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Rowlands CF, Allen S, Balmaña J, Domchek SM, Evans DG, Hanson H, Hoogerbrugge N, James PA, Nathanson KL, Robson M, Tischkowitz M, Foulkes WD, Turnbull C. Population-based germline breast cancer gene association studies and meta-analysis to inform wider mainstream testing. Ann Oncol 2024:S0923-7534(24)01014-7. [PMID: 38986768 DOI: 10.1016/j.annonc.2024.07.244] [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: 04/24/2024] [Revised: 06/20/2024] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Germline genetic testing, previously restricted to familial and young-onset breast cancer, is now offered increasingly broadly to patients with 'population-type' breast cancer in mainstream oncology clinics, with wide variation in the genes included. PATIENTS AND METHODS Weighted meta-analysis was carried out for three population-based case-control studies (BRIDGES, CARRIERS and UK Biobank) comprising in total 101 397 women with breast cancer and 312 944 women without breast cancer, to quantify 37 putative breast cancer susceptibility genes (BCSGs) for the frequency of pathogenic variants (PVs) in unselected, 'population-type' breast cancer cases and their association with breast cancer and its subtypes. RESULTS Meta-analysed odds ratios (ORs) and frequencies of PVs in 'population-type' breast cancer cases were generated for BRCA1 (OR 8.73, 95% confidence interval (CI) 7.47-10.20; 1 in 101), BRCA2 (OR 5.68, 95% CI 5.13-6.30; 1 in 68) and PALB2 (OR 4.30, 95% CI 3.68-5.03; 1 in 187). For both CHEK2 (OR 2.40, 95% CI 2.21-2.62; 1 in 73) and ATM (OR 2.16, 95% CI 1.93-2.41; 1 in 132) subgroup analysis showed a stronger association with oestrogen receptor-positive disease. The magnitude of association and frequency of PVs were low for RAD51C (OR 1.53, 95% CI 1.29-2.04; 1 in 913), RAD51D (OR 1.76, 95% CI 1.29-2.41; 1 in 1079) and BARD1 (OR 2.34, 95% CI 1.85-2.97; 1 in 672); frequencies and associations were higher when the analysis was restricted to triple-negative breast cancers. The PV frequency in 'population-type' breast cancer cases was very low for 'syndromic' BCSGs TP53 (1 in 1844), STK11 (1 in 11 525), CDH1 (1 in 2668), PTEN (1 in 3755) and NF1 (1 in 1470), with metrics of association also modest ranging from OR 3.62 (95% CI 1.98-6.61) for TP53 down to OR 1.60 (95% CI 0.48-5.30) for STK11. CONCLUSIONS These metrics reflecting 'population-type' breast cancer will be informative in defining the appropriate gene set as we continue to expand to germline testing to an increasingly unselected group of breast cancer cases.
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Affiliation(s)
- C F Rowlands
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - S Allen
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - J Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona; Medical Oncology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Hospital Campus, Barcelona, Spain
| | - S M Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, USA
| | - D G Evans
- Manchester Academic Health Science Centre, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester
| | - H Hanson
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Exeter; Peninsula Regional Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - N Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - P A James
- Parkville Familial Cancer Centre, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Melbourne, Australia
| | - K L Nathanson
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia; Abramson Cancer Center, Perelman School of Medicine, Philadelphia
| | - M Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York; Weill Cornell Medical College, New York, USA
| | - M Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - W D Foulkes
- Department of Human Genetics, McGill University, Montréal, Canada; Department of Oncology, McGill University, Montréal, Canada; Department of Medicine, McGill University, Montréal, Canada
| | - C Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
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Stastna B, Dolezalova T, Matejkova K, Nemcova B, Zemankova P, Janatova M, Kleiblova P, Soukupova J, Kleibl Z. Germline pathogenic variants in the MRE11, RAD50, and NBN (MRN) genes in cancer predisposition: A systematic review and meta-analysis. Int J Cancer 2024. [PMID: 38924040 DOI: 10.1002/ijc.35066] [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: 02/28/2024] [Revised: 05/22/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
The MRE11, RAD50, and NBN genes encode the MRN complex sensing DNA breaks and directing their repair. While carriers of biallelic germline pathogenic variants (gPV) develop rare chromosomal instability syndromes, the cancer risk in heterozygotes remains controversial. We performed a systematic review and meta-analysis of 53 studies in patients with different cancer diagnoses to better understand the cancer risk. We found an increased risk (odds ratio, 95% confidence interval) for gPV carriers in NBN for melanoma (7.14; 3.30-15.43), pancreatic cancer (4.03; 2.14-7.58), hematological tumors (3.42; 1.14-10.22), and prostate cancer (2.44, 1.84-3.24), but a low risk for breast cancer (1.29; 1.00-1.66) and an insignificant risk for ovarian cancer (1.53; 0.76-3.09). We found no increased breast cancer risk in carriers of gPV in RAD50 (0.93; 0.74-1.16; except of c.687del carriers) and MRE11 (0.87; 0.66-1.13). The secondary burden analysis compared the frequencies of gPV in MRN genes in patients from 150 studies with those in the gnomAD database. In NBN gPV carriers, this analysis additionally showed a high risk for brain tumors (5.06; 2.39-9.52), a low risk for colorectal (1.64; 1.26-2.10) and hepatobiliary (2.16; 1.02-4.06) cancers, and no risk for endometrial, and gastric cancer. The secondary burden analysis showed also a moderate risk for ovarian cancer (3.00; 1.27-6.08) in MRE11 gPV carriers, and no risk for ovarian and hepatobiliary cancers in RAD50 gPV carriers. These findings provide a robust clinical evidence of cancer risks to guide personalized clinical management in heterozygous carriers of gPV in the MRE11, RAD50, and NBN genes.
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Affiliation(s)
- Barbora Stastna
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tatana Dolezalova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Katerina Matejkova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Barbora Nemcova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Petra Zemankova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marketa Janatova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Jana Soukupova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
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Agaoglu NB, Unal B, Hayes CP, Walker M, Ng OH, Doganay L, Can ND, Rana HQ, Ghazani AA. Genomic disparity impacts variant classification of cancer susceptibility genes in Turkish breast cancer patients. Cancer Med 2024; 13:e6852. [PMID: 38308423 PMCID: PMC10905328 DOI: 10.1002/cam4.6852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 11/23/2023] [Accepted: 12/10/2023] [Indexed: 02/04/2024] Open
Abstract
OBJECTIVE Turkish genome is underrepresented in large genomic databases. This study aims to evaluate the effect of allele frequency in the Turkish population in determining the clinical utility of germline findings in breast cancer, including invasive lobular carcinoma (ILC), mixed invasive ductal and lobular carcinoma (IDC-L), and ductal carcinoma (DC). METHODS Two clinic-based cohorts from the Umraniye Research and Training Hospital (URTH) were used in this study: a cohort consisting of 132 women with breast cancer and a non-cancer cohort consisting of 492 participants. The evaluation of the germline landscape was performed by analysis of 27 cancer genes. The frequency and type of variants in the breast cancer cohort were compared to those in the non-cancer cohort to investigate the effect of population genetics. The variant allele frequencies in Turkish Variome and gnomAD were statistically evaluated. RESULTS The genetic analysis identified 121 variants in the breast cancer cohort (actionable = 32, VUS = 89) and 223 variants in the non-cancer cohort (actionable = 25, VUS = 188). The occurrence of 21 variants in both suggested a possible genetic population effect. Evaluation of allele frequency of 121 variants from the breast cancer cohort showed 22% had a significantly higher value in Turkish Variome compared to gnomAD (p < 0.0001, 95% CI) with a mean difference of 60 times (ranging from 1.37-354.4). After adjusting for variant allele frequency using the ancestry-appropriate database, 6.7% (5/75) of VUS was reclassified to likely benign. CONCLUSION To our knowledge, this is the first study of population genetic effects in breast cancer subtypes in Turkish women. Our findings underscore the need for a large genomic database representing Turkish population-specific variants. It further highlights the significance of the ancestry-appropriate population database for accurate variant assessment in clinical settings.
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Affiliation(s)
- Nihat B. Agaoglu
- Department of Medical Genetics, Division of Cancer GeneticsUmraniye Training and Research HospitalIstanbulTurkey
| | - Busra Unal
- Department of Medical Genetics, Division of Cancer GeneticsUmraniye Training and Research HospitalIstanbulTurkey
- Division of GeneticsBrigham and Women's HospitalBostonMassachusettsUSA
| | - Connor P. Hayes
- Division of GeneticsBrigham and Women's HospitalBostonMassachusettsUSA
| | - McKenzie Walker
- Division of GeneticsBrigham and Women's HospitalBostonMassachusettsUSA
| | - Ozden Hatirnaz Ng
- Department of Medical Biology, School of MedicineAcibadem UniversityIstanbulTurkey
| | - Levent Doganay
- Department of Medical Genetics, Division of Cancer GeneticsUmraniye Training and Research HospitalIstanbulTurkey
| | - Nisan D. Can
- Department of Molecular Biology Genetics and BiotechnologyIstanbul Technical UniversityIstanbulTurkey
| | - Huma Q. Rana
- Division of Cancer Genetics and PreventionDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of MedicineBrigham and Women's HospitalBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Arezou A. Ghazani
- Division of GeneticsBrigham and Women's HospitalBostonMassachusettsUSA
- Department of MedicineBrigham and Women's HospitalBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
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