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Caeser R, Chiang J, Tan ES, Tai ES, Ngeow J. Cascade testing for hereditary cancer in Singapore: how population genomics help guide clinical policy. Fam Cancer 2024; 23:133-140. [PMID: 38662262 DOI: 10.1007/s10689-024-00376-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/26/2024]
Abstract
Hereditary Cancer makes up around 5-10% of all cancers. It is important to diagnose hereditary cancer in a timely fashion, as not only do patients require long-term care from a young age, but their relatives also require management. The main approach to capture at-risk relatives is cascade testing. It involves genetic testing of relatives of the first detected carrier of a pathogenic variant in a family i.e. the proband. The current standard of care for cascade testing is a patient-mediated approach. Probands are then advised to inform and encourage family members to undergo genetic testing. In Singapore, cascade testing is inefficient, around 10-15%, lower than the 30% global average. Here, we describe the cascade testing process and its effort to increase testing in Singapore. Precision Health Research, Singapore (PRECISE), was set up to coordinate Singapore's National Precision Medicine strategy and has awarded five clinical implementation pilots, with one of them seeking to identify strategies for how cascade testing for hereditary cancer can be increased in a safe and cost-efficient manner. Achieving this will be done through addressing barriers such as cost, manpower shortages, exploring a digital channel for contacting at-risk relatives, and getting a deeper insight into why genetic testing gets declined. If successful, it will likely result in care pathways that are a cost-effective public health intervention for identifying individuals at risk. Surveillance and management of those unaffected at-risk individuals, if caught early, will result in improved patient outcomes, and further reduce the healthcare burden for the economy.
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Affiliation(s)
- Rebecca Caeser
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Jianbang Chiang
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Ee Shien Tan
- Duke-National University of Singapore (NUS) Medical School, National University of Singapore, Singapore, Singapore
- Genetics Service, Department of Pediatrics, Kadang Kerbau (KK) Women's and Children's Hospital, Singapore, Singapore
| | - E Shyong Tai
- Duke-National University of Singapore (NUS) Medical School, National University of Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Precision Health Research, Singapore, Singapore
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.
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Chiang J, Chia TH, Yuen J, Shaw T, Li ST, Binte Ishak ND, Chew EL, Chong ST, Chan SH, Ngeow J. Impact of Variant Reclassification in Cancer Predisposition Genes on Clinical Care. JCO Precis Oncol 2022; 5:577-584. [PMID: 34994607 DOI: 10.1200/po.20.00399] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Genetic testing has clinical utility in the management of patients with hereditary cancer syndromes. However, the increased likelihood of encountering a variant of uncertain significance in individuals of non-European descent such as Asians may be challenging to both clinicians and patients. This study aims to evaluate the impact of variant reclassification in an Asian country with variants of uncertain significance reported in cancer predisposition genes. METHODS A retrospective analysis of patients seen at the Cancer Genetics Service at the National Cancer Centre Singapore between February 2014 and March 2020 was conducted. The frequency, direction, and time to variant reclassification were evaluated by comparing the reclassified report against the original report. RESULTS A total of 1,412 variants of uncertain significance were reported in 49.9% (845 of 1,695) of patients. Over 6 years, 6.7% (94 of 1,412) of variants were reclassified. Most variants of uncertain significance (94.1%, 80 of 85) were downgraded to benign or likely benign variant, with a smaller proportion of variants of uncertain significance (5.9%, 5 of 85) upgraded to pathogenic or likely pathogenic variant. Actionable variants of uncertain significance upgrades and pathogenic or likely pathogenic variant downgrades, which resulted in management changes, happened in 31.0% (39 of 126) of patients. The median and mean time taken for reclassification were 1 and 1.62 year(s), respectively. CONCLUSION We propose a clinical guideline to standardize management of patients reported to have variants of uncertain significance. Management should be based on the patient's personal history, family history, and variant interpretation. For clinically relevant or suspicious variants of uncertain significance, follow-up is recommended every 2 years, as actionable reclassifications may happen during this period.
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Affiliation(s)
- Jianbang Chiang
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Tze Hao Chia
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jeanette Yuen
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Tarryn Shaw
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Shao-Tzu Li
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Nur Diana Binte Ishak
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Ee Ling Chew
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Siao Ting Chong
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Sock Hoai Chan
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore.,Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Singapore, Singapore
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Sullivan T, Thirthagiri E, Chong CE, Stauffer S, Reid S, Southon E, Hassan T, Ravichandran A, Wijaya E, Lim J, Taib NAM, Fadzli F, Yip CH, Hartman M, Li J, van Dam RM, North SL, Das R, Easton DF, Biswas K, Teo SH, Sharan SK. Epidemiological and ES cell-based functional evaluation of BRCA2 variants identified in families with breast cancer. Hum Mutat 2021; 42:200-212. [PMID: 33314489 PMCID: PMC7919386 DOI: 10.1002/humu.24154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 09/29/2020] [Accepted: 11/28/2020] [Indexed: 01/06/2023]
Abstract
The discovery of high-risk breast cancer susceptibility genes, such as Breast cancer associated gene 1 (BRCA1) and Breast cancer associated gene 2 (BRCA2) has led to accurate identification of individuals for risk management and targeted therapy. The rapid decline in sequencing costs has tremendously increased the number of individuals who are undergoing genetic testing world-wide. However, given the significant differences in population-specific variants, interpreting the results of these tests can be challenging especially for novel genetic variants in understudied populations. Here we report the characterization of novel variants in the Malaysian and Singaporean population that consist of different ethnic groups (Malays, Chinese, Indian, and other indigenous groups). We have evaluated the functional significance of 14 BRCA2 variants of uncertain clinical significance by using multiple in silico prediction tools and examined their frequency in a cohort of 7840 breast cancer cases and 7928 healthy controls. In addition, we have used a mouse embryonic stem cell (mESC)-based functional assay to assess the impact of these variants on BRCA2 function. We found these variants to be functionally indistinguishable from wild-type BRCA2. These variants could fully rescue the lethality of Brca2-null mESCs and exhibited no sensitivity to six different DNA damaging agents including a poly ADP ribose polymerase inhibitor. Our findings strongly suggest that all 14 evaluated variants are functionally neutral. Our findings should be valuable in risk assessment of individuals carrying these variants.
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Affiliation(s)
- Teresa Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Eswary Thirthagiri
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.,Servier, Kuala Lumpur, Malaysia.,Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Chan-Eng Chong
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Stacey Stauffer
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Susan Reid
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Tiara Hassan
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Aravind Ravichandran
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India.,SASTRA University, Thirumalaisamudram, Thanjavur, Tamil Nadu, India
| | | | - Joanna Lim
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Nur Aishah Mohd Taib
- Breast Cancer Research Unit, UM Cancer Research Institute, University of Malaya Medical Center, Kuala Lumpur, Malaysia
| | - Farhana Fadzli
- Breast Cancer Research Unit, UM Cancer Research Institute, University of Malaya Medical Center, Kuala Lumpur, Malaysia
| | | | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore.,Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - Jingmei Li
- Genome Institute of Singapore, Human Genetics, Singapore, Singapore.,Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Susan L North
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Ranabir Das
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia.,Breast Cancer Research Unit, UM Cancer Research Institute, University of Malaya Medical Center, Kuala Lumpur, Malaysia
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
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Reinterpretation of BRCA1 and BRCA2 variants of uncertain significance in patients with hereditary breast/ovarian cancer using the ACMG/AMP 2015 guidelines. Breast Cancer 2019; 26:510-519. [PMID: 30725392 DOI: 10.1007/s12282-019-00951-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/25/2019] [Indexed: 01/19/2023]
Abstract
BACKGROUND Although BRCA1 or BRCA2 (BRCA1/2) genetic testing plays an important role in determining treatment modalities in patients with hereditary breast and ovarian cancer, sequence variants with unknown clinical significance or variant of uncertain significance (VUS) have limited use in medical decision-making. With vast quantities of gene-related data being updated, the clinical significance of VUS may change over time. We reinterpreted the sequence variant previously reported as BRCA1/2 VUS results in patients with breast or ovarian cancer and assessed whether the clinical significance of VUS was changed. METHODS We retrospectively reviewed medical records of 423 breast or ovarian cancer patients who underwent BRCA1/2 genetic testing from 2010 to 2017. The VUSs in BRCA1/2 were reanalyzed using the 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology standards and guidelines (ACMG/AMP 2015 guidelines) and the VUS was reclassified into five categories: "pathogenic", "likely pathogenic", "VUS", "likely benign", and "benign". RESULTS A total of 75 patients (48 sequence types of VUS) were identified as carrying either one or more VUS in BRCA1/2. Among the 75 patients, two patients (2.7%) were reclassified as "likely pathogenic", 30 patients (40.0%) were reclassified as either "benign" or "likely benign", and the remaining 43 patients (57.3%) were still classified as VUS category. CONCLUSIONS Since the clinical significance of VUS in BRCA1/2 may vary from time to time, reinterpretation of the VUS results could contribute to clinical decision-making.
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