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Lee NY, Hum M, Amali AA, Lim WK, Wong M, Myint MK, Tay RJ, Ong PY, Samol J, Lim CW, Ang P, Tan MH, Lee SC, Lee ASG. Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility. Hum Genomics 2022; 16:61. [PMID: 36424660 PMCID: PMC9685974 DOI: 10.1186/s40246-022-00435-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/14/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND For the majority of individuals with early-onset or familial breast cancer referred for genetic testing, the genetic basis of their familial breast cancer remains unexplained. To identify novel germline variants associated with breast cancer predisposition, whole-exome sequencing (WES) was performed. METHODS WES on 290 BRCA1/BRCA2-negative Singaporeans with early-onset breast cancer and/or a family history of breast cancer was done. Case-control analysis against the East-Asian subpopulation (EAS) from the Genome Aggregation Database (gnomAD) identified variants enriched in cases, which were further selected by occurrence in cancer gene databases. Variants were further evaluated in repeated case-control analyses using a second case cohort from the database of Genotypes and Phenotypes (dbGaP) comprising 466 early-onset breast cancer patients from the United States, and a Singapore SG10K_Health control cohort. RESULTS Forty-nine breast cancer-associated germline pathogenic variants in 37 genes were identified in Singapore cases versus gnomAD (EAS). Compared against SG10K_Health controls, 13 of 49 variants remain significantly enriched (False Discovery Rate (FDR)-adjusted p < 0.05). Comparing these 49 variants in dbGaP cases against gnomAD (EAS) and SG10K_Health controls revealed 23 concordant variants that were significantly enriched (FDR-adjusted p < 0.05). Fourteen variants were consistently enriched in breast cancer cases across all comparisons (FDR-adjusted p < 0.05). Seven variants in GPRIN2, NRG1, MYO5A, CLIP1, CUX1, GNAS and MGA were confirmed by Sanger sequencing. CONCLUSIONS In conclusion, we have identified pathogenic variants in genes associated with breast cancer predisposition. Importantly, many of these variants were significant in a second case cohort from dbGaP, suggesting that the strategy of using case-control analysis to select variants could potentially be utilized for identifying variants associated with cancer susceptibility.
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Affiliation(s)
- Ning Yuan Lee
- grid.410724.40000 0004 0620 9745Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
| | - Melissa Hum
- grid.410724.40000 0004 0620 9745Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
| | - Aseervatham Anusha Amali
- grid.410724.40000 0004 0620 9745Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
| | - Wei Kiat Lim
- grid.410724.40000 0004 0620 9745Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
| | - Matthew Wong
- grid.410724.40000 0004 0620 9745Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
| | - Matthew Khine Myint
- grid.410724.40000 0004 0620 9745Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
| | - Ru Jin Tay
- Lucence Diagnostics Pte Ltd, 211 Henderson Road, Singapore, 159552 Singapore
| | - Pei-Yi Ong
- grid.440782.d0000 0004 0507 018XDepartment of Hematology-Oncology, National University Cancer Institute, Singapore (NCIS), National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074 Singapore
| | - Jens Samol
- grid.240988.f0000 0001 0298 8161Medical Oncology Department, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433 Singapore ,grid.21107.350000 0001 2171 9311Johns Hopkins University, Baltimore, MD 21218 USA
| | - Chia Wei Lim
- grid.240988.f0000 0001 0298 8161Department of Personalised Medicine, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433 Singapore
| | - Peter Ang
- grid.415572.00000 0004 0620 9577Oncocare Cancer Centre, Gleneagles Medical Centre, 6 Napier Road, Singapore, 258499 Singapore
| | - Min-Han Tan
- Lucence Diagnostics Pte Ltd, 211 Henderson Road, Singapore, 159552 Singapore
| | - Soo-Chin Lee
- grid.440782.d0000 0004 0507 018XDepartment of Hematology-Oncology, National University Cancer Institute, Singapore (NCIS), National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074 Singapore ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Dr, Singapore, 117597 Singapore ,grid.4280.e0000 0001 2180 6431Cancer Science Institute, Singapore (CSI), National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
| | - Ann S. G. Lee
- grid.410724.40000 0004 0620 9745Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore ,grid.4280.e0000 0001 2180 6431Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117593 Singapore ,grid.428397.30000 0004 0385 0924SingHealth Duke-NUS Oncology Academic Clinical Programme (ONCO ACP), Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857 Singapore
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