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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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Lerner-Ellis J, Sopik V, Wong A, Lázaro C, Narod SA, Charames GS. Retesting of women who are negative for a BRCA1 and BRCA2 mutation using a 20-gene panel. J Med Genet 2019; 57:380-384. [PMID: 31784482 DOI: 10.1136/jmedgenet-2019-106403] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/24/2019] [Accepted: 10/04/2019] [Indexed: 11/04/2022]
Abstract
BACKGROUND The value of retesting women who previously tested negative for a pathogenic variant (mutation) in BRCA1 and BRCA2 using an expanded panel of breast and ovarian cancer genes is unclear. METHODS We studied 110 BRCA1/2-negative women who were retested using a panel of 20 breast and/or ovarian cancer susceptibility genes at the Advanced Molecular Diagnostics Laboratory (AMDL) at Mount Sinai Hospital in Toronto between March 2017 and March 2019. All patients had previously tested negative for BRCA pathogenic variants at the AMDL between January 2012 and March 2018 and were subsequently referred for retesting by their physician. RESULTS Overall, six pathogenic variants in genes other than BRCA1 and BRCA2 were found (prevalence 5.5%). There were two pathogenic variants found in RAD51C, and one found in each of BRIP1, PALB2, PMS2 and PTEN. The prevalence of pathogenic variants was 6.5% for women affected with cancer (6 of 93), including 4.9% for women with breast cancer (4 of 82) and 22.2% for women with ovarian cancer (2 of 9). None of the 17 unaffected women had a clinically significant or pathogenic variant. There were 44 women (40%) for whom the result of the panel test was inconclusive due to the detection of a variant of uncertain significance. CONCLUSIONS Our findings indicate that the retesting of BRCA1/2-negative individuals with an expanded panel of 20 breast and ovarian cancer genes can produce clinically relevant results, with a yield of 5.5% for pathogenic variants in genes other than BRCA1 and BRCA2.
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Affiliation(s)
- Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada .,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Victoria Sopik
- Women's College Research Institute, Women's College Hospital, Toronto, Ontario, Canada
| | - Andrew Wong
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Conxi Lázaro
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Women's College Research Institute, Women's College Hospital, Toronto, Ontario, Canada.,Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hospital Duran i Reynals, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet, Barcelona, Spain
| | - Steven A Narod
- Women's College Research Institute, Women's College Hospital, Toronto, Ontario, Canada
| | - George S Charames
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
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Flores KG, Steffen LE, McLouth CJ, Vicuña BE, Gammon A, Kohlmann W, Vigil L, Dayao ZR, Royce ME, Kinney AY. Factors Associated with Interest in Gene-Panel Testing and Risk Communication Preferences in Women from BRCA1/2 Negative Families. J Genet Couns 2016; 26:480-490. [PMID: 27496122 DOI: 10.1007/s10897-016-0001-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 07/18/2016] [Indexed: 12/12/2022]
Abstract
Scientific advances have allowed the development of multiplex gene-panels to assess many genes simultaneously in women who have tested negative for BRCA1/2. We examined correlates of interest in testing for genes that confer modest and moderate breast cancer risk and risk communication preferences for women from BRCA negative families. Female first-degree relatives of breast cancer patients who tested negative for BRCA1/2 mutations (N = 149) completed a survey assessing multiplex genetic testing interest and risk communication preferences. Interest in testing was high (70 %) and even higher if results could guide risk-reducing behavior changes such as taking medications (79 %). Participants preferred to receive genomic risk communications from a variety of sources including: primary care physicians (83 %), genetic counselors (78 %), printed materials (71 %) and the web (60 %). Factors that were independently associated with testing interest were: perceived lifetime risk of developing cancer (odds ratio (OR) = 1.67: 95 % confidence interval (CI) 1.06-2.65) and high cancer worry (OR = 3.12: CI 1.28-7.60). Findings suggest that women from BRCA1/2 negative families are a unique population and may be primed for behavior change. Findings also provide guidance for clinicians who can help develop genomic risk communications, promote informed decision making and customize behavioral interventions.
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Affiliation(s)
- Kristina G Flores
- University of New Mexico Comprehensive Cancer Center, University of New Mexico, MSC07 4025, 2325 Camino de Salud NE, Albuquerque, NM, 87131-0001, USA.
| | - Laurie E Steffen
- University of New Mexico Comprehensive Cancer Center, University of New Mexico, MSC07 4025, 2325 Camino de Salud NE, Albuquerque, NM, 87131-0001, USA.,Department of Psychology, University of New Mexico, Albuquerque, NM, USA
| | | | - Belinda E Vicuña
- University of New Mexico Comprehensive Cancer Center, University of New Mexico, MSC07 4025, 2325 Camino de Salud NE, Albuquerque, NM, 87131-0001, USA.,Department of Psychology, University of New Mexico, Albuquerque, NM, USA
| | - Amanda Gammon
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Wendy Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Lucretia Vigil
- University of New Mexico Comprehensive Cancer Center, University of New Mexico, MSC07 4025, 2325 Camino de Salud NE, Albuquerque, NM, 87131-0001, USA
| | - Zoneddy R Dayao
- University of New Mexico Comprehensive Cancer Center, University of New Mexico, MSC07 4025, 2325 Camino de Salud NE, Albuquerque, NM, 87131-0001, USA.,Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Melanie E Royce
- University of New Mexico Comprehensive Cancer Center, University of New Mexico, MSC07 4025, 2325 Camino de Salud NE, Albuquerque, NM, 87131-0001, USA.,Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Anita Y Kinney
- University of New Mexico Comprehensive Cancer Center, University of New Mexico, MSC07 4025, 2325 Camino de Salud NE, Albuquerque, NM, 87131-0001, USA.,Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
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