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Bruinsma F, Harraka P, Jordan S, Park DJ, Pope B, Steen J, Milne RL, Giles GG, Winship I, Tucker KM, Southey MC, Nguyen-Dumont T. Prevalence of Germline Pathogenic Variants in Renal Cancer Predisposition Genes in a Population-Based Study of Renal Cell Carcinoma. Cancers (Basel) 2024; 16:2985. [PMID: 39272843 PMCID: PMC11393909 DOI: 10.3390/cancers16172985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
Renal cell carcinoma (RCC) has been associated with germline pathogenic or likely pathogenic (PLP) variants in recognised cancer susceptibility genes. Studies of RCC using gene panel sequencing have been highly variable in terms of study design, genes included, and reported prevalence of PLP variant carriers (4-26%). Studies that restricted their analysis to established RCC predisposition genes identified variants in 1-6% of cases. This work assessed the prevalence of clinically actionable PLP variants in renal cancer predisposition genes in an Australian population-based sample of RCC cases. Germline DNA from 1029 individuals diagnosed with RCC who were recruited through the Victoria and Queensland cancer registries were screened using a custom amplicon-based panel of 21 genes. Mean age at cancer diagnosis was 60 ± 10 years, and two-thirds (690, 67%) of the participants were men. Eighteen participants (1.7%) were found to carry a PLP variant. Genes with PLP variants included BAP1, FH, FLCN, MITF, MSH6, SDHB, TSC1, and VHL. Most carriers of PLP variants did not report a family history of the disease. Further exploration of the clinical utility of gene panel susceptibility testing for all RCCs is warranted.
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Affiliation(s)
- Fiona Bruinsma
- Cancer Epidemiology Division, Cancer Council Victoria, East Melbourne, VIC 3002, Australia
- Burnet Institute, Melbourne, VIC 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Philip Harraka
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Susan Jordan
- School of Public Health, The University of Queensland, Herston, QLD 4006, Australia
| | - Daniel J Park
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Bernard Pope
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC 3010, Australia
- Victoria Comprehensive Cancer Centre, The University of Melbourne Centre for Cancer Research, Melbourne, VIC 3010, Australia
- Department of Surgery, Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jason Steen
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, East Melbourne, VIC 3002, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, East Melbourne, VIC 3002, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Ingrid Winship
- Department of Medicine, Melbourne Medical School, The University of Melbourne, Melbourne, VIC 3010, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC 3052, Australia
| | - Katherine M Tucker
- Hereditary Cancer Centre, Nelune Comprehensive Cancer Centre, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- Division of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, East Melbourne, VIC 3002, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC 3010, Australia
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Siraj AK, Bu R, Parvathareddy SK, Iqbal K, Azam S, Qadri Z, Al-Rasheed M, Haqawi W, Diaz M, Victoria IG, Al-Badawi IA, Tulbah A, Al-Dayel F, Ajarim D, Al-Kuraya KS. PALB2 germline mutations in a large cohort of Middle Eastern breast-ovarian cancer patients. Sci Rep 2023; 13:7666. [PMID: 37169825 PMCID: PMC10175539 DOI: 10.1038/s41598-023-34693-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 05/05/2023] [Indexed: 05/13/2023] Open
Abstract
The PALB2 gene is a breast cancer (BC) and ovarian cancer (OC) predisposition gene involved in the homologous recombination repair pathway. However, the prevalence and clinicopathological association of PALB2 pathogenic/likely pathogenic (PV/LPV) variants in Middle East is still not fully explored. Total 918 BC/OC patients from Saudi Arabia were selected for PALB2 mutations screening using capture sequencing technology. Five heterozygous PVs or LPVs were identified in six cases, accounting for 0.65% (6/918) of entire cohort. Two cases (33.3%) harbored PVs and four cases (66.7%) carried LPVs. Four PVs/LPVs (80%) were frameshift along with one novel splicing LPV (c.2835-2_2835-1delinsTT). One recurrent LPV (c.3425delT: p.L1142fs) was identified in two cases. All six affected carriers have breast cancer diagnosis with median age of 39.5 years (range 34-49 years). Only two cases (33%) have documented family history of cancer. Breast cancer phenotype was invasive ductal unilateral cancer in all cases with 66.7% of hormone receptor positive and 16% of triple negative tumors. Germline PVs/LPVs in the PALB2 gene were observed in low frequency of 0.65% in Saudi BC and/or OC. Our study confirms one recurrent LPV and one novel LPV in Saudi breast cancer patients.
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Affiliation(s)
- Abdul K Siraj
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Rong Bu
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Sandeep Kumar Parvathareddy
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Kaleem Iqbal
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Saud Azam
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Zeeshan Qadri
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Maha Al-Rasheed
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Wael Haqawi
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Mark Diaz
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Ingrid G Victoria
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Ismail A Al-Badawi
- Department of Obstetrics-Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Asma Tulbah
- Department of Pathology, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Fouad Al-Dayel
- Department of Pathology, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Dahish Ajarim
- Oncology Center, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Khawla S Al-Kuraya
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia.
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3
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Yang P, Qiao Y, Liao H, Huang Y, Meng M, Chen Y, Zhou Q. The Cancer/Testis Antigen CT45A1 Promotes Transcription of Oncogenic Sulfatase-2 Gene in Breast Cancer Cells and Is Sensible Targets for Cancer Therapy. J Breast Cancer 2023; 26:168-185. [PMID: 37095619 PMCID: PMC10139848 DOI: 10.4048/jbc.2023.26.e5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/17/2022] [Accepted: 01/31/2023] [Indexed: 02/16/2023] Open
Abstract
PURPOSE Invasive breast carcinomas (BRCAs) are highly lethal. The molecular mechanisms underlying progression of invasive BRCAs are unclear, and effective therapies are highly desired. The cancer-testis antigen CT45A1 promotes overexpression of pro-metastatic sulfatase-2 (SULF2) and breast cancer metastasis to the lungs, but its mechanisms are largely unknown. In this study, we aimed to elucidate the mechanism of CT45A1-induced SULF2 overexpression and provide evidence for targeting CT45A1 and SULF2 for breast cancer therapy. METHODS The effect of CT45A1 on SULF2 expression was assessed using reverse transcription polymerase chain reaction and western blot. The mechanism of CT45A1-induced SULF2 gene transcription was studied using protein-DNA binding assay and a luciferase activity reporter system. The interaction between CT45A1 and SP1 proteins was assessed using immunoprecipitation and western blot. Additionally, the suppression of breast cancer cell motility by SP1 and SULF2 inhibitors was measured using cell migration and invasion assays. RESULTS CT45A1 and SULF2 are aberrantly overexpressed in patients with BRCA; importantly, overexpression of CT45A1 is closely associated with poor prognosis. Mechanistically, gene promoter demethylation results in overexpression of both CT45A1 and SULF2. CT45A1 binds directly to the core sequence GCCCCC in the promoter region of SULF2 gene and activates the promoter. Additionally, CT45A1 interacts with the oncogenic master transcription factor SP1 to drive SULF2 gene transcription. Interestingly, SP1 and SULF2 inhibitors suppress breast cancer cell migration, invasion, and tumorigenicity. CONCLUSION Overexpression of CT45A1 is associated with poor prognosis in patients with BRCA. CT45A1 promotes SULF2 overexpression by activating the promoter and interacting with SP1. Additionally, SP1 and SULF2 inhibitors suppress breast cancer cell migration, invasion, and tumorigenesis. Our findings provide new insight into the mechanisms of breast cancer metastasis and highlight CT45A1 and SULF2 as sensible targets for developing novel therapeutics against metastatic breast cancer.
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Affiliation(s)
- Ping Yang
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong, P.R. China
| | - Yingnan Qiao
- Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, Soochow University, Suzhou, P.R. China
| | - Huaidong Liao
- Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, Soochow University, Suzhou, P.R. China
| | - Yizheng Huang
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong, P.R. China
| | - Mei Meng
- Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, Soochow University, Suzhou, P.R. China
| | - Yu Chen
- Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, Soochow University, Suzhou, P.R. China
| | - Quansheng Zhou
- Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, Soochow University, Suzhou, P.R. China
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, P.R. China
- 2011 Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
- National Clinical Research Center for Hematologic Diseases, The Affiliated Hospital of Soochow University, Suzhou, P.R. China
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4
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Gonzalez A, Del Greco F, Vargas-Roig L, Brun B, Tabares G, Mampel A, Montes C, Martin C, Lopez M, Rossi N, Bruno L, Ponce C, Quaglio P, Yanzi A, Acevedo S, Lugo L, Lopez Breccia P, Avila S, Sisterna S, Del Castillo MS, Vazquez M, Nuñez LM. PALB2 germline mutations in a multi-gene panel testing cohort of 1905 breast-ovarian cancer patients in Argentina. Breast Cancer Res Treat 2022; 194:403-412. [PMID: 35610400 DOI: 10.1007/s10549-022-06620-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/30/2022] [Indexed: 11/24/2022]
Abstract
PURPOSE PALB2 variants have been scarcely described in Argentinian and Latin-American reports. In this study, we describe molecular and clinical characteristics of PALB2 mutations found in multi-gene panels (MP) from breast-ovarian cancer (BOC) families in different institutions from Argentina. METHODS We retrospectively identified PALB2 pathogenic (PV) and likely pathogenic (LPV) variants from a cohort of 1905 MP results, provided by one local lab (Heritas) and SITHER (Hereditary Tumor Information System) public database. All patients met hereditary BOC clinical criteria for testing, according to current guidelines. RESULTS The frequency of PALB2 mutations is 2.78% (53/1905). Forty-eight (90.5%) are PV and five (9.5%) are LPV. Most of the 18 different mutations (89%) are nonsense and frameshift types and 2 variants are novel. One high-rate recurrent PV (Y551*) is present in 43% (23/53) of the unrelated index cases. From the 53 affected carriers, 94% have BC diagnosis with 14% of bilateral cases. BC phenotype is mainly invasive ductal (78%) with 62% of hormone-receptor positive and 22% of triple negative tumors. Self-reported ethnic background of the cohort is West European (66%) and native Latin-American (20%) which is representative of Buenos Aires and other big urban areas of the country. CONCLUSION This is the first report describing molecular and clinical characteristics of PALB2 carriers in Argentina. Frequency of PALB2 PV in Argentinian HBOC families is higher than in other reported populations. Y551* is a recurrent mutation that seems to be responsible for almost 50% of PALB2 cases.
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Affiliation(s)
| | | | | | | | | | | | - Cecilia Montes
- Instituto Modelo de Ginecología Y Obstetricia, Córdoba, Argentina
| | - Claudia Martin
- Hospital Privado Universitario de Córdoba, Córdoba, Argentina
| | | | - Norma Rossi
- Fundación Para el Progreso de La Medicina, Córdoba, Argentina
| | - Luisina Bruno
- Instituto de Oncología Alexander Fleming, Buenos Aires, Argentina
| | - Carolina Ponce
- Instituto de Oncología Alexander Fleming, Buenos Aires, Argentina
| | | | | | | | - Lilia Lugo
- Clínica San Gerónimo, Santa Fe, Argentina
| | | | - Silvia Avila
- Facultad de Ciencias Médicas, Universidad Nacional del Comahue, Neuquén, Argentina.,Heritas - CONICET, Rosario, Argentina.,Hospital Alemán de Buenos Aires, Buenos Aires, Argentina
| | | | | | | | - Lina M Nuñez
- Hospital Alemán de Buenos Aires, Buenos Aires, Argentina.
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5
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Tischkowitz M, Balmaña J, Foulkes WD, James P, Ngeow J, Schmutzler R, Voian N, Wick MJ, Stewart DR, Pal T. Management of individuals with germline variants in PALB2: a clinical practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1416-1423. [PMID: 33976419 DOI: 10.1038/s41436-021-01151-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
PURPOSE PALB2 germline pathogenic variants are associated with increased breast cancer risk and smaller increased risk of pancreatic and likely ovarian cancer. Resources for health-care professionals managing PALB2 heterozygotes are currently limited. METHODS A workgroup of experts sought to outline management of PALB2 heterozygotes based on current evidence. Peer-reviewed publications from PubMed were identified to guide recommendations, which arose by consensus and the collective expertise of the authors. RESULTS PALB2 heterozygotes should be offered BRCA1/2-equivalent breast surveillance. Risk-reducing mastectomy can be considered guided by personalized risk estimates. Pancreatic cancer surveillance should be considered, but ideally as part of a clinical trial. Typically, ovarian cancer surveillance is not recommended, and risk-reducing salpingo-oophorectomy should only rarely be considered before the age of 50. Given the mechanistic similarities, PALB2 heterozygotes should be considered for therapeutic regimens and trials as those for BRCA1/2. CONCLUSION This guidance is similar to those for BRCA1/2. While the range of the cancer risk estimates overlap with BRCA1/2, point estimates are lower in PALB2 so individualized estimates are important for management decisions. Systematic prospective data collection is needed to determine as yet unanswered questions such as the risk of contralateral breast cancer and survival after cancer diagnosis.
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Affiliation(s)
- Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO) and Medical Oncology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Hospital Campus, Barcelona, Spain
| | - William D Foulkes
- Departments of Human Genetics, Oncology and Medicine, McGill University, Montréal, QC, Canada
| | - Paul James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.,Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Joanne Ngeow
- Genomic Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Rita Schmutzler
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,University Hospital of Cologne, Center of Integrated Oncology, CIO and Center of Familial Breast and Ovarian Cancer, Cologne, Germany
| | - Nicoleta Voian
- Genetic Risk Clinic, Providence Cancer Institute, Portland, OR, USA
| | - Myra J Wick
- Departments of Obstetrics and Gynecology and Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Tuya Pal
- Department of Medicine, Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
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Genetic testing in Poland and Ukraine: should comprehensive germline testing of BRCA1 and BRCA2 be recommended for women with breast and ovarian cancer? Genet Res (Camb) 2020; 102:e6. [PMID: 32772980 PMCID: PMC7443769 DOI: 10.1017/s0016672320000075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Purpose To characterize the spectrum of BRCA1 and BRCA2 pathogenic germline variants in women from south-west Poland and west Ukraine affected with breast or ovarian cancer. Testing in women at high risk of breast and ovarian cancer in these regions is currently mainly limited to founder mutations. Methods Unrelated women affected with breast and/or ovarian cancer from Poland (n = 337) and Ukraine (n = 123) were screened by targeted sequencing. Excluded from targeted sequencing were 34 Polish women who had previously been identified as carrying a founder mutation in BRCA1. No prior testing had been conducted among the Ukrainian women. Thus, this study screened BRCA1 and BRCA2 in the germline DNA of 426 women in total. Results We identified 31 and 18 women as carriers of pathogenic/likely pathogenic (P/LP) genetic variants in BRCA1 and BRCA2, respectively. We observed five BRCA1 and eight BRCA2 P/LP variants (13/337, 3.9%) in the Polish women. Combined with the 34/337 (10.1%) founder variants identified prior to this study, the overall P/LP variant frequency in the Polish women was thus 14% (47/337). Among the Ukrainian women, 16/123 (13%) women were identified as carrying a founder mutation and 20/123 (16.3%) were found to carry non-founder P/LP variants (10 in BRCA1 and 10 in BRCA2). Conclusions These results indicate that genetic testing in women at high risk of breast and ovarian cancer in Poland and Ukraine should not be limited to founder mutations. Extended testing will enhance risk stratification and management for these women and their families.
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Vagena A, Papamentzelopoulou M, Kalfakakou D, Kollia P, Papadimitriou C, Psyrri A, Apostolou P, Fountzilas G, Konstantopoulou I, Yannoukakos D, Fostira F. PALB2 c.2257C>T truncating variant is a Greek founder and is associated with high breast cancer risk. J Hum Genet 2019; 64:767-773. [DOI: 10.1038/s10038-019-0612-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/15/2019] [Accepted: 04/19/2019] [Indexed: 12/20/2022]
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Macedo GS, Alemar B, Ashton-Prolla P. Reviewing the characteristics of BRCA and PALB2-related cancers in the precision medicine era. Genet Mol Biol 2019; 42:215-231. [PMID: 31067289 PMCID: PMC6687356 DOI: 10.1590/1678-4685-gmb-2018-0104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/24/2018] [Indexed: 12/24/2022] Open
Abstract
Germline mutations in BRCA1 and BRCA2 (BRCA) genes confer high risk of developing cancer, especially breast and ovarian tumors. Since the cloning of these tumor suppressor genes over two decades ago, a significant amount of research has been done. Most recently, monoallelic loss-of-function mutations in PALB2 have also been shown to increase the risk of breast cancer. The identification of BRCA1, BRCA2 and PALB2 as proteins involved in DNA double-strand break repair by homologous recombination and of the impact of complete loss of BRCA1 or BRCA2 within tumors have allowed the development of novel therapeutic approaches for patients with germline or somatic mutations in said genes. Despite the advances, especially in the clinical use of PARP inhibitors, key gaps remain. Now, new roles for BRCA1 and BRCA2 are emerging and old concepts, such as the classical two-hit hypothesis for tumor suppression, have been questioned, at least for some BRCA functions. Here aspects regarding cancer predisposition, cellular functions, histological and genomic findings in BRCA and PALB2-related tumors will be presented, in addition to an up-to-date review of the evolution and challenges in the development and clinical use of PARP inhibitors.
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Affiliation(s)
- Gabriel S Macedo
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Precision Medicine Program, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Barbara Alemar
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Precision Medicine Program, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
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9
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Targeted massively parallel sequencing characterises the mutation spectrum of PALB2 in breast and ovarian cancer cases from Poland and Ukraine. Fam Cancer 2019; 17:345-349. [PMID: 29052111 PMCID: PMC5999175 DOI: 10.1007/s10689-017-0050-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Loss-of-function germline mutations in the PALB2 gene are associated with an increase of breast cancer risk. The purpose of this study was to characterise the spectrum of PALB2 mutations in women affected with breast or ovarian cancer from South-West Poland and West Ukraine. We applied Hi-Plex, an amplicon-based enrichment method for targeted massively parallel sequencing, to screen the coding exons and proximal intron–exon junctions of PALB2 in germline DNA from unrelated women affected with breast cancer (n = 338) and ovarian cancer (n = 89) from Poland (n = 304) and Ukraine (n = 123). These women were at high-risk of carrying a genetic predisposition to breast and/or ovarian cancer due to a family history and/or early-onset disease. Targeted-sequencing identified two frameshift deletions: PALB2:c.509_510del; p.R170Ifs in three women affected with breast cancer and PALB2:c.172_175del;p.Q60Rfs in one woman affected with ovarian cancer. A number of other previously described missense (some predicted to be damaging by PolyPhen-2 and CADD) and synonymous mutations were also identified in this population. This study is consistent with previous reports that PALB2:c.509_510del and PALB2:c.172_175del are recurrent mutations associated with breast cancer predisposition in Polish women with a family history of the disease. Our study contributes to the accumulating evidence indicating that PALB2 should be included in genetic testing for breast cancer susceptibility in these populations to enhance risk assessment and management of women at high-risk of developing breast cancer. This data could also contribute to ongoing work that is assessing the possible association between ovarian cancer risk and PALB2 mutations for which there is currently no evidence.
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10
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Song F, Li M, Liu G, Swapna G, Daigham NS, Xia B, Montelionep GT, Bunting SF. Antiparallel Coiled-Coil Interactions Mediate the Homodimerization of the DNA Damage-Repair Protein PALB2. Biochemistry 2018; 57:6581-6591. [PMID: 30289697 PMCID: PMC6652205 DOI: 10.1021/acs.biochem.8b00789] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Deficits in DNA damage-repair pathways are the root cause of several human cancers. In mammalian cells, DNA double-strand break repair is carried out by multiple mechanisms, including homologous recombination (HR). The partner and localizer of BRCA2 (PALB2), which is an essential factor for HR, binds to the breast cancer susceptibility 1 (BRCA1) protein at DNA double-strand breaks. At the break site, PALB2 also associates with the breast cancer susceptibility 2 (BRCA2) protein to form a multiprotein complex that facilitates HR. The BRCA1-PALB2 interaction is mediated by association of predicted helical coiled-coil regions in both proteins. PALB2 can also homodimerize through the formation of a coiled coil by the self-association of helical elements at the N-terminus of the PALB2 protein, and this homodimerization has been proposed to regulate the efficiency of HR. We have produced a segment of PALB2, designated PALB2cc (PALB2 coiled coil segment) that forms α-helical structures, which assemble into stable homodimers. PALB2cc also forms heterodimers with a helical segment of BRCA1, called BRCA1cc (BRCA1 coiled coil segment). The three-dimensional structure of the homodimer formed by PALB2cc was determined by solution NMR spectroscopy. This PALB2cc homodimer is a classical antiparallel coiled-coil leucine zipper. NMR chemical-shift perturbation studies were used to study dimer formation for both the PALB2cc homodimer and the PALB2cc/BRCA1cc heterodimer. The mutation of residue Leu24 of PALB2cc significantly reduces its homodimer stability, but has a more modest effect on the stability of the heterodimer formed between PALB2cc and BRCA1cc. We show that mutation of Leu24 leads to genomic instability and reduced cell viability after treatment with agents that induce DNA double-strand breaks. These studies may allow the identification of distinct mutations of PALB2cc that selectively disrupt homodimeric versus heterodimeric interactions, and reveal the specific role of PALB2cc homodimerization in HR.
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Affiliation(s)
- Fei Song
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Minxing Li
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Gaohua Liu
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - G.V.T. Swapna
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Nourhan S. Daigham
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Gaetano T. Montelionep
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Samuel F. Bunting
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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11
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Pope BJ, Hammet F, Nguyen-Dumont T, Park DJ. Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing. Methods Mol Biol 2018; 1712:53-70. [PMID: 29224068 DOI: 10.1007/978-1-4939-7514-3_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguyen-Dumont et al., Biotechniques 58:33-36, 2015). At its core is the principle of using gene-specific primers (GSPs) to "seed" (or target) the reaction and universal primers to "drive" the majority of the reaction. In this manner, effects on amplification efficiencies across the target amplicons can, to a large extent, be restricted to early seeding cycles. Product sizes are defined within a relatively narrow range to enable high-specificity size selection, replication uniformity across target sites (including in the context of fragmented input DNA such as that derived from fixed tumor specimens (Nguyen-Dumont et al., Biotechniques 55:69-74, 2013; Nguyen-Dumont et al., Anal Biochem 470:48-51, 2015), and application of high-specificity genetic variant calling algorithms (Pope et al., Source Code Biol Med 9:3, 2014; Park et al., BMC Bioinformatics 17:165, 2016). Hi-Plex offers a streamlined workflow that is suitable for testing large numbers of specimens without the need for automation.
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Affiliation(s)
- Bernard J Pope
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Fleur Hammet
- Genomic Technologies Group, Genetic Epidemiology Laboratory, Department of Medicine, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Tu Nguyen-Dumont
- Genomic Technologies Group, Genetic Epidemiology Laboratory, Department of Medicine, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daniel J Park
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia. .,Genomic Technologies Group, Genetic Epidemiology Laboratory, Department of Medicine, The University of Melbourne, Parkville, VIC, 3010, Australia.
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12
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Abstract
An apparently balanced t(2;3)(q37.3;q13.2) translocation that appears to segregate with renal cell carcinoma (RCC) has indicated potential areas to search for the elusive genetic basis of clear cell RCC. We applied Hi-Plex targeted sequencing to analyse germline DNA from 479 individuals affected with clear cell RCC for this breakpoint translocation and genetic variants in neighbouring genes on chromosome 2, ACKR3 and COPS8. While only synonymous variants were found in COPS8, one of the missense variants in ACKR3:c.892C>T, observed in 4/479 individuals screened (0.8%), was predicted likely to damage ACKR3 function. Identification of causal genes for RCC has potential clinical utility, where risk assessment and risk management can offer better outcomes, with surveillance for at-risk relatives and nephron sparing surgery through earlier intervention.
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13
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Nguyen-Dumont T, Myszka A, Karpinski P, Sasiadek MM, Akopyan H, Hammet F, Tsimiklis H, Park DJ, Pope BJ, Slezak R, Kitsera N, Siekierzynska A, Southey MC. FANCM and RECQL genetic variants and breast cancer susceptibility: relevance to South Poland and West Ukraine. BMC MEDICAL GENETICS 2018; 19:12. [PMID: 29351780 PMCID: PMC5775547 DOI: 10.1186/s12881-018-0524-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 01/09/2018] [Indexed: 12/17/2022]
Abstract
Background FANCM and RECQL have recently been reported as breast cancer susceptibility genes and it has been suggested that they should be included on gene panel tests for breast cancer predisposition. However, the clinical value of testing for mutations in RECQL and FANCM remains to be determined. In this study, we have characterised the spectrum of FANCM and RECQL mutations in women affected with breast or ovarian cancer from South-West Poland and West Ukraine. Methods We applied Hi-Plex, an amplicon-based enrichment method for targeted massively parallel sequencing, to screen the coding exons and proximal intron-exon junctions of FANCM and RECQL in germline DNA from unrelated women affected with breast cancer (n = 338) and ovarian cancer (n = 89) from Poland (n = 304) and Ukraine (n = 123). These women were at high-risk of carrying a genetic predisposition to breast and/or ovarian cancer due to a family history and/or early-onset disease. Results Among 427 women screened, we identified one carrier of the FANCM:c.1972C > T nonsense mutation (0.23%), and two carriers of the frameshift insertion FANCM:c.1491dup (0.47%). None of the variants we observed in RECQL were predicted to be loss-of-function mutations by standard variant effect prediction tools. Conclusions Our study of the Polish and Ukrainian populations has identified a carrier frequency of truncating mutations in FANCM consistent with previous reports. Although initial reports suggesting that mutations in RECQL could be associated with increased breast cancer risk included women from Poland and identified the RECQL:c.1667_1667 + 3delAGTA mutation in 0.23–0.35% of breast cancer cases, we did not observe any carriers in our study cohort. Continued screening, both in research and diagnostic settings, will enable the accumulation of data that is needed to establish the clinical utility of including RECQL and FANCM on gene panel tests. Electronic supplementary material The online version of this article (10.1186/s12881-018-0524-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tú Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Aleksander Myszka
- Institute of Obstetrics and Emergency Medicine, University of Rzeszow, Rzeszow, Poland
| | - Pawel Karpinski
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Maria M Sasiadek
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Hayane Akopyan
- Institute of Obstetrics and Emergency Medicine, University of Rzeszow, Rzeszow, Poland.,Institute of Hereditary Pathology of National Academy of Medical Sciences, Lviv, Ukraine
| | - Fleur Hammet
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Helen Tsimiklis
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Daniel J Park
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia.,Melbourne Bioinformatics, The University of Melbourne, Carlton, Victoria, Australia
| | - Bernard J Pope
- Melbourne Bioinformatics, The University of Melbourne, Carlton, Victoria, Australia
| | - Ryszard Slezak
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Nataliya Kitsera
- Institute of Hereditary Pathology of National Academy of Medical Sciences, Lviv, Ukraine
| | | | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia.
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14
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Germline mutations of PALB2 gene in a sequential series of Chinese patients with breast cancer. Breast Cancer Res Treat 2017; 166:865-873. [PMID: 28825143 DOI: 10.1007/s10549-017-4425-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/25/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND PALB2 (Partner and Localizer of BRCA2) is recently recognized as a breast cancer predisposition gene. Germline loss-of-function mutations in PALB2 lead to increased breast cancer risk. Since the germline mutation frequency of PALB2 is much less than BRCA1/2, the distinct mutation spectrum of PALB2 is still obscure. To verify the utility of PALB2 genetic testing in Chinese population, we assessed the mutational frequency, spectrum, and predictors of the PALB2 gene in a sequential series of Chinese breast cancer patients from our Research DNA Bank. METHODS We examined breast cancer samples (n = 2279) collected from 2000 through 2016 from Chinese patients who agreed to participate in research DNA banking. To identify the mutations, complete coding sequence and intron-exon boundaries of PALB2 were screened with Next-Generation Sequencing. Personal and family histories were synchronously collected for mutation identification. RESULTS Among the 2279 breast cancer patients, 305 patients were familial breast cancer cases and the rest 1967 patients were sporadic breast cancer cases. PALB2 loss-of-function mutation carriers accounted for 1.31% (n = 4) and 0.56% (n = 11) in familial and sporadic breast cancer cohort separately. In total, 30 missenses, four nonsenses, three frameshifts, three splicings, and one inframe deletions of PALB2 were identified in this study. Among the deleterious mutations, PALB2 c.1744C>T, c.2748+1G>A, c.2749-1G>C, c.3114-1G>A were newly identified in sporadic breast cancer, and c.3271delC newly found in familial breast cancer. Based on in silico analysis, we found two potentially damaging missense variants with high frequency: c.1213C>G, c.3054G>C, and classified six new potentially damaging missense variants. CONCLUSIONS Our data presented the germline mutation status of PALB2 in Chinese breast cancer patients, suggesting that loss-of-function germline mutations of PALB2 are important in both familial and sporadic breast cancer. Clinically, these data may be helpful in genetic counseling of breast cancer patients with PALB2 germline mutation.
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15
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Foo TK, Tischkowitz M, Simhadri S, Boshari T, Zayed N, Burke KA, Berman SH, Blecua P, Riaz N, Huo Y, Ding YC, Neuhausen SL, Weigelt B, Reis-Filho JS, Foulkes WD, Xia B. Compromised BRCA1-PALB2 interaction is associated with breast cancer risk. Oncogene 2017; 36:4161-4170. [PMID: 28319063 PMCID: PMC5519427 DOI: 10.1038/onc.2017.46] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 01/30/2017] [Accepted: 01/31/2017] [Indexed: 12/14/2022]
Abstract
The major breast cancer suppressor proteins BRCA1 and BRCA2 play essential roles in homologous recombination (HR)-mediated DNA repair, which is thought to be critical for tumor suppression. The two BRCA proteins are linked by a third tumor suppressor, PALB2, in the HR pathway. While truncating mutations in these genes are generally pathogenic, interpretations of missense variants remains a challenge. To date, patient-derived missense variants that disrupt PALB2 binding have been identified in BRCA1 and BRCA2; however, there has not been sufficient evidence to prove their pathogenicity in humans, and no variants in PALB2 that disrupt either its BRCA1 or BRCA2 binding have been reported. Here, we report on the identification of a novel PALB2 variant, c.104T>C [p.L35P], that segregated in a family with a strong history of breast cancer. Functional analyses showed that L35P abrogates the PALB2-BRCA1 interaction and completely disables its abilities to promote HR and confer resistance to platinum salts and PARP inhibitors. Whole-exome sequencing of a breast cancer from a c.104T>C carrier revealed a second, somatic, truncating mutation affecting PALB2, and the tumor displays hallmark genomic features of tumors with BRCA mutations and HR defects, cementing the pathogenicity of L35P. Parallel analyses of other germline variants in the PALB2 N-terminal BRCA1-binding domain identified multiple variants that affect HR function to varying degrees, suggesting their possible contribution to cancer development. Our findings establish L35P as the first pathogenic missense mutation in PALB2 and directly demonstrate the requirement of the PALB2-BRCA1 interaction for breast cancer suppression.
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Affiliation(s)
- T K Foo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - M Tischkowitz
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - S Simhadri
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - T Boshari
- Department of Medical Genetics and Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - N Zayed
- Department of Medical Genetics and Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - K A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S H Berman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - P Blecua
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Y Huo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Y C Ding
- Department of Population Sciences, Beckman Research Institute at the City of Hope, Duarte, CA, USA
| | - S L Neuhausen
- Department of Population Sciences, Beckman Research Institute at the City of Hope, Duarte, CA, USA
| | - B Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - W D Foulkes
- Department of Medical Genetics and Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - B Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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16
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Silvestri V, Zelli V, Valentini V, Rizzolo P, Navazio AS, Coppa A, Agata S, Oliani C, Barana D, Castrignanò T, Viel A, Russo A, Tibiletti MG, Zanna I, Masala G, Cortesi L, Manoukian S, Azzollini J, Peissel B, Bonanni B, Peterlongo P, Radice P, Palli D, Giannini G, Chillemi G, Montagna M, Ottini L. Whole-exome sequencing and targeted gene sequencing provide insights into the role of PALB2 as a male breast cancer susceptibility gene. Cancer 2016; 123:210-218. [PMID: 27648926 DOI: 10.1002/cncr.30337] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Male breast cancer (MBC) is a rare disease whose etiology appears to be largely associated with genetic factors. BRCA1 and BRCA2 mutations account for about 10% of all MBC cases. Thus, a fraction of MBC cases are expected to be due to genetic factors not yet identified. To further explain the genetic susceptibility for MBC, whole-exome sequencing (WES) and targeted gene sequencing were applied to high-risk, BRCA1/2 mutation-negative MBC cases. METHODS Germ-line DNA of 1 male and 2 female BRCA1/2 mutation-negative breast cancer (BC) cases from a pedigree showing a first-degree family history of MBC was analyzed with WES. Targeted gene sequencing for the validation of WES results was performed for 48 high-risk, BRCA1/2 mutation-negative MBC cases from an Italian multicenter study of MBC. A case-control series of 433 BRCA1/2 mutation-negative MBC and female breast cancer (FBC) cases and 849 male and female controls was included in the study. RESULTS WES in the family identified the partner and localizer of BRCA2 (PALB2) c.419delA truncating mutation carried by the proband, her father, and her paternal uncle (all affected with BC) and the N-acetyltransferase 1 (NAT1) c.97C>T nonsense mutation carried by the proband's maternal aunt. Targeted PALB2 sequencing detected the c.1984A>T nonsense mutation in 1 of the 48 BRCA1/2 mutation-negative MBC cases. NAT1 c.97C>T was not found in the case-control series. CONCLUSIONS These results add strength to the evidence showing that PALB2 is involved in BC risk for both sexes and indicate that consideration should be given to clinical testing of PALB2 for BRCA1/2 mutation-negative families with multiple MBC and FBC cases. Cancer 2017;123:210-218. © 2016 American Cancer Society.
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Affiliation(s)
| | - Veronica Zelli
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Virginia Valentini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Piera Rizzolo
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Anna Sara Navazio
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Anna Coppa
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Simona Agata
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV, Padua, Italy
| | - Cristina Oliani
- Oncology Unit, Local Health and Social Care Unit ULSS5 Ovest Vicentino, Montecchio Maggiore, Italy
| | - Daniela Barana
- Oncology Unit, Local Health and Social Care Unit ULSS5 Ovest Vicentino, Montecchio Maggiore, Italy
| | - Tiziana Castrignanò
- Supercomputing Applications and Innovation Department, Interuniversity Consortium for Super Computing CINECA, Rome, Italy
| | - Alessandra Viel
- Unit of Functional Onco-Genomics and Genetics, Aviano Oncology Reference Center CRO, National Cancer Institute, Aviano, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical and Oncological Sciences, University of Palermo, Palermo, Italy
| | | | - Ines Zanna
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute ISPO, Florence, Italy
| | - Giovanna Masala
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute ISPO, Florence, Italy
| | - Laura Cortesi
- Department of Oncology and Haematology, University of Modena and Reggio Emilia, Modena, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, National Cancer Institute INT, Milan, Italy
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, National Cancer Institute INT, Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, National Cancer Institute INT, Milan, Italy
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, European Institute of Oncology IEO, Milan, Italy
| | - Paolo Peterlongo
- Italian Foundation for Cancer Research (FIRC) Institute of Molecular Oncology INT, Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, National Cancer Institute INT, Milan, Italy
| | - Domenico Palli
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute ISPO, Florence, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Giovanni Chillemi
- Supercomputing Applications and Innovation Department, Interuniversity Consortium for Super Computing CINECA, Rome, Italy
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV, Padua, Italy
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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17
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Association of PALB2 sequence variants with the risk of early-onset breast cancer in patients from Turkey. Mol Biol Rep 2016; 43:1273-1284. [DOI: 10.1007/s11033-016-4061-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/16/2016] [Indexed: 02/05/2023]
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18
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Park DJ, Li R, Lau E, Georgeson P, Nguyen-Dumont T, Pope BJ. UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing. BMC Bioinformatics 2016; 17:165. [PMID: 27083325 PMCID: PMC4833922 DOI: 10.1186/s12859-016-1014-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 04/06/2016] [Indexed: 11/24/2022] Open
Abstract
Background Previously, we described ROVER, a DNA variant caller which identifies genetic variants from PCR-targeted massively parallel sequencing (MPS) datasets generated by the Hi-Plex protocol. ROVER permits stringent filtering of sequencing chemistry-induced errors by requiring reported variants to appear in both reads of overlapping pairs above certain thresholds of occurrence. ROVER was developed in tandem with Hi-Plex and has been used successfully to screen for genetic mutations in the breast cancer predisposition gene PALB2. ROVER is applied to MPS data in BAM format and, therefore, relies on sequence reads being mapped to a reference genome. In this paper, we describe an improvement to ROVER, called UNDR ROVER (Unmapped primer-Directed ROVER), which accepts MPS data in FASTQ format, avoiding the need for a computationally expensive mapping stage. It does so by taking advantage of the location-specific nature of PCR-targeted MPS data. Results The UNDR ROVER algorithm achieves the same stringent variant calling as its predecessor with a significant runtime performance improvement. In one indicative sequencing experiment, UNDR ROVER (in its fastest mode) required 8-fold less sequential computation time than the ROVER pipeline and 13-fold less sequential computation time than a variant calling pipeline based on the popular GATK tool. UNDR ROVER is implemented in Python and runs on all popular POSIX-like operating systems (Linux, OS X). It requires as input a tab-delimited format file containing primer sequence information, a FASTA format file containing the reference genome sequence, and paired FASTQ files containing sequence reads. Primer sequences at the 5′ end of reads associate read-pairs with their targeted amplicon and, thus, their expected corresponding coordinates in the reference genome. The primer-intervening sequence of each read is compared against the reference sequence from the same location and variants are identified using the same algorithm as ROVER. Specifically, for a variant to be ‘called’ it must appear at the same location in both of the overlapping reads above user-defined thresholds of minimum number of reads and proportion of reads. Conclusions UNDR ROVER provides the same rapid and accurate genetic variant calling as its predecessor with greatly reduced computational costs.
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Affiliation(s)
- Daniel J Park
- Genetic Epidemiology Laboratory, School of Biomedical Sciences, Medical Building, The University of Melbourne, Melbourne, Victoria, 3010, Australia.,Victorian Life Sciences Computation Initiative, The University of Melbourne, Melbourne, Victoria, 3053, Australia
| | - Roger Li
- Department of Computing and Information Systems, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Edmund Lau
- Victorian Life Sciences Computation Initiative, The University of Melbourne, Melbourne, Victoria, 3053, Australia
| | - Peter Georgeson
- Victorian Life Sciences Computation Initiative, The University of Melbourne, Melbourne, Victoria, 3053, Australia
| | - Tú Nguyen-Dumont
- Genetic Epidemiology Laboratory, School of Biomedical Sciences, Medical Building, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Bernard J Pope
- Department of Computing and Information Systems, The University of Melbourne, Melbourne, Victoria, 3010, Australia. .,Victorian Life Sciences Computation Initiative, The University of Melbourne, Melbourne, Victoria, 3053, Australia.
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19
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Mutation analysis of PALB2 gene in French breast cancer families. Breast Cancer Res Treat 2015; 154:463-71. [DOI: 10.1007/s10549-015-3625-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/26/2015] [Indexed: 11/25/2022]
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20
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Thompson ER, Gorringe KL, Rowley SM, Wong-Brown MW, McInerny S, Li N, Trainer AH, Devereux L, Doyle MA, Li J, Lupat R, Delatycki MB, Mitchell G, James PA, Scott RJ, Campbell IG. Prevalence of PALB2 mutations in Australian familial breast cancer cases and controls. Breast Cancer Res 2015; 17:111. [PMID: 26283626 PMCID: PMC4539664 DOI: 10.1186/s13058-015-0627-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/04/2015] [Indexed: 12/30/2022] Open
Abstract
Introduction PALB2 is emerging as a high-penetrance breast cancer predisposition gene in the order of BRCA1 and BRCA2. However, large studies that have evaluated the full gene rather than just the most common variants in both cases and controls are required before all truncating variants can be included in familial breast cancer variant testing. Methods In this study we analyse almost 2000 breast cancer cases sourced from individuals referred to familial cancer clinics, thus representing typical cases presenting in clinical practice. These cases were compared to a similar number of population-based cancer-free controls. Results We identified a significant excess of truncating variants in cases (1.3 %) versus controls (0.2 %), including six novel variants (p = 0.0001; odds ratio (OR) 6.58, 95 % confidence interval (CI) 2.3–18.9). Three of the four control individuals carrying truncating variants had at least one relative with breast cancer. There was no excess of missense variants in cases overall, but the common c.1676A > G variant (rs152451) was significantly enriched in cases and may represent a low-penetrance polymorphism (p = 0.002; OR 1.24 (95 % CI 1.09–1.47). Conclusions Our findings support truncating variants in PALB2 as high-penetrance breast cancer susceptibility alleles, and suggest that a common missense variant may also lead to a low level of increased breast cancer risk.
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Affiliation(s)
- Ella R Thompson
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, East Melbourne, VIC, 8006, Australia. .,The Sir Peter MacCallum Department of Oncology, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Kylie L Gorringe
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, East Melbourne, VIC, 8006, Australia. .,The Sir Peter MacCallum Department of Oncology, St Andrews Place, East Melbourne, VIC, 3002, Australia. .,Department of Pathology, University of Melbourne, Corner GrattonStree and Royal Parade, Melbourne, VIC, 3010, Australia.
| | - Simone M Rowley
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, East Melbourne, VIC, 8006, Australia.
| | - Michelle W Wong-Brown
- Discipline of Medical Genetics and Centre for Information-Based Medicine, The University of Newcastle and Hunter Medical Research Institute, 1 Kookaburra Circuit, Newcastle, NSW, 2305, Australia.
| | - Simone McInerny
- Familial Cancer Centre, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Na Li
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, East Melbourne, VIC, 8006, Australia. .,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, Hubei, China.
| | - Alison H Trainer
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, East Melbourne, VIC, 8006, Australia. .,Familial Cancer Centre, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Lisa Devereux
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, East Melbourne, VIC, 8006, Australia. .,LifePool, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Maria A Doyle
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Jason Li
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Richard Lupat
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | | | | | - Gillian Mitchell
- The Sir Peter MacCallum Department of Oncology, St Andrews Place, East Melbourne, VIC, 3002, Australia. .,Familial Cancer Centre, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia. .,Hereditary Cancer Program, BC Cancer Agency, 600 West 10th Avenue, Vancouver, BC, V5Z 4E6, Canada.
| | - Paul A James
- The Sir Peter MacCallum Department of Oncology, St Andrews Place, East Melbourne, VIC, 3002, Australia. .,Department of Pathology, University of Melbourne, Corner GrattonStree and Royal Parade, Melbourne, VIC, 3010, Australia. .,Familial Cancer Centre, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Rodney J Scott
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, Hubei, China. .,Division of Genetics, Hunter Area Pathology Service, Lookout Road, Newcastle, NSW, 2305, Australia.
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, East Melbourne, VIC, 8006, Australia. .,The Sir Peter MacCallum Department of Oncology, St Andrews Place, East Melbourne, VIC, 3002, Australia. .,Department of Pathology, University of Melbourne, Corner GrattonStree and Royal Parade, Melbourne, VIC, 3010, Australia.
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Interpretation of genomic variation and disease association: the great missense mutation challenge! Breast Cancer Res Treat 2015; 151:475-6. [PMID: 25900795 DOI: 10.1007/s10549-015-3394-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 04/16/2015] [Indexed: 10/23/2022]
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Two PALB2 germline mutations found in both BRCA1+ and BRCAx familial breast cancer. Breast Cancer Res Treat 2015; 151:219-24. [PMID: 25833210 DOI: 10.1007/s10549-015-3358-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
Abstract
Partner and localizer of BRCA2 (PALB2), plays an important functional role in DNA damage repair. Recent studies indicate that germline mutations in PALB2 predispose individuals to a high risk of developing familial breast cancer. Therefore, comprehensive identification of PALB2 germline mutations is potentially important for understanding their roles in tumorigenesis and for testing their potential utility as clinical targets. Most of the previous studies of PALB2 have focused on familial breast cancer cases with normal/wild-type BRCA1 and BRCA2 (BRCAx). We hypothesize that PALB2 genetic mutations also exist in individuals with BRCA mutations (BRCA+). To test this hypothesis, PALB2 germline mutations were screened in 107 exome data sets collected from familial breast cancer families who were either BRCA1+ or BRCAx. Two novel heterozygous mutations predicted to alter the function of PALB2 were identified (c.2014G>C, p.E672Q and c.2993G>A, p.G998E). Notably, both of these mutations co-existed in BRCA1+ and BRCA1x families. These studies show that mutations in PALB2 can occur independent of the status of BRCA1 mutations, and they highlight the importance to include BRCA1+ families in PALB2 mutation screens.
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Prevalence of PALB2 mutations in the Creighton University Breast Cancer Family Registry. Breast Cancer Res Treat 2015; 150:637-41. [DOI: 10.1007/s10549-015-3347-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 03/12/2015] [Indexed: 10/23/2022]
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