1
|
Paulo P, Cardoso M, Brandão A, Pinto P, Falconi A, Pinheiro M, Cerveira N, Silva R, Santos C, Pinto C, Peixoto A, Maia S, Teixeira MR. Genetic landscape of homologous recombination repair genes in early-onset/familial prostate cancer patients. Genes Chromosomes Cancer 2023; 62:710-720. [PMID: 37436117 DOI: 10.1002/gcc.23190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/19/2023] [Accepted: 06/28/2023] [Indexed: 07/13/2023] Open
Abstract
Prostate cancer (PrCa) is one of the three most frequent and deadliest cancers worldwide. The discovery of PARP inhibitors for the treatment of tumors with deleterious variants in homologous recombination repair (HRR) genes has placed PrCa on the roadmap of precision medicine. However, the overall contribution of HRR genes to the 10%-20% of carcinomas arising in men with early-onset/familial PrCa has not been fully clarified. We used targeted next-generation sequencing (T-NGS) covering eight HRR genes (ATM, BRCA1, BRCA2, BRIP1, CHEK2, NBN, PALB2, and RAD51C) and an analysis pipeline querying both small and large genomic variations to clarify their global and relative contribution to hereditary PrCa predisposition in a series of 462 early-onset/familial PrCa cases. Deleterious variants were found in 3.9% of the patients, with CHEK2 and ATM being the most frequently mutated genes (38.9% and 22.2% of the carriers, respectively), followed by PALB2 and NBN (11.1% of the carriers, each), and finally by BRCA2, RAD51C, and BRIP1 (5.6% of the carriers, each). Using the same NGS data, exonic rearrangements were found in two patients, one pathogenic in BRCA2 and one of unknown significance in BRCA1. These results contribute to clarify the genetic heterogeneity that underlies PrCa predisposition in the early-onset and familial disease, respectively.
Collapse
Affiliation(s)
- Paula Paulo
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
| | - Marta Cardoso
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
| | - Andreia Brandão
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
| | - Pedro Pinto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
| | - Ariane Falconi
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
| | - Manuela Pinheiro
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
| | - Nuno Cerveira
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Rui Silva
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
| | - Catarina Santos
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Carla Pinto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Ana Peixoto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Sofia Maia
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
- Medical Genetics Unit, Hospital Pediátrico de Coimbra, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Manuel R Teixeira
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| |
Collapse
|
2
|
Li N, Zethoven M, McInerny S, Healey E, DeSilva D, Devereux L, Scott RJ, James PA, Campbell IG. Contribution of large genomic rearrangements in PALB2 to familial breast cancer: implications for genetic testing. J Med Genet 2023; 60:112-118. [PMID: 35396271 DOI: 10.1136/jmedgenet-2021-108399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/08/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND PALB2 is the most important contributor to familial breast cancer after BRCA1 and BRCA2. Large genomic rearrangements (LGRs) in BRCA1 and BRCA2 are routinely assessed in clinical testing and are a significant contributor to the yield of actionable findings. In contrast, the contribution of LGRs in PALB2 has not been systematically studied. METHODS We performed targeted sequencing and real-time qPCR validation to identify LGRs in PALB2 in 5770 unrelated patients with familial breast cancer and 5741 cancer-free control women from the same Australian population. RESULTS Seven large deletions ranging in size from 0.96 kbp to 18.07 kbp involving PALB2 were identified in seven cases, while no LGRs were identified in any of the controls. Six LGRs were considered pathogenic as they included one or more exons of PALB2 and disrupted the WD40 domain at the C terminal end of the PALB2 protein while one LGR only involved a partial region of intron 10 and was considered a variant of unknown significance. Altogether, pathogenic LGRs identified in this study accounted for 10.3% (6 of 58) of the pathogenic PALB2 variants detected among the 5770 families with familial breast cancer. CONCLUSIONS Our data show that a clinically important proportion of PALB2 pathogenic mutations in Australian patients with familial breast cancer are LGRs. Such observations have provided strong support for inclusion of PALB2 LGRs in routine clinical genetic testing.
Collapse
Affiliation(s)
- Na Li
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Magnus Zethoven
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Bioinformatics Core Facility, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Simone McInerny
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Eliza Healey
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Dilanka DeSilva
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Lisa Devereux
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Lifepool, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia.,Division of Molecular Medicine, Pathology North, Newcastle, New South Wales, Australia.,Discipline of Medical Genetics, The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
3
|
Eyries M, Ariste O, Legrand G, Basset N, Guillerm E, Perrier A, Duros C, Cohen-Haguenauer O, de la Grange P, Coulet F. Detection of a pathogenic Alu element insertion in PALB2 gene from targeted NGS diagnostic data. Eur J Hum Genet 2022; 30:1187-1190. [PMID: 35277653 PMCID: PMC9553905 DOI: 10.1038/s41431-022-01064-3] [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] [Received: 09/27/2021] [Revised: 01/11/2022] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
Despite routine analysis of a large panel of genes, pathogenic variants are only detected in approximately 20% of families with hereditary breast and/or ovarian cancer. Mobile element insertions (MEI) are known to cause genetic diseases in humans, but remain challenging to detect. Retrospective analysis of targeted next-generation sequencing (NGS) data from 359 patients was performed using a dedicated MEI detection pipeline. We detected one MEI in exon 9 of the PALB2 gene in a woman with a family history of breast cancer. The pathogenic variant, c.2872_2888delins114AluL2, disrupts the PALB2 coding sequence and leads to the production of a truncated protein, p.(Gln958Valfs*38). This is the first report of a pathogenic MEI in PALB2. This study illustrates that MEI analysis may help to improve molecular diagnostic yield and can be performed from targeted NGS data used for routine diagnosis.
Collapse
Affiliation(s)
- Mélanie Eyries
- Sorbonne Université, Département de génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, F-75013, Paris, France.
| | | | - Gaelle Legrand
- Sorbonne Université, Département de génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - Noémie Basset
- Sorbonne Université, Département de génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - Erell Guillerm
- Sorbonne Université, Département de génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - Alexandre Perrier
- Sorbonne Université, Département de génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - Caroline Duros
- Hôpital Saint-Louis-Lariboisière-Fernand-Widal, Service d'oncologie médicale Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France
| | - Odile Cohen-Haguenauer
- Hôpital Saint-Louis-Lariboisière-Fernand-Widal, Service d'oncologie médicale Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France
| | | | - Florence Coulet
- Sorbonne Université, Département de génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| |
Collapse
|
4
|
Identification and Characterization of an Exonic Duplication in PALB2 in a Man with Synchronous Breast and Prostate Cancer. Int J Mol Sci 2022; 23:ijms23020667. [PMID: 35054852 PMCID: PMC8775416 DOI: 10.3390/ijms23020667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/04/2023] Open
Abstract
PALB2 (partner and localizer of BRCA2), as indicated by its name, is a BRCA2-interacting protein that plays an important role in homologous recombination (HR) and DNA double-strand break (DSB) repair. While pathogenic variants of PALB2 have been well proven to confer an increased risk of breast cancer, data on its involvement in prostate cancer (PrC) have not been clearly demonstrated. We investigated, using targeted next generation sequencing (NGS), a 59-year-old Caucasian man who developed synchronous breast and prostate cancers. This genetic investigation allowed to identify an intragenic germline heterozygous duplication in PALB2, implicating intronic repetitive sequences spanning exon 11. This variant was confirmed by multiplex ligation probe amplification (MLPA), and genomic breakpoints have been identified and characterized at the nucleotide level (c.3114-811_3202-1756dup) using an approach based on walking PCR, long range PCR, and Sanger sequencing. RT-PCR using mRNA extracted from lymphocytes and followed by Sanger sequencing revealed a tandem duplication r.3114_3201dup; p.(Gly1068Glufs * 14). This duplication results in the synthesis of a truncated, and most-likely, non-functional protein. These findings expand the phenotypic spectrum of PALB2 variants and may improve the yield of genetic diagnoses in this field.
Collapse
|
5
|
Kwong A, Au CH, Shin VY, Ho DN, Wong EYL, Ho CYS, Chung Y, Chan TL, Ma ESK. Rapid Breakpoint Mapping of a Novel Germline PALB2 Duplication by PCR-Free Long-Read Sequencing for Interpretation of Its Pathogenicity. JCO Precis Oncol 2022; 5:1044-1047. [PMID: 34994627 DOI: 10.1200/po.20.00454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen Hospital, Hong Kong, China.,Department of Surgery and Cancer Genetics Centre, Hong Kong Sanatorium and Hospital, Hong Kong, China.,Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Chun Hang Au
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Vivian Y Shin
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen Hospital, Hong Kong, China
| | - Dona N Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Elaine Y L Wong
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Cecilia Y S Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Yvonne Chung
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Tsun Leung Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong, China.,Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Edmond S K Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong, China.,Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| |
Collapse
|
6
|
Garcia-Pelaez J, Barbosa-Matos R, São José C, Sousa S, Gullo I, Hoogerbrugge N, Carneiro F, Oliveira C. Gastric cancer genetic predisposition and clinical presentations: Established heritable causes and potential candidate genes. Eur J Med Genet 2021; 65:104401. [PMID: 34871783 DOI: 10.1016/j.ejmg.2021.104401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 11/10/2021] [Accepted: 11/28/2021] [Indexed: 12/12/2022]
Abstract
Tumour risk syndromes (TRS) are characterized by an increased risk of early-onset cancers in a familial context. High cancer risk is mostly driven by loss-of-function variants in a single cancer-associated gene. Presently, predisposition to diffuse gastric cancer (DGC) is explained by CDH1 and CTNNA1 pathogenic and likely pathogenic variants (P/LP), causing Hereditary Diffuse Gastric Cancer (HDGC); while APC promoter 1B single nucleotide variants predispose to Gastric Adenocarcinoma and Proximal Polyposis of the Stomach (GAPPS). Familial Intestinal Gastric Cancer (FIGC), recognized as a GC-predisposing disease, remains understudied and genetically unsolved. GC can also occur in the spectrum of other TRS. Identification of heritable causes allows defining diagnostic testing criteria, helps to clinically classify GC families into the appropriate TRS, and allows performing pre-symptomatic testing identifying at-risk individuals for downstream surveillance, risk reduction and/or treatment. However, most of HDGC, some GAPPS, and most FIGC patients/families remain unsolved, expecting a heritable factor to be discovered. The missing heritability in GC-associated tumour risk syndromes (GC-TRS) is likely explained not by a single major gene, but by a diversity of genes, some, predisposing to other TRS. This would gain support if GC-enriched small families or apparently isolated early-onset GC cases were hiding a family history compatible with another TRS. Herein, we revisited current knowledge on GC-TRS, and searched in the literature for individuals/families bearing P/LP variants predisposing for other TRS, but whose probands display a clinical presentation and/or family history also fitting GC-TRS criteria. We found 27 families with family history compatible with HDGC or FIGC, harbouring 28 P/LP variants in 16 TRS-associated genes, mainly associated with DNA repair. PALB2 or BRCA2 were the most frequently mutated candidate genes in individuals with family history compatible with HDGC and FIGC, respectively. Consolidation of PALB2 and BRCA2 as HDGC- or FIGC-associated genes, respectively, holds promise and worth additional research. This analysis further highlighted the influence, that proband's choice and small or unreported family history have, for a correct TRS diagnosis, genetic screening, and disease management. In this review, we provide a rational for identification of particularly relevant candidate genes in GC-TRS.
Collapse
Affiliation(s)
- José Garcia-Pelaez
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Doctoral Programme in Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Rita Barbosa-Matos
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; International Doctoral Programme in Molecular and Cellular Biotechnology Applied to Health Sciences from Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Celina São José
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Doctoral Programme in Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Sónia Sousa
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Irene Gullo
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; FMUP - Faculty of Medicine of the University of Porto, Porto, Portugal; Centro Hospitalar e Universitário S. João, Porto, Portugal
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Fátima Carneiro
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; FMUP - Faculty of Medicine of the University of Porto, Porto, Portugal; Centro Hospitalar e Universitário S. João, Porto, Portugal
| | - Carla Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; FMUP - Faculty of Medicine of the University of Porto, Porto, Portugal.
| |
Collapse
|
7
|
The Genetic Analyses of French Canadians of Quebec Facilitate the Characterization of New Cancer Predisposing Genes Implicated in Hereditary Breast and/or Ovarian Cancer Syndrome Families. Cancers (Basel) 2021; 13:cancers13143406. [PMID: 34298626 PMCID: PMC8305212 DOI: 10.3390/cancers13143406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 12/19/2022] Open
Abstract
The French Canadian population of the province of Quebec has been recognized for its contribution to research in medical genetics, especially in defining the role of heritable pathogenic variants in cancer predisposing genes. Multiple carriers of a limited number of pathogenic variants in BRCA1 and BRCA2, the major risk genes for hereditary breast and/or ovarian cancer syndrome families, have been identified in French Canadians, which is in stark contrast to the array of over 2000 different pathogenic variants reported in each of these genes in other populations. As not all such cancer syndrome families are explained by BRCA1 and BRCA2, newly proposed gene candidates identified in other populations have been investigated for their role in conferring risk in French Canadian cancer families. For example, multiple carriers of distinct variants were identified in PALB2 and RAD51D. The unique genetic architecture of French Canadians has been attributed to shared ancestry due to common ancestors of early settlers of this population with origins mainly from France. In this review, we discuss the merits of genetically characterizing cancer predisposing genes in French Canadians of Quebec. We focused on genes that have been implicated in hereditary breast and/or ovarian cancer syndrome families as they have been the most thoroughly characterized cancer syndromes in this population. We describe how genetic analyses of French Canadians have facilitated: (i) the classification of variants in BRCA1 and BRCA2; (ii) the identification and classification of variants in newly proposed breast and/or ovarian cancer predisposing genes; and (iii) the identification of a new breast cancer predisposing gene candidate, RECQL. The genetic architecture of French Canadians provides a unique opportunity to evaluate new candidate cancer predisposing genes regardless of the population in which they were identified.
Collapse
|
8
|
van den Akker J, Hon L, Ondov A, Mahkovec Z, O'Connor R, Chan RC, Lock J, Zimmer AD, Rostamianfar A, Ginsberg J, Leon A, Topper S. Intronic Breakpoint Signatures Enhance Detection and Characterization of Clinically Relevant Germline Structural Variants. J Mol Diagn 2021; 23:612-629. [PMID: 33621668 DOI: 10.1016/j.jmoldx.2021.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/14/2020] [Accepted: 01/27/2021] [Indexed: 12/16/2022] Open
Abstract
The relevance of large copy number variants (CNVs) to hereditary disorders has been long recognized, and population sequencing efforts have chronicled many common structural variants (SVs). However, limited data are available on the clinical contribution of rare germline SVs. Here, a detailed characterization of SVs identified using targeted next-generation sequencing was performed. Across 50 genes associated with hereditary cancer and cardiovascular disorders, a minimum of 828 unique SVs were reported, including 584 fully characterized SVs. Almost 40% of CNVs were <5 kb, with one in three deletions impacting a single exon. Additionally, 36 mid-range deletions/duplications (50 to 250 bp), 21 mobile element insertions, 6 inversions, and 27 complex rearrangements were detected. This data set was used to model SV detection in a bioinformatics pipeline solely relying on read depth, which revealed that genome sequencing (30×) allows detection of 71%, a 500× panel only targeting coding regions 53%, and exome sequencing (100×) <20% of characterized SVs. SVs accounted for 14.1% of all unique pathogenic variants, supporting the importance of SVs in hereditary disorders. Robust SV detection requires an ensemble of variant-calling algorithms that utilize sequencing of intronic regions. These algorithms should use distinct data features representative of each class of mutational mechanism, including recombination between two sequences sharing high similarity, covariants inserted between CNV breakpoints, and complex rearrangements containing inverted sequences.
Collapse
|
9
|
Richardson ME, Chong H, Mu W, Conner BR, Hsuan V, Willett S, Lam S, Tsai P, Pesaran T, Chamberlin AC, Park MS, Gray P, Karam R, Elliott A. DNA breakpoint assay reveals a majority of gross duplications occur in tandem reducing VUS classifications in breast cancer predisposition genes. Genet Med 2018; 21:683-693. [PMID: 30054569 PMCID: PMC6752314 DOI: 10.1038/s41436-018-0092-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/04/2018] [Indexed: 01/17/2023] Open
Abstract
PURPOSE Gross duplications are ambiguous in terms of clinical interpretation due to the limitations of the detection methods that cannot infer their context, namely, whether they occur in tandem or are duplicated and inserted elsewhere in the genome. We investigated the proportion of gross duplications occurring in tandem in breast cancer predisposition genes with the intent of informing their classifications. METHODS The DNA breakpoint assay (DBA) is a custom, paired-end, next-generation sequencing (NGS) method designed to capture and detect deep-intronic DNA breakpoints in gross duplications in BRCA1, BRCA2, ATM, CDH1, PALB2, and CHEK2. RESULTS DBA allowed us to ascertain breakpoints for 44 unique gross duplications from 147 probands. We determined that the duplications occurred in tandem in 114 (78%) carriers from this cohort, while the remainder have unknown tandem status. Among the tandem gross duplications that were eligible for reclassification, 95% of them were upgraded to pathogenic. CONCLUSION DBA is a novel, high-throughput, NGS-based method that informs the tandem status, and thereby the classification of, gross duplications. This method revealed that most gross duplications in the investigated genes occurred in tandem and resulted in a pathogenic classification, which helps to secure the necessary treatment options for their carriers.
Collapse
Affiliation(s)
- Marcy E Richardson
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA.
| | - Hansook Chong
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Wenbo Mu
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Blair R Conner
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Vickie Hsuan
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Sara Willett
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Stephanie Lam
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Pei Tsai
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Tina Pesaran
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Adam C Chamberlin
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Min-Sun Park
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Phillip Gray
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Rachid Karam
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Aaron Elliott
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| |
Collapse
|
10
|
Mandelker D, Zhang L. The emerging significance of secondary germline testing in cancer genomics. J Pathol 2018; 244:610-615. [PMID: 29293272 DOI: 10.1002/path.5031] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 12/13/2022]
Abstract
Many clinical laboratories now sequence the tumors from advanced cancer patients to identify oncogenic drivers and guide targeted therapies and clinical trials. One limitation of tumor sequencing is that it cannot distinguish between tumor-specific somatic (acquired) mutations and patients' germline (constitutional) variants. To definitively identify somatic variants, some clinical labs sequence both a normal sample from a patient and their tumor to subtract the germline variants from the somatic variants. Having a paired normal sample also allows for the identification of secondary germline mutations in cancer patients who may not meet the current clinical guidelines for genetic testing of cancer predisposition syndromes. Such simultaneous detection of somatic alterations and germline mutations during tumor-normal sequencing can guide therapeutic decision making for cancer patients and the identification and screening of at-risk family members. Here, we review the clinical workflow, advantages and disadvantages, and clinical utility of tumor-normal sequencing in the management of cancer patients. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
11
|
Bleuyard JY, Butler RM, Esashi F. Perturbation of PALB2 function by the T413S mutation found in small cell lung cancer. Wellcome Open Res 2017; 2:110. [PMID: 29387807 PMCID: PMC5721578 DOI: 10.12688/wellcomeopenres.13113.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2017] [Indexed: 12/22/2022] Open
Abstract
Background: Germline mutations in the
PALB2 gene are associated with the genetic disorder Fanconi anaemia and increased predisposition to cancer. Disease-associated variants are mainly protein-truncating mutations, whereas a few missense substitutions are reported to perturb its interaction with breast cancer susceptibility proteins BRCA1 and BRCA2, which play essential roles in homology-directed repair (HDR). More recently, PALB2 was shown to associate with active genes independently of BRCA1, and through this mechanism, safeguards these regions from DNA replicative stresses. However, it is unknown whether PALB2 tumour suppressor function requires its chromatin association. Methods: Mining the public database of cancer mutations, we identified four potentially deleterious cancer-associated missense mutations within the PALB2 chromatin association motif (ChAM). To assess the impact of these mutations on PALB2 function, we generated cell lines expressing PALB2 variants harbouring corresponding ChAM mutations, and evaluated PALB2 chromatin association properties and the cellular resistance to camptothecin (CPT). Additionally, we examined the accumulation of γH2A.X and the RAD51 recombinase as readouts of DNA damage signalling and HDR, respectively. Results: We demonstrate that a small-cell lung cancer (SCLC)-associated T413S mutation in PALB2 impairs its chromatin association and confers reduced resistance to CPT, the only FDA-approved drug for relapsed SCLC. Unexpectedly, we found a less efficient γH2A.X nuclear foci formation in PALB2 T413S expressing cells, whereas a near-normal level of RAD51 nuclear foci was visible. Conclusions: These findings support the importance of PALB2 chromatin association in the suppression of tumours, including SCLC, an unusually aggressive type of cancer with poor prognosis. PALB2 T413S has little impact on RAD51 recruitment, likely due to its intact interaction with BRCA1 and BRCA2. However, this mutant shows inefficient DNA stress signalling. This finding sheds new light on the function of PALB2, playing a role in efficient DNA stress signalling through constitutive chromatin association.
Collapse
Affiliation(s)
- Jean-Yves Bleuyard
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Rosie M Butler
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, SE1 9RT, UK
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| |
Collapse
|
12
|
Bleuyard JY, Butler RM, Esashi F. Perturbation of PALB2 function by the T413S mutation found in small cell lung cancer. Wellcome Open Res 2017. [PMID: 29387807 DOI: 10.12688/wellcomeopenres.13113.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background: Germline mutations in the PALB2 gene are associated with the genetic disorder Fanconi anaemia and increased predisposition to cancer. Disease-associated variants are mainly protein-truncating mutations, whereas a few missense substitutions are reported to perturb its interaction with breast cancer susceptibility proteins BRCA1 and BRCA2, which play essential roles in homology-directed repair (HDR). More recently, PALB2 was shown to associate with active genes independently of BRCA1, and through this mechanism, safeguards these regions from DNA replicative stresses. However, it is unknown whether PALB2 tumour suppressor function requires its chromatin association. Methods: Mining the public database of cancer mutations, we identified four potentially deleterious cancer-associated missense mutations within the PALB2 chromatin association motif (ChAM). To assess the impact of these mutations on PALB2 function, we generated cell lines expressing PALB2 variants harbouring corresponding ChAM mutations, and evaluated PALB2 chromatin association properties and the cellular resistance to camptothecin (CPT). Additionally, we examined the accumulation of γH2A.X and the RAD51 recombinase as readouts of DNA damage signalling and HDR, respectively. Results: We demonstrate that a small-cell lung cancer (SCLC)-associated T413S mutation in PALB2 impairs its chromatin association and confers reduced resistance to CPT, the only FDA-approved drug for relapsed SCLC. Unexpectedly, we found a less efficient γH2A.X nuclear foci formation in PALB2 T413S expressing cells, whereas a near-normal level of RAD51 nuclear foci was visible. Conclusions: These findings support the importance of PALB2 chromatin association in the suppression of tumours, including SCLC, an unusually aggressive type of cancer with poor prognosis. PALB2 T413S has little impact on RAD51 recruitment, likely due to its intact interaction with BRCA1 and BRCA2. However, this mutant shows inefficient DNA stress signalling. This finding sheds new light on the function of PALB2, playing a role in efficient DNA stress signalling through constitutive chromatin association.
Collapse
Affiliation(s)
- Jean-Yves Bleuyard
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Rosie M Butler
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, SE1 9RT, UK
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| |
Collapse
|
13
|
Morgan RG, Venturelli M, Gross C, Tarperi C, Schena F, Reggiani C, Naro F, Pedrinolla A, Monaco L, Richardson RS, Donato AJ. Age-Associated ALU Element Instability in White Blood Cells Is Linked to Lower Survival in Elderly Adults: A Preliminary Cohort Study. PLoS One 2017; 12:e0169628. [PMID: 28060910 PMCID: PMC5218400 DOI: 10.1371/journal.pone.0169628] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/20/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND ALU element instability could contribute to gene function variance in aging, and may partly explain variation in human lifespan. OBJECTIVE To assess the role of ALU element instability in human aging and the potential efficacy of ALU element content as a marker of biological aging and survival. DESIGN Preliminary cohort study. METHODS We measured two high frequency ALU element subfamilies, ALU-J and ALU-Sx, by a single qPCR assay and compared ALU-J/Sx content in white blood cell (WBCs) and skeletal muscle cell (SMCs) biopsies from twenty-three elderly adults with sixteen healthy sex-balanced young adults; all-cause survival rates of elderly adults predicted by ALU-J/Sx content in both tissues; and cardiovascular disease (CVD)- and cancer-specific survival rates of elderly adults predicted by ALU-J/Sx content in both tissues, as planned subgroup analyses. RESULTS We found greater ALU-J/Sx content variance in WBCs from elderly adults than young adults (P < 0.001) with no difference in SMCs (P = 0.94). Elderly adults with low WBC ALU-J/Sx content had worse four-year all-cause and CVD-associated survival than those with high ALU-J/Sx content (both P = 0.03 and hazard ratios (HR) ≥ 3.40), while WBC ALU-J/Sx content had no influence on cancer-associated survival (P = 0.42 and HR = 0.74). SMC ALU-J/Sx content had no influence on all-cause, CVD- or cancer -associated survival (all P ≥ 0.26; HR ≤ 2.07). CONCLUSIONS These initial findings demonstrate that ALU element instability occurs with advanced age in WBCs, but not SMCs, and imparts greater risk of all-cause mortality that is likely driven by an increased risk for CVD and not cancer.
Collapse
Affiliation(s)
- R. Garrett Morgan
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Geriatric Research, Education, and Clinical Center, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, United States of America
| | - Massimo Venturelli
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Department of Neurological and Movement Sciences, University of Verona, Verona, Italy
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Cole Gross
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Cantor Tarperi
- Department of Neurological and Movement Sciences, University of Verona, Verona, Italy
| | - Federico Schena
- Department of Neurological and Movement Sciences, University of Verona, Verona, Italy
| | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Fabio Naro
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University, Rome, Italy
| | | | - Lucia Monaco
- Department of Physiology and Pharmacology, Sapienza University of Rome, Italy
| | - Russell S. Richardson
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Geriatric Research, Education, and Clinical Center, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, United States of America
- Department of Health, Kinesiology, and Recreation, University of Utah, Salt Lake City, Utah, United States of America
| | - Anthony J. Donato
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Geriatric Research, Education, and Clinical Center, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, United States of America
- Department of Health, Kinesiology, and Recreation, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
| |
Collapse
|
14
|
Lux MP, Fasching PA, Schrauder MG, Hein A, Jud SM, Rauh C, Beckmann MW. The PI3K Pathway: Background and Treatment Approaches. Breast Care (Basel) 2016; 11:398-404. [PMID: 28228706 DOI: 10.1159/000453133] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Two-thirds of all breast cancer patients with metastases have a hormone receptor (HR)-positive/human epidermal growth factor receptor 2 (HER2)-negative subtype. Endocrine therapy is the treatment of choice in these patients since in addition to its effectiveness it can also maintain the patients' quality of life over a longer term. However, 44-62% of postmenopausal patients with metastatic breast carcinoma have primary tamoxifen resistance. After 3-5 years, 30-40% of the patients receiving tamoxifen treatment develop secondary resistance. Understanding the way in which resistance develops is therefore essential for developing treatment approaches that can prevent or reverse endocrine resistance. The phosphatidylinositol 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) signaling pathway plays a central role here. As a result of the numerous interactions involved, complex issues arise that need to be taken into account in the development and use of therapeutic agents. In addition, this signaling pathway is the one that most frequently undergoes mutations in breast cancer. The prognostic and predictive significance of individual mutations has not yet been fully explained, but it might provide a basis for patient selection in clinical studies. Initial research results on the use of PI3K inhibitors suggest that this may be a highly promising therapeutic approach, with an acceptable side effect profile.
Collapse
Affiliation(s)
- Michael P Lux
- University Breast Center for Franconia, Department of Gynecology, Erlangen University Hospital, CCC Erlangen-EMN, Erlangen, Germany
| | - Peter A Fasching
- University Breast Center for Franconia, Department of Gynecology, Erlangen University Hospital, CCC Erlangen-EMN, Erlangen, Germany
| | - Michael G Schrauder
- University Breast Center for Franconia, Department of Gynecology, Erlangen University Hospital, CCC Erlangen-EMN, Erlangen, Germany
| | - Alexander Hein
- University Breast Center for Franconia, Department of Gynecology, Erlangen University Hospital, CCC Erlangen-EMN, Erlangen, Germany
| | - Sebastian M Jud
- University Breast Center for Franconia, Department of Gynecology, Erlangen University Hospital, CCC Erlangen-EMN, Erlangen, Germany
| | - Claudia Rauh
- University Breast Center for Franconia, Department of Gynecology, Erlangen University Hospital, CCC Erlangen-EMN, Erlangen, Germany
| | - Matthias W Beckmann
- University Breast Center for Franconia, Department of Gynecology, Erlangen University Hospital, CCC Erlangen-EMN, Erlangen, Germany
| |
Collapse
|