring pathologic variants in other HR genes may also benefit from PARPi therapy. The objective of this study is to assess the feasibility of primary-tumour testing by examining the concordance of variant detection between germline and tumour-variant status using a custom hereditary cancer gene panel (HCP). From April 2019 to November 2020, HCP variant testing was performed on 146 HGSC formalin-fixed, paraffin-embedded tissue samples using next-generation sequencing. Of those, 78 patients also underwent HCP germline testing using blood samples. A pathogenic variant was detected in 41.1% (60/146) of tumours tested, with 68.3% (41/60) having either a BRCA1 or BRCA2 variant (n = 36), or BRCA1/2 plus a second variant (n = 5), and 31.2% (19/60) carrying a pathogenic variant in another HCP gene. The overall variant rate among the paired germline and tumour samples was 43.6% (34/78), with the remaining 56% (44/78) having no pathogenic variant detected in the germline or tumour. The overall BRCA1/2 variant rate for paired samples was 33.3% (26/78), with germline variants detected in 11.5% (9/78). A non-BRCA1/2 germline variant in another HCP gene was detected in 9.0% (7/78). All germline variants were detected in the tumour, demonstrating 100% concordance. These data provide evidence supporting the feasibility of primary-tumour testing for detecting germline and somatic variants in HCP genes in patients with HGSC, which can be used to guide clinical decision-making, and may provide opportunity for improving patient triage and clinical genetic referral practices.
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Affiliation(s)
- Emily A. Goebel
- Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, ON N6A 5A5, Canada
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
- Correspondence: (E.A.G.); (B.S.)
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Oleksandra Dzyubak
- Department of Obstetrics and Gynecology, London Health Sciences Centre and Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5W9, Canada
| | - C. Meg McLachlin
- Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, ON N6A 5A5, Canada
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Jacob McGee
- Department of Obstetrics and Gynecology, London Health Sciences Centre and Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5W9, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
- Correspondence: (E.A.G.); (B.S.)
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4
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Tran VT, Nguyen ST, Pham XD, Phan TH, Nguyen VC, Nguyen HT, Nguyen HP, Doan PTT, Le TA, Nguyen BT, Jasmine TX, Nguyen DS, Nguyen HDL, Nguyen NM, Do DX, Tran VU, Nguyen HHT, Le MP, Nguyen YN, Do TTT, Truong DK, Tang HS, Phan MD, Nguyen HN, Giang H, Tu LN. Pathogenic Variant Profile of Hereditary Cancer Syndromes in a Vietnamese Cohort. Front Oncol 2022; 11:789659. [PMID: 35070997 PMCID: PMC8767154 DOI: 10.3389/fonc.2021.789659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/09/2021] [Indexed: 12/30/2022] Open
Abstract
Background Hereditary cancer syndromes (HCS) are responsible for 5-10% of cancer cases. Genetic testing to identify pathogenic variants associated with cancer predisposition has not been routinely available in Vietnam. Consequently, the prevalence and genetic landscape of HCS remain unknown. Methods 1165 Vietnamese individuals enrolled in genetic testing at our laboratory in 2020. We performed analysis of germline mutations in 17 high- and moderate- penetrance genes associated with HCS by next generation sequencing. Results A total of 41 pathogenic variants in 11 genes were detected in 3.2% individuals. The carrier frequency was 4.2% in people with family or personal history of cancer and 2.6% in those without history. The percentage of mutation carriers for hereditary colorectal cancer syndromes was 1.3% and for hereditary breast and ovarian cancer syndrome was 1.6%. BRCA1 and BRCA2 mutations were the most prevalent with the positive rate of 1.3% in the general cohort and 5.1% in breast or ovarian cancer patients. Most of BRCA1 mutations located at the BRCA C-terminus domains and the top recurrent mutation was NM_007294.3:c.5251C>T (p.Arg1751Ter). One novel variant NM_000038.6(APC):c.6665C>A (p.Pro2222His) was found in a breast cancer patient with a strong family history of cancer. A case study of hereditary cancer syndrome was illustrated to highlight the importance of genetic testing. Conclusion This is the first largest analysis of carrier frequency and mutation spectrum of HCS in Vietnam. The findings demonstrate the clinical significance of multigene panel testing to identify carriers and their at-risk relatives for better cancer surveillance and management strategies.
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Affiliation(s)
| | - Sao Trung Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | - Huu Thinh Nguyen
- University Medical Center Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Huu Phuc Nguyen
- University Medical Center Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Phuong Thao Thi Doan
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | - Duy Sinh Nguyen
- Department of Oncology, Faculty of Medicine, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hong-Dang Luu Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Ngoc Mai Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Duy Xuan Do
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Vu Uyen Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hue Hanh Thi Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Minh Phong Le
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Yen Nhi Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | | | | | - Hung Sang Tang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Minh-Duy Phan
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hoai-Nghia Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Lan N Tu
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
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5
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Pereira F, Teixeira MR, Dinis Ribeiro M, Brandão C. Multi-Gene Panel Testing in Gastroenterology: Are We Ready for the Results? GE-PORTUGUESE JOURNAL OF GASTROENTEROLOGY 2021; 28:403-409. [PMID: 34901447 DOI: 10.1159/000513966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/11/2020] [Indexed: 12/30/2022]
Abstract
Genetic testing aims to identify patients at risk for inherited cancer susceptibility. In the last decade, there was a significant increase in the request of broader panels of genes as multi-gene panel testing became widely available. However, physicians may be faced with genetic findings for which there is lack of management evidence, despite some progress in understanding their clinical relevance. In this short review, we discuss the advantages and the drawbacks related to multi-gene panel testing in the setting of a Gastrointestinal Familial Cancer Risk clinic. We also summarize the available recommendations on management of pathogenic variant carriers.
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Affiliation(s)
- Flávio Pereira
- Department of Gastroenterology, Amato Lusitano Hospital, Castelo Branco, Portugal
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal.,Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Mário Dinis Ribeiro
- Department of Gastroenterology, Portuguese Oncology Institute, Porto, Portugal
| | - Catarina Brandão
- Department of Gastroenterology, Portuguese Oncology Institute, Porto, Portugal
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6
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Lai E, Ziranu P, Spanu D, Dubois M, Pretta A, Tolu S, Camera S, Liscia N, Mariani S, Persano M, Migliari M, Donisi C, Demurtas L, Pusceddu V, Puzzoni M, Scartozzi M. BRCA-mutant pancreatic ductal adenocarcinoma. Br J Cancer 2021; 125:1321-1332. [PMID: 34262146 PMCID: PMC8575931 DOI: 10.1038/s41416-021-01469-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 05/28/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Despite continued research, pancreatic ductal adenocarcinoma (PDAC) remains one of the main causes of cancer death. Interest is growing in the role of the tumour suppressors breast cancer 1 (BRCA1) and BRCA2-typically associated with breast and ovarian cancer-in the pathogenesis of PDAC. Indeed, both germline and sporadic mutations in BRCA1/2 have been found to play a role in the development of PDAC. However, data regarding BRCA1/2-mutant PDAC are lacking. In this review, we aim to outline the specific landscape of BRCA-mutant PDAC, focusing on heritability, clinical features, differences between BRCA1 and 2 mutations and between germline and sporadic alterations, as well as established therapeutic strategies and those that are still under evaluation.
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Affiliation(s)
- Eleonora Lai
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy
| | - Pina Ziranu
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy
| | - Dario Spanu
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy
| | - Marco Dubois
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy
| | - Andrea Pretta
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy
- Medical Oncology Unit, Sapienza University of Rome, Rome, Italy
- Department of Medical Oncology, Institut Jules Bordet-Université Libre de Bruxelles (ULB), Brussells, Belgium
| | - Simona Tolu
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy
- Medical Oncology Unit, Sapienza University of Rome, Rome, Italy
| | - Silvia Camera
- Department of Medical Oncology, San Raffaele Scientific Institute, Milan, Italy
| | - Nicole Liscia
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy
- Medical Oncology Unit, Sapienza University of Rome, Rome, Italy
| | - Stefano Mariani
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy
| | - Mara Persano
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy
| | - Marco Migliari
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy
| | - Clelia Donisi
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy
| | - Laura Demurtas
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy
| | - Valeria Pusceddu
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy
| | - Marco Puzzoni
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy
| | - Mario Scartozzi
- Medical Oncology Unit, University Hospital and University of Cagliari, Cagliari, Italy.
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7
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Zeng J, Zhang Y, Shang Y, Mai J, Shi S, Lu M, Bu C, Zhang Z, Zhang Z, Li Y, Du Z, Xiao J. CancerSCEM: a database of single-cell expression map across various human cancers. Nucleic Acids Res 2021; 50:D1147-D1155. [PMID: 34643725 PMCID: PMC8728207 DOI: 10.1093/nar/gkab905] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/15/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022] Open
Abstract
With the proliferating studies of human cancers by single-cell RNA sequencing technique (scRNA-seq), cellular heterogeneity, immune landscape and pathogenesis within diverse cancers have been uncovered successively. The exponential explosion of massive cancer scRNA-seq datasets in the past decade are calling for a burning demand to be integrated and processed for essential investigations in tumor microenvironment of various cancer types. To fill this gap, we developed a database of Cancer Single-cell Expression Map (CancerSCEM, https://ngdc.cncb.ac.cn/cancerscem), particularly focusing on a variety of human cancers. To date, CancerSCE version 1.0 consists of 208 cancer samples across 28 studies and 20 human cancer types. A series of uniformly and multiscale analyses for each sample were performed, including accurate cell type annotation, functional gene expressions, cell interaction network, survival analysis and etc. Plus, we visualized CancerSCEM as a user-friendly web interface for users to browse, search, online analyze and download all the metadata as well as analytical results. More importantly and unprecedentedly, the newly-constructed comprehensive online analyzing platform in CancerSCEM integrates seven analyze functions, where investigators can interactively perform cancer scRNA-seq analyses. In all, CancerSCEM paves an informative and practical way to facilitate human cancer studies, and also provides insights into clinical therapy assessments.
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Affiliation(s)
- Jingyao Zeng
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yadong Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunfei Shang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jialin Mai
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuo Shi
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingming Lu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Congfan Bu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhewen Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zaichao Zhang
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Yang Li
- Beijing Tongren Eye Center, Beijing key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Zhenglin Du
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingfa Xiao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,China National Center for Bioinformation, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Abstract
A new software package provides more accurate cancer risk prediction profiles and has the ability to integrate more genes and cancer types in the future.
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9
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Perkhofer L, Golan T, Cuyle PJ, Matysiak-Budnik T, Van Laethem JL, Macarulla T, Cauchin E, Kleger A, Beutel AK, Gout J, Stenzinger A, Van Cutsem E, Bellmunt J, Hammel P, O’Reilly EM, Seufferlein T. Targeting DNA Damage Repair Mechanisms in Pancreas Cancer. Cancers (Basel) 2021; 13:4259. [PMID: 34503069 PMCID: PMC8428219 DOI: 10.3390/cancers13174259] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022] Open
Abstract
Impaired DNA damage repair (DDR) is increasingly recognised as a hallmark in pancreatic ductal adenocarcinoma (PDAC). It is estimated that around 14% of human PDACs harbour mutations in genes involved in DDR, including, amongst others, BRCA1/2, PALB2, ATM, MSH2, MSH6 and MLH1. Recently, DDR intervention by PARP inhibitor therapy has demonstrated effectiveness in germline BRCA1/2-mutated PDAC. Extending this outcome to the significant proportion of human PDACs with somatic or germline mutations in DDR genes beyond BRCA1/2 might be beneficial, but there is a lack of data, and consequently, no clear recommendations are provided in the field. Therefore, an expert panel was invited by the European Society of Digestive Oncology (ESDO) to assess the current knowledge and significance of DDR as a target in PDAC treatment. The aim of this virtual, international expert meeting was to elaborate a set of consensus recommendations on testing, diagnosis and treatment of PDAC patients with alterations in DDR pathways. Ahead of the meeting, experts completed a 27-question survey evaluating the key issues. The final recommendations herein should aid in facilitating clinical practice decisions on the management of DDR-deficient PDAC.
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Affiliation(s)
- Lukas Perkhofer
- Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany; (L.P.); (A.K.); (A.K.B.); (J.G.)
| | - Talia Golan
- Oncology Institute, Sheba Medical Center, Tel Aviv University, Tel Aviv 52621, Israel;
| | - Pieter-Jan Cuyle
- Digestive Oncology Department, Imelda General Hospital, 2820 Bonheiden, Belgium;
- University Hospitals Gasthuisberg Leuven and KU Leuven, 3000 Leuven, Belgium;
| | - Tamara Matysiak-Budnik
- IMAD, Department of Gastroenterology and Digestive Oncology, Hôtel Dieu, CHU de Nantes, 44000 Nantes, France; (T.M.-B.); (E.C.)
| | - Jean-Luc Van Laethem
- GI Cancer Unit, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium;
| | - Teresa Macarulla
- Vall d’Hebrón University Hospital and Vall d’Hebron Institute of Oncology, 08035 Barcelona, Spain;
| | - Estelle Cauchin
- IMAD, Department of Gastroenterology and Digestive Oncology, Hôtel Dieu, CHU de Nantes, 44000 Nantes, France; (T.M.-B.); (E.C.)
| | - Alexander Kleger
- Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany; (L.P.); (A.K.); (A.K.B.); (J.G.)
| | - Alica K. Beutel
- Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany; (L.P.); (A.K.); (A.K.B.); (J.G.)
| | - Johann Gout
- Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany; (L.P.); (A.K.); (A.K.B.); (J.G.)
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany;
| | - Eric Van Cutsem
- University Hospitals Gasthuisberg Leuven and KU Leuven, 3000 Leuven, Belgium;
| | - Joaquim Bellmunt
- Medical Oncology, University Hospital del Mar, 08003 Barcelona, Spain;
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | | | - Eileen M. O’Reilly
- Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
- Department of Medicine, David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Thomas Seufferlein
- Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany; (L.P.); (A.K.); (A.K.B.); (J.G.)
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10
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Bhai P, Levy MA, Rooney K, Carere DA, Reilly J, Kerkhof J, Volodarsky M, Stuart A, Kadour M, Panabaker K, Schenkel LC, Lin H, Ainsworth P, Sadikovic B. Analysis of Sequence and Copy Number Variants in Canadian Patient Cohort With Familial Cancer Syndromes Using a Unique Next Generation Sequencing Based Approach. Front Genet 2021; 12:698595. [PMID: 34326862 PMCID: PMC8314385 DOI: 10.3389/fgene.2021.698595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Background Hereditary cancer predisposition syndromes account for approximately 10% of cancer cases. Next generation sequencing (NGS) based multi-gene targeted panels is now a frontline approach to identify pathogenic mutations in cancer predisposition genes in high-risk families. Recent evolvement of NGS technologies have allowed simultaneous detection of sequence and copy number variants (CNVs) using a single platform. In this study, we have analyzed frequency and nature of sequence variants and CNVs, in a Canadian cohort of patients, suspected with hereditary cancer syndrome, referred for genetic testing following specific genetic testing guidelines based on patient's personal and/or family history of cancer. Methods A 2870 patients were subjected to a single NGS based multi-gene targeted hereditary cancer panel testing algorithm to identify sequence variants and CNVs in cancer predisposition genes at our reference laboratory in Southwestern Ontario. CNVs identified by NGS were confirmed by alternative techniques like Multiplex ligation-dependent probe amplification (MLPA). Results A 15% (431/2870) patients had a pathogenic variant and 36% (1032/2870) had a variant of unknown significance (VUS), in a cancer susceptibility gene. A total of 287 unique pathogenic variant were identified, out of which 23 (8%) were novel. CNVs identified by NGS based approach accounted for 9.5% (27/287) of pathogenic variants, confirmed by alternate techniques with high accuracy. Conclusion This study emphasizes the utility of NGS based targeted testing approach to identify both sequence and CNVs in patients suspected with hereditary cancer syndromes in clinical setting and expands the mutational spectrum of high and moderate penetrance cancer predisposition genes.
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Affiliation(s)
- Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Kathleen Rooney
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Deanna Alexis Carere
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Michael Volodarsky
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Mike Kadour
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, ON, Canada
| | - Karen Panabaker
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Laila C Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Hanxin Lin
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Peter Ainsworth
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, ON, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
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11
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Clinical Multigene Testing for Prostate Cancer. Urol Clin North Am 2021; 48:297-309. [PMID: 34210486 DOI: 10.1016/j.ucl.2021.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Germline genetic testing for prostate cancer (PC) is increasingly important as the clinical utility of germline variants in this patient population is understood better. To better characterize the clinical landscape of germline testing in PC, published clinical cohorts of PC who underwent clinical germline genetic analysis at point of care are reviewed. Limitations and heterogeneity of these cohorts are highlighted and pathogenic results with established or potential clinical utility in PC noted. The need for additional germline genetic studies is underscored, because the number of PC patients studied lags greatly behind the high prevalence of the disease.
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12
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Mantilla WA, Sanabria-Salas MC, Baldion AM, Sua LF, Gonzalez DM, Lema M. NGS in Lung, Breast, and Unknown Primary Cancer in Colombia: A Multidisciplinary Consensus on Challenges and Opportunities. JCO Glob Oncol 2021; 7:1012-1023. [PMID: 34185572 PMCID: PMC8457807 DOI: 10.1200/go.21.00046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/16/2021] [Accepted: 05/25/2021] [Indexed: 12/24/2022] Open
Abstract
Given the benefits and likely future applications, there is an urgent need to expand the use of next-generation sequencing (NGS) in breast, lung, and unknown primary cancers in Colombia. The objective of this review is to address the barriers limiting access to the use of NGS in Colombia, specifically for patients with breast, lung, and unknown primary cancers in the public health care system. A selected Panel of Colombian experts in NGS were provided with a series of relevant questions to address in a multiday conference. Each narrative was discussed and edited by the Panel through numerous drafts and rounds of discussion until consensus was achieved. There are limitations to the widespread adoption of innovative technology inherent to the Colombian health care system. Barriers identified to implementing NGS in Colombia include availability, accessibility, and affordability; limited infrastructure; training and awareness of health personnel; quality-control procedures; and collection of local data. Stakeholders must align to adapt the implementation of NGS to the constraints of resource-limited environments. Diagnostic algorithms were developed to guide molecular testing for lung, breast, and unknown primary cancers. Recommendations on overcoming the barriers to the widespread adoption of NGS include country-specific molecular testing guidelines, creating a national genetic registry, improving infrastructure, and creating health policy that favors the adoption of innovative technology.
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Affiliation(s)
| | | | - Ana Margarita Baldion
- Head of the Pathology Section, Department of Pathology and Laboratory Medicine, Hospital Universitario Fundacion Santa Fe de Bogota, Bogotá, Colombia
| | - Luz F. Sua
- Department of Pathology and Laboratory Medicine, Fundación Valle del Lili, and Faculty of Health Sciences, Universidad ICESI, Cali, Colombia
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13
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Vidal AF, Ferraz RS, El-Husny A, Silva CS, Vinasco-Sandoval T, Magalhães L, Raiol-Moraes M, Barra WF, Pereira CLBL, de Assumpção PP, de Brito LM, Vialle RA, Santos S, Ribeiro-Dos-Santos Â, Ribeiro-Dos-Santos AM. Comprehensive analysis of germline mutations in northern Brazil: a panel of 16 genes for hereditary cancer-predisposing syndrome investigation. BMC Cancer 2021; 21:363. [PMID: 33827469 PMCID: PMC8028728 DOI: 10.1186/s12885-021-08089-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/23/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Next generation sequencing (NGS) has been a handy tool in clinical practice, mainly due to its efficiency and cost-effectiveness. It has been widely used in genetic diagnosis of several inherited diseases, and, in clinical oncology, it may enhance the discovery of new susceptibility genes and enable individualized care of cancer patients. In this context, we explored a pan-cancer panel in the investigation of germline variants in Brazilian patients presenting clinical criteria for hereditary cancer syndromes or familial history. METHODS Seventy-one individuals diagnosed or with familial history of hereditary cancer syndromes were submitted to custom pan-cancer panel including 16 high and moderate penetrance genes previously associated with hereditary cancer syndromes (APC, BRCA1, BRCA2, CDH1, CDKN2A, CHEK2, MSH2, MSH6, MUTYH, PTEN, RB1, RET, TP53, VHL, XPA and XPC). All pathogenic variants were validated by Sanger sequencing. RESULTS We identified a total of eight pathogenic variants among 12 of 71 individuals (16.9%). Among the mutation-positive subjects, 50% were diagnosed with breast cancer and had mutations in BRCA1, CDH1 and MUTYH. Notably, 33.3% were individuals diagnosed with polyposis or who had family cases and harbored pathogenic mutations in APC and MUTYH. The remaining individuals (16.7%) were gastric cancer patients with pathogenic variants in CDH1 and MSH2. Overall, 54 (76.05%) individuals presented at least one variant uncertain significance (VUS), totalizing 81 VUS. Of these, seven were predicted to have disease-causing potential. CONCLUSION Overall, analysis of all these genes in NGS-panel allowed the identification not only of pathogenic variants related to hereditary cancer syndromes but also of some VUS that need further clinical and molecular investigations. The results obtained in this study had a significant impact on patients and their relatives since it allowed genetic counselling and personalized management decisions.
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Affiliation(s)
- Amanda Ferreira Vidal
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Rafaella Sousa Ferraz
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Antonette El-Husny
- Bettina Ferro de Souza University Hospital, Federal University of Pará, Belém, Pará, Brazil
| | - Caio Santos Silva
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Tatiana Vinasco-Sandoval
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Leandro Magalhães
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Milene Raiol-Moraes
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Williams Fernandes Barra
- João de Barros Barreto University Hospital, Federal University of Pará, Belém, Pará, Brazil
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil
| | - Cynthia Lara Brito Lins Pereira
- João de Barros Barreto University Hospital, Federal University of Pará, Belém, Pará, Brazil
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil
| | | | - Leonardo Miranda de Brito
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Ricardo Assunção Vialle
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Sidney Santos
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil
| | - André M Ribeiro-Dos-Santos
- Laboratory of Human and Medical Genetics, Graduate Program Genetics and Molecular Biology, Federal University of Pará, Belém, Pará, Brazil.
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14
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Milo Rasouly H, Aggarwal V, Bier L, Goldstein DB, Gharavi AG. Cases in Precision Medicine: Genetic Testing to Predict Future Risk for Disease in a Healthy Patient. Ann Intern Med 2021; 174:540-547. [PMID: 33460345 DOI: 10.7326/m20-5713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Genetic testing is performed more routinely in clinical practice, and direct-to-consumer tests are widely available. It has obvious appeal as a preventive health measure. Clinicians and their healthy patients increasingly inquire about genetic testing as a tool for predicting diseases, such as cancer, heart disease, or dementia. Despite demonstrated utility for diagnosis in the setting of many diseases, genetic testing still has many limitations as a predictive tool for healthy persons. This article uses a hypothetical case to review key considerations for predictive genetic testing.
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Affiliation(s)
- Hila Milo Rasouly
- Columbia University Irving Medical Center, New York, New York (H.M.R., A.G.G.)
| | - Vimla Aggarwal
- Hammer Health Sciences, New York, New York (V.A., L.B., D.B.G.)
| | - Louise Bier
- Hammer Health Sciences, New York, New York (V.A., L.B., D.B.G.)
| | | | - Ali G Gharavi
- Columbia University Irving Medical Center, New York, New York (H.M.R., A.G.G.)
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15
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Rainone M, Singh I, Salo-Mullen EE, Stadler ZK, O'Reilly EM. An Emerging Paradigm for Germline Testing in Pancreatic Ductal Adenocarcinoma and Immediate Implications for Clinical Practice: A Review. JAMA Oncol 2021; 6:764-771. [PMID: 32053139 DOI: 10.1001/jamaoncol.2019.5963] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Importance Pancreatic ductal adenocarcinoma (PDAC) is a malignant neoplasm with a rising incidence and is a leading public health challenge. Pancreatic ductal adenocarcinoma has been well characterized genomically, with findings of therapeutic actionability that have substantive implications for clinical practice based on recent high-level evidence. Observations Pathogenic germline alterations (PGAs) are relatively common in individuals with PDAC, as evidenced in multiple recent data sets, with a frequency of approximately 10%. The most common PGAs are in BRCA1, BRCA2, and ATM and more rarely in PALB2, MLH1, MSH2, MSH6, PMS2, CDKN2A, and TP53, among others, with an aggregate frequency of 3.8% to 9.7%. These PGAs are of key interest owing to therapeutic actionability and the downstream identification of at-risk family members and possible hereditary cancer syndromes. Approximately 3% to 7% of individuals with PDAC harbor a BRCA1 or BRCA2 mutation, which are among the most frequently mutated genes in PDAC. Recent updates to the American Society of Clinical Oncology and the National Comprehensive Cancer Network guidelines recommend risk assessment for all individuals with PDAC irrespective of personal or family history or ethnicity. Treatment implications include the use of checkpoint inhibitor therapy for mismatch repair-deficient PDAC and the validation of poly-ADP (adenosine diphosphate)-ribose polymerase inhibitor (PARPi) therapy as a maintenance strategy in platinum-sensitive PDAC. Conclusions and Relevance With increasing evidence and slow improvement of outcomes, PDAC has entered the era of precision medicine. Germline mutations have been identified in key genes with an aggregate frequency of 3.8% to 9.7%, several of which are therapeutically actionable with platinum, PARPi, and checkpoint inhibitor therapy. Potential therapeutic targets need to be actively sought and identified.
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Affiliation(s)
- Michael Rainone
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Mount Sinai St Luke's and Mount Sinai West Hospitals, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Isha Singh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Mount Sinai St Luke's and Mount Sinai West Hospitals, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Erin E Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eileen M O'Reilly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medicine, New York, New York
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16
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Sun S, Li ST, Ngeow J. Factors shaping at-risk individuals' decisions to undergo genetic testing for cancer in Asia. HEALTH & SOCIAL CARE IN THE COMMUNITY 2020; 28:1569-1577. [PMID: 32196825 DOI: 10.1111/hsc.12981] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 01/10/2020] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
This study aims to enrich our understanding of factors influencing medically indicated at-risk individuals' decisions to take genetic tests (or not) in the context of cancer treatment and prevention. While previous studies have explored this topic in communities in Europe and the United States, we know relatively little about the situation in Asia. In this study, we conducted in-depth interviews with 24 women who underwent genetic testing for hereditary breast and ovarian cancer syndromes in Singapore. Grounded theory with thematic analysis was applied. Six encouraging and three discouraging factors are identified in the analysis. The six encouraging factors are: desire to create awareness for self and family; perceived benefits for self and family; strong family history of cancer; presence of family support; medical professional recommendation and adequate amount of time to consider undertaking the test. The three discouraging factors are: high costs of tests; perceived lack of ability to cope with test results; and insufficient information about genetic testing. Taken together, the findings in this study add to the current literature by providing empirical evidence regarding the importance of holding family included pre-test counselling and providing adequate time for patients to decide to undergo genetic testing for hereditary cancer syndromes.
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Affiliation(s)
- Shirley Sun
- Sociology, School of Social Sciences, Nanyang Technology University, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Shao-Tzu Li
- Division of Medical Oncology, Cancer Genetics Service, National Cancer Centre Singapore, Singapore
| | - Joanne Ngeow
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Division of Medical Oncology, Cancer Genetics Service, National Cancer Centre Singapore, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
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17
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Akcay IM, Celik E, Agaoglu NB, Alkurt G, Kizilboga Akgun T, Yildiz J, Enc F, Kir G, Canbek S, Kilic A, Zemheri E, Ezberci F, Ozcelik M, Dinler Doganay G, Doganay L. Germline pathogenic variant spectrum in 25 cancer susceptibility genes in Turkish breast and colorectal cancer patients and elderly controls. Int J Cancer 2020; 148:285-295. [PMID: 32658311 DOI: 10.1002/ijc.33199] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/21/2020] [Accepted: 06/23/2020] [Indexed: 12/19/2022]
Abstract
Inherited pathogenic variants account for 5% to 10% of all breast cancer (BC) and colorectal cancer (CRC) cases. Here, we sought to profile the pathogenic variants in 25 cancer susceptibility genes in Turkish population. Germline pathogenic variants were screened in 732 BC patients, 189 CRC patients and 490 cancer-free elderly controls, using next-generation sequencing-based multigene panel testing and multiplex ligation-dependent probe amplification testing. Pathogenic variants were detected in 17.2% of high-risk BC patients and 26.4% of high-risk CRC patients. More than 95% of these variants were clinically actionable. BRCA1/2 and mismatch repair genes (MLH1, MSH2 and MSH6) accounted for two-thirds of all pathogenic variants detected in high-risk BC and CRC patients, respectively. Pathogenic variants in PALB2, CHEK2, ATM and TP53 were also prevalent in high-risk BC patients (4.5%). BRCA1 exons 17-18 deletion and CHEK2 c.592+3A>T were the most common variants predisposing to BC, and they are likely to be founder variants. Three frequent MUTYH pathogenic variants (c.884C>T, c.1437_1439delGGA and c.1187G>A) were responsible for all MUTYH biallelic cases (4.4% of high-risk CRC patients). The total pathogenic variant frequency was very low in controls (2.4%) and in low-risk BC (3.9%) and CRC (6.1%) patients. Our study depicts the pathogenic variant spectrum and prevalence in Turkish BC and CRC patients, guiding clinicians and health authorities for genetic testing applications and variant classification in Turkish population.
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Affiliation(s)
- Izzet Mehmet Akcay
- Department of Molecular Biology-Genetics & Biotechnology, Istanbul Technical University, Istanbul, Turkey.,GLAB (Genomic Laboratory), Health Directorate of Istanbul, Istanbul, Turkey
| | - Elifnaz Celik
- Department of Molecular Biology-Genetics & Biotechnology, Istanbul Technical University, Istanbul, Turkey.,GLAB (Genomic Laboratory), Health Directorate of Istanbul, Istanbul, Turkey
| | - Nihat Bugra Agaoglu
- GLAB (Genomic Laboratory), Health Directorate of Istanbul, Istanbul, Turkey.,Department of Clinical Genetics, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Gizem Alkurt
- Department of Molecular Biology-Genetics & Biotechnology, Istanbul Technical University, Istanbul, Turkey.,GLAB (Genomic Laboratory), Health Directorate of Istanbul, Istanbul, Turkey
| | - Tugba Kizilboga Akgun
- Department of Molecular Biology-Genetics & Biotechnology, Istanbul Technical University, Istanbul, Turkey.,GLAB (Genomic Laboratory), Health Directorate of Istanbul, Istanbul, Turkey
| | - Jale Yildiz
- Department of Molecular Biology-Genetics & Biotechnology, Istanbul Technical University, Istanbul, Turkey.,GLAB (Genomic Laboratory), Health Directorate of Istanbul, Istanbul, Turkey
| | - Feruze Enc
- Department of Gastroenterology, Goztepe Teaching and Research Hospital, Medeniyet University, Istanbul, Turkey
| | - Gozde Kir
- Department of Pathology, Goztepe Teaching and Research Hospital, Medeniyet University, Istanbul, Turkey
| | - Sezin Canbek
- GLAB (Genomic Laboratory), Health Directorate of Istanbul, Istanbul, Turkey.,Department of Clinical Genetics, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Ali Kilic
- Department of General Surgery, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Ebru Zemheri
- Department of Pathology, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Fikret Ezberci
- Department of General Surgery, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Melike Ozcelik
- Department of Oncology, Kartal Lutfi Kirdar Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Oncology, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Gizem Dinler Doganay
- Department of Molecular Biology-Genetics & Biotechnology, Istanbul Technical University, Istanbul, Turkey.,GLAB (Genomic Laboratory), Health Directorate of Istanbul, Istanbul, Turkey
| | - Levent Doganay
- GLAB (Genomic Laboratory), Health Directorate of Istanbul, Istanbul, Turkey.,Department of Gastroenterology and Hepatology, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
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18
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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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19
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Velázquez C, Lastra E, Avila Cobos F, Abella L, de la Cruz V, Hernando BA, Hernández L, Martínez N, Infante M, Durán M. A comprehensive custom panel evaluation for routine hereditary cancer testing: improving the yield of germline mutation detection. J Transl Med 2020; 18:232. [PMID: 32522261 PMCID: PMC7288470 DOI: 10.1186/s12967-020-02391-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022] Open
Abstract
Background In the context of our Regional Program of Hereditary Cancer, individuals fulfilling the criteria are tested for germline mutations to subsequently establish the clinical management. Our standard diagnostic approach focuses on sequencing a few classic high-risk genes, a method that frequently renders uninformative genetic results. This study aims to examine the improved yield offered by an On-Demand panel. Methods We designed an On-Demand panel for the analysis of 35-genes associated with inherited cancer susceptibility in a total of 128 cases of Hereditary Breast and Ovarian Cancer (HBOC) and Hereditary Nonpolyposis Colorectal Cancer (HNPCC). Results Eighteen deleterious mutations were detected, in both routinely (BRCA2, MLH1, MSH2, PMS2) and non-routinely (ATM, BLM, BRIP1, CHEK2, MUTYH) tested genes. The screening extended to 35 genes rendered by patients carrying several- up to 6-Variants of Unknown Significance (VUS). Moreover, we confirmed the splicing disruption at RNA level for a not previously reported BRIP1 splicing mutation. Using an On-Demand panel, we identified 18 pathogenic mutation carriers, seven of which would have gone unnoticed with traditional analysis. Conclusions Our results reinforce the utility of NGS gene panels in the diagnostic routine to increase the performance of genetic testing, especially in individuals from families with overlapping cancer phenotypes.
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Affiliation(s)
- Carolina Velázquez
- Cancer Genetics Group, Institute of Genetics and Molecular Biology (UVa-CSIC), Sanz y Forés 3, 47003, Valladolid, Spain. .,IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France.
| | - Enrique Lastra
- Unit of Genetic Counseling in Cancer, Complejo Hospitalario de Burgos, Burgos, Spain
| | | | - Luis Abella
- Unit of Genetic Counseling in Cancer, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - Virginia de la Cruz
- Unit of Genetic Counseling in Cancer, Hospital Universitario Rio Hortega, Valladolid, Spain
| | | | - Lara Hernández
- Cancer Genetics Group, Institute of Genetics and Molecular Biology (UVa-CSIC), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Noemí Martínez
- Cancer Genetics Group, Institute of Genetics and Molecular Biology (UVa-CSIC), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Mar Infante
- Cancer Genetics Group, Institute of Genetics and Molecular Biology (UVa-CSIC), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Mercedes Durán
- Cancer Genetics Group, Institute of Genetics and Molecular Biology (UVa-CSIC), Sanz y Forés 3, 47003, Valladolid, Spain
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Abstract
For most individuals, cancer development is multifactorial; however, up to 10% of all cancers are related to an inherited genetic mutation. As health care shifts to having a greater emphasis on prevention, care providers, including general surgeons, will need to play a role in identifying patients at high risk for cancer development. Genetic testing provides a tool to determine those patients with a genetic mutation and to whom appropriate preventive care and treatment may be offered. It is imperative for general surgeons to understand the role genetics plays in the care of individual patients and their relatives.
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Affiliation(s)
- Christine Van Cott
- Department of Surgery, St. Vincent's Medical Center, Bridgeport, CT, USA; Frank H. Netter MD School of Medicine, Quinnipiac University, North Haven, CT, USA.
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21
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DeSouza B, Georgiou D. Advances in Hereditary Colorectal Cancer: Opportunities and Challenges for Clinical Translation. CURRENT GENETIC MEDICINE REPORTS 2020. [DOI: 10.1007/s40142-020-00183-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Sciacovelli M, Schmidt C, Maher ER, Frezza C. Metabolic Drivers in Hereditary Cancer Syndromes. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2020. [DOI: 10.1146/annurev-cancerbio-030419-033612] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cancer is a multifaceted disease in which inherited genetic variants can be important drivers of tumorigenesis. The discovery that germline mutations of metabolic genes predispose to familial forms of cancer caused a shift in our understanding of how metabolism contributes to tumorigenesis, providing evidence that metabolic alterations can be oncogenic. In this review, we focus on mitochondrial enzymes whose mutations predispose to familial cancer, and we fully appraise their involvement in cancer formation and progression. Elucidating the molecular mechanisms that orchestrate transformation in these diverse tumors may answer key biological questions about tumor formation and evolution, leading to the identification of new therapeutic targets of intervention.
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Affiliation(s)
- Marco Sciacovelli
- MRC (Medical Research Council) Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, United Kingdom;,
| | - Christina Schmidt
- MRC (Medical Research Council) Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, United Kingdom;,
| | - Eamonn R. Maher
- Department of Medical Genetics, NIHR (National Institute of Health Research) Cambridge Biomedical Research Centre, and Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Christian Frezza
- MRC (Medical Research Council) Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, United Kingdom;,
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23
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Cetani F, Pardi E, Aretini P, Saponaro F, Borsari S, Mazoni L, Apicella M, Civita P, La Ferla M, Caligo MA, Lessi F, Mazzanti CM, Torregossa L, Oppo A, Marcocci C. Whole exome sequencing in familial isolated primary hyperparathyroidism. J Endocrinol Invest 2020; 43:231-245. [PMID: 31486992 DOI: 10.1007/s40618-019-01107-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/29/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Familial isolated hyperparathyroidism (FIHP) is a rare inherited disease accounting for 1% of all cases of primary hyperparathyroidism (PHPT). It is genetically heterogeneous being associated with mutations in different genes, including MEN1, CDC73, CASR, and recently GCM2. The aim of the study was to further investigate the molecular pathogenesis in Italian FIHP kindreds. METHODS We used whole exome sequencing (WES) in the probands of seven unrelated FIHP kindreds. We carried out a separate family-based exome analysis in a large family characterized by the co-occurrence of PHPT with multiple tumors apparently unrelated to the disease. Selected variants were also screened in 18 additional FIHP kindreds. The clinical, biochemical, and pathological characteristics of the families were also investigated. RESULTS Three different variants in GCM2 gene were found in two families, but only one (p.Tyr394Ser), already been shown to be pathogenic in vitro, segregated with the disease. Six probands carried seven heterozygous missense mutations segregating with the disease in the FAT3, PARK2, HDAC4, ITPR2 and TBCE genes. A genetic variant in the APC gene co-segregating with PHPT (p.Val530Ala) was detected in a family whose affected relatives had additional tumors, including colonic polyposis. CONCLUSION We confirm the role of GCM2 germline mutations in the pathogenesis of FIHP, although at a lower rate than in the previous WES study. Further studies are needed to establish the prevalence and the role in the predisposition to FIHP of the novel variants in additional genes.
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Affiliation(s)
- F Cetani
- University Hospital of Pisa, Endocrine Unit 2, Via Paradisa 2, 56124, Pisa, Italy.
| | - E Pardi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - P Aretini
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - F Saponaro
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - S Borsari
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - L Mazoni
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - M Apicella
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - P Civita
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - M La Ferla
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - M A Caligo
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - F Lessi
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - C M Mazzanti
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - L Torregossa
- Division of Surgical Pathology, University Hospital of Pisa, Pisa, Italy
| | - A Oppo
- Endocrinology Unit, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - C Marcocci
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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24
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Challenges in reporting pathogenic/potentially pathogenic variants in 94 cancer predisposing genes - in pediatric patients screened with NGS panels. Sci Rep 2020; 10:223. [PMID: 31937788 PMCID: PMC6959212 DOI: 10.1038/s41598-019-57080-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/17/2019] [Indexed: 11/08/2022] Open
Abstract
The benefit of reporting unsolicited findings in Next Generation Sequencing (NGS) related to cancer genes in children may have implications for family members, nevertheless, could also cause distress. We aimed to retrospectively investigate germline variants in 94 genes implicated in oncogenesis, in patients referred to NGS testing for various rare genetic diseases and reevaluate the utility of reporting different classes of pathogenicity. We used in silico prediction software to classify variants and conducted manual review to examine unsolicited findings frequencies in 145 children with rare diseases, that underwent sequencing - using a 4813 gene panel. The anonymized reanalysis revealed 18250 variants, of which 126 were considered after filtering. Six pathogenic variants (in BRCA1,BMPR1A,FANCA,FANCC,NBN genes) with cancer related phenotype and three unsolicited variants (in BRCA2,PALB2,RAD50 genes) were reported to patients. Additionally, three unsolicited variants in ATR, BLM (in two individuals), and FANCB genes presented potential cancer susceptibility, were not reported to patients. In retrospect, 4.8% (7/145) of individuals in our cohort had unsolicited NGS findings related to cancer. More efforts are needed to create an updatable consensus in reporting variants in cancer predisposing genes, especially for children. Consent process is crucial to inform of both value and risk of additional genetic information.
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Tischler J, Crew KD, Chung WK. Cases in Precision Medicine: The Role of Tumor and Germline Genetic Testing in Breast Cancer Management. Ann Intern Med 2019; 171:925-930. [PMID: 31634909 PMCID: PMC7458587 DOI: 10.7326/m18-2417] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Personalization of care through precision medicine and, more specifically, genetic testing is altering the treatment of breast cancer. Genetic testing is used in germline and tumor testing, with each providing distinct data to guide management. Germline testing supports more accurate risk evaluation to inform screening and risk-reducing medical and surgical strategies. Tumor testing can inform cancer recurrence risk assessment and cancer treatment options. This article reviews how genetic testing informs treatment and potential risks for a patient with breast cancer and her family. Hereditary cancer genetic testing of family members should include a discussion of potential results, adverse effects, clinical management options, and insurance coverage and address concerns about privacy or discrimination. Genetic professionals are available to assist with educating, testing, and treating patients with increased cancer risk.
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Affiliation(s)
- Jonah Tischler
- Vagelos College of Physicians and Surgeons, Columbia University, New York, New York (J.T.)
| | - Katherine D Crew
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York (K.D.C., W.K.C.)
| | - Wendy K Chung
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York (K.D.C., W.K.C.)
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26
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Grady MC, Kolla KA, Peshkin BN. Multigene Cancer Panels: Implications for Pre- and Post-test Genetic Counseling. CURRENT GENETIC MEDICINE REPORTS 2019. [DOI: 10.1007/s40142-019-00173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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27
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Peshkin BN, Isaacs C, Schwartz MD. Re: Cascade Genetic Testing of Relatives for Hereditary Cancer Risk: Results of an Online Initiative. J Natl Cancer Inst 2019; 111:872-873. [DOI: 10.1093/jnci/djz028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 02/20/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Beth N Peshkin
- See the Notes section for the full list of authors’ affiliations
| | - Claudine Isaacs
- See the Notes section for the full list of authors’ affiliations
| | - Marc D Schwartz
- See the Notes section for the full list of authors’ affiliations
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28
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Tsaousis GN, Papadopoulou E, Apessos A, Agiannitopoulos K, Pepe G, Kampouri S, Diamantopoulos N, Floros T, Iosifidou R, Katopodi O, Koumarianou A, Markopoulos C, Papazisis K, Venizelos V, Xanthakis I, Xepapadakis G, Banu E, Eniu DT, Negru S, Stanculeanu DL, Ungureanu A, Ozmen V, Tansan S, Tekinel M, Yalcin S, Nasioulas G. Analysis of hereditary cancer syndromes by using a panel of genes: novel and multiple pathogenic mutations. BMC Cancer 2019; 19:535. [PMID: 31159747 PMCID: PMC6547505 DOI: 10.1186/s12885-019-5756-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 05/27/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Hereditary cancer predisposition syndromes are responsible for approximately 5-10% of all diagnosed cancer cases. In the past, single-gene analysis of specific high risk genes was used for the determination of the genetic cause of cancer heritability in certain families. The application of Next Generation Sequencing (NGS) technology has facilitated multigene panel analysis and is widely used in clinical practice, for the identification of individuals with cancer predisposing gene variants. The purpose of this study was to investigate the extent and nature of variants in genes implicated in hereditary cancer predisposition in individuals referred for testing in our laboratory. METHODS In total, 1197 individuals from Greece, Romania and Turkey were referred to our laboratory for genetic testing in the past 4 years. The majority of referrals included individuals with personal of family history of breast and/or ovarian cancer. The analysis of genes involved in hereditary cancer predisposition was performed using a NGS approach. Genomic DNA was enriched for targeted regions of 36 genes and sequencing was carried out using the Illumina NGS technology. The presence of large genomic rearrangements (LGRs) was investigated by computational analysis and Multiplex Ligation-dependent Probe Amplification (MLPA). RESULTS A pathogenic variant was identified in 264 of 1197 individuals (22.1%) analyzed while a variant of uncertain significance (VUS) was identified in 34.8% of cases. Clinically significant variants were identified in 29 of the 36 genes analyzed. Concerning the mutation distribution among individuals with positive findings, 43.6% were located in the BRCA1/2 genes whereas 21.6, 19.9, and 15.0% in other high, moderate and low risk genes respectively. Notably, 25 of the 264 positive individuals (9.5%) carried clinically significant variants in two different genes and 6.1% had a LGR. CONCLUSIONS In our cohort, analysis of all the genes in the panel allowed the identification of 4.3 and 8.1% additional pathogenic variants in other high or moderate/low risk genes, respectively, enabling personalized management decisions for these individuals and supporting the clinical significance of multigene panel analysis in hereditary cancer predisposition.
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Affiliation(s)
| | | | | | | | | | | | | | - Theofanis Floros
- Oncology Department, Athens Naval and Veterans Hospital, Athens, Greece
| | | | | | | | | | | | | | | | | | - Eugeniu Banu
- Spitalul Sfantul Constantin Brasov, Brasov, Romania
| | - Dan Tudor Eniu
- Institutul Oncologic Prof. Dr. I. Chiricuta, Cluj, Romania
| | - Serban Negru
- University of Medicine and Pharmacy of Timisoara, Timisoara, Romania
| | | | | | - Vahit Ozmen
- Faculty of Medicine Istanbul University, Istanbul, Turkey
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Zimmermann MT. The Importance of Biologic Knowledge and Gene Expression Context for Genomic Data Interpretation. Front Genet 2018; 9:670. [PMID: 30619486 PMCID: PMC6305277 DOI: 10.3389/fgene.2018.00670] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/04/2018] [Indexed: 11/13/2022] Open
Abstract
Background: Genomic sequencing, including whole exome sequencing (WES), is enabling a higher resolution for defining diseases, understand mechanisms, and improving the practice of clinical care. However, WES routinely identifies genomic variants with uncertain functional effects. Furthering uncertainty in WES data interpretation is that many genes can express multiple transcripts and their relative expression may differ by body tissue. In order to interpret WES data, we not only need to understand which transcript is most relevant, but what tissue is most relevant. Methods: In this work, we quantify how frequently differences in transcript and tissue expression affect WES data interpretation at gene, pathway, disease, and biologic network levels. We combined and analyzed multiple large and publically available datasets to inform genomic data interpretation. Results: Across well-established biologic pathways and genes with pathogenic disease variants, 54 and 40% have a different protein coding effect by transcript selection for, respectively, 25 and 50% of the genes contained. Additionally, strong differences in human tissue expression levels affect 33 and 19% of the same set of pathways and diseases for, respectively, 25 and 50% of the genes contained. Conclusion: Whole exome sequencing identifies genomic variants, but to interpret the functional effects of those variants in high-resolution, we recommend building transcript selection and cross-tissue gene expression levels into hypotheses and analyses. Using current large-scale data, we show how extensively interpretation of genomic variants may differ according to transcript and tissue, across most pathways and disease. Thus, their inclusion is necessary for WES data interpretation.
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Affiliation(s)
- Michael T. Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, United States
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30
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Affiliation(s)
- Veroushka Ballester
- Department of Medicine, Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, New York
| | - Marcia Cruz-Correa
- Departments of Medicine, Biochemistry and Surgery, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico; Division of Cancer Biology, University of Puerto Rico Comprehensive Cancer Center, San Juan, Puerto Rico.
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