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Zhao B, Li J, Sinha S, Qin Z, Kou SH, Xiao F, Lei H, Chen T, Cao W, Ding X, Wang SM. Pathogenic variants in human DNA damage repair genes mostly arose in recent human history. BMC Cancer 2024; 24:415. [PMID: 38575974 PMCID: PMC10993466 DOI: 10.1186/s12885-024-12160-6] [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: 09/21/2023] [Accepted: 03/21/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Genome stability is maintained by the DNA damage repair (DDR) system composed of multiple DNA repair pathways of hundreds of genes. Germline pathogenic variation (PV) in DDR genes damages function of the affected DDR genes, leading to genome instability and high risk of diseases, in particular, cancer. Knowing evolutionary origin of the PVs in human DDR genes is essential to understand the etiology of human diseases. However, answer to the issue remains largely elusive. In this study, we analyzed evolutionary origin for the PVs in human DDR genes. METHODS We identified 169 DDR genes by referring to various databases and identified PVs in the DDR genes of modern humans from ClinVar database. We performed a phylogenetic analysis to analyze the conservation of human DDR PVs in 100 vertebrates through cross-species genomic data comparison using the phyloFit program of the PHAST package and visualized the results using the GraphPad Prism software and the ggplot module. We identified DDR PVs from over 5000 ancient humans developed a database to host the DDR PVs ( https://genemutation.fhs.um.edu.mo/dbDDR-AncientHumans ). Using the PV data, we performed a molecular archeological analysis to compare the DDR PVs between modern humans and ancient humans. We analyzed evolution selection of DDR genes across 20 vertebrates using the CodeML in PAML for phylogenetic analysis. RESULTS Our phylogenic analysis ruled out cross-species conservation as the origin of human DDR PVs. Our archeological approach identified rich DDR PVs shared between modern and ancient humans, which were mostly dated within the last 5000 years. We also observed similar pattern of quantitative PV distribution between modern and ancient humans. We further detected a set of ATM, BRCA2 and CHEK2 PVs shared between human and Neanderthals. CONCLUSIONS Our study reveals that human DDR PVs mostly arose in recent human history. We propose that human high cancer risk caused by DDR PVs can be a by-product of human evolution.
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Affiliation(s)
- Bojin Zhao
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Jiaheng Li
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Siddharth Sinha
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Zixin Qin
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Si Hoi Kou
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Fengxia Xiao
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Huijun Lei
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Tianhui Chen
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310018, China
| | - Wenming Cao
- Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310018, China
| | - Xiaofan Ding
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - San Ming Wang
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China.
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Wu Z, Zhang Q, Jin Y, Zhang X, Chen Y, Yang C, Tang X, Jiang H, Wang X, Zhou X, Yu F, Wang B, Guan M. Population-based BRCA germline mutation screening in the Han Chinese identifies individuals at risk of BRCA mutation-related cancer: experience from a clinical diagnostic center from greater Shanghai area. BMC Cancer 2024; 24:411. [PMID: 38566028 PMCID: PMC10988807 DOI: 10.1186/s12885-024-12089-w] [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: 11/01/2023] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Deleterious BRCA1/2 (BRCA) mutation raises the risk for BRCA mutation-related malignancies, including breast, ovarian, prostate, and pancreatic cancer. Germline variation of BRCA exhibits substantial ethnical diversity. However, there is limited research on the Chinese Han population, constraining the development of strategies for BRCA mutation screening in this large ethnic group. METHODS We profile the BRCA mutational spectrum, including single nucleotide variation, insertion/deletion, and large genomic rearrangements in 2,080 apparently healthy Chinese Han individuals and 522 patients with BRCA mutation-related cancer, to determine the BRCA genetic background of the Chinese Han population, especially of the East Han. Incident cancer events were monitored in 1,005 participants from the healthy group, comprising 11 BRCA pathogenic/likely pathogenic (PLP) variant carriers and 994 PLP-free individuals, including 3 LGR carriers. RESULTS Healthy Chinese Han individuals demonstrated a distinct BRCA mutational spectrum compared to cancer patients, with a 0.53% (1 in 189) prevalence of pathogenic/likely pathogenic (PLP) variant, alongside a 3 in 2,080 occurrence of LGR. BRCA1 c. 5470_5477del demonstrated high prevalence (0.44%) in the North Han Chinese and penetrance for breast cancer. None of the 3 LGR carriers developed cancer during the follow-up. We calculated a relative risk of 135.55 (95% CI 25.07 to 732.88) for the development of BRCA mutation-related cancers in the BRCA PLP variant carriers (mean age 42.91 years, median follow-up 10 months) compared to PLP-free individuals (mean age 48.47 years, median follow-up 16 months). CONCLUSION The unique BRCA mutational profile in the Chinese Han highlights the potential for standardized population-based BRCA variant screening to enhance BRCA mutation-related cancer prevention and treatment.
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Affiliation(s)
- Zhiyuan Wu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Qingyun Zhang
- Central Laboratory, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Yiting Jin
- Department of General Surgery, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Xinju Zhang
- Central Laboratory, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Yanli Chen
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Can Yang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Xuemei Tang
- Central Laboratory, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Haowen Jiang
- Department of Urology, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Xiaoyi Wang
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Xinli Zhou
- Department of Oncology, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Feng Yu
- Health Management Center, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Bing Wang
- Health Management Center, Huashan Hospital, Fudan University, 200040, Shanghai, China.
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, 200040, Shanghai, China.
- Central Laboratory, Huashan Hospital, Fudan University, 200040, Shanghai, China.
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3
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Martin FJ, Saffie IM, Hurtado MA, Avila-Jaque D, Lagos RA, Selman CA, Huserman JZ, Castillo VA, Chahuán BJ. Variants in BRCA1/2 in a hospital-based cohort in Chile and national literature review. Ecancermedicalscience 2024; 18:1683. [PMID: 38566764 PMCID: PMC10984842 DOI: 10.3332/ecancer.2024.1683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Indexed: 04/04/2024] Open
Abstract
Purpose The aim was to assess the diagnostic yield of next generation sequencing (NGS) multi-gene panels for breast and ovarian cancer in a high-complexity cancer centre in Chile. Additionally, our goal was to broaden the genotypic spectrum of BRCA variants already identified in Chilean families. Methods Retrospective analysis was conducted on the genetic test results of 722 individuals from Fundación Arturo López Pérez's genetic counselling unit between 2016 and 2021. A comprehensive literature review encompassing articles analysing the frequency of germinal pathogenic variants in BRCA1/2 within the Chilean population was undertaken. Results 23.5% of the panels had positive results, with 60% due to pathogenic variants in the BRCA1/2 genes. Seven previously unreported variants in BRCA1 from Chilean studies were identified.One or more variants of uncertain significance were detected in 31% of the results, and 11.5% of the families in this cohort presented copy number variants (CNVs) in BRCA1/2.8 studies analysed the frequency of pathogenic variants in BRCA1/2 in the Chilean population between 2006 and 2023, with a frequency between 7.1% and 17.1%.51 BRCA1 variants in 149 families have been reported in Chile and 38 BRCA2 variants in 132 families. Nine founder pathogenic variants identified by one study were present in 51.9% of the total Chilean families reported. Conclusion Our findings advocate for the integration of NGS multi-gene panel testing as a primary strategy within our population. This approach allows for the comprehensive assessment of single nucleotide variants and CNVs in BRCA1/2, alongside other high and moderately penetrant genes associated with breast and ovarian cancer.
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Affiliation(s)
- Fernanda J Martin
- Unidad Asesoramiento Genético Oncológico, Fundación Arturo López Pérez, Santiago 7500921, Chile
- https://orcid.org/0000-0002-7167-8850
| | - Isabel M Saffie
- Cirugía de mama, Fundación Arturo López Pérez, Santiago 7500921, Chile
- https://orcid.org/0000-0002-4723-5750
| | - Mabel A Hurtado
- Unidad Asesoramiento Genético Oncológico, Fundación Arturo López Pérez, Santiago 7500921, Chile
- Cirugía de mama, Fundación Arturo López Pérez, Santiago 7500921, Chile
| | - Diana Avila-Jaque
- Sección de Genética, Hospital San Juan de Dios, Santiago 8350488, Chile
- https://orcid.org/0009-0002-7787-6847
| | - Rodrigo A Lagos
- Unidad estadística, Fundación Arturo López Pérez, Santiago 7500921, Chile
- https://orcid.org/0000-0002-5806-6227
| | - Carolina A Selman
- Subdirección Unidades Diagnósticas, Fundación Arturo López Pérez, Santiago 7500921, Chile
| | - Jonathan Z Huserman
- Departamento Genética, Hospital Base San José Osorno, Osorno 5311523, Chile
- https://orcid.org/0000-0002-9355-3282
| | - Valentina A Castillo
- Departamento Genética, Hospital Clínico Universidad de Chile, Santiago 8380453, Chile
- Departamento Genética, Hospital Dr. Sótero del Río, Santiago 8150000, Chile
| | - Badir J Chahuán
- Unidad Asesoramiento Genético Oncológico, Fundación Arturo López Pérez, Santiago 7500921, Chile
- Cirugía de mama, Fundación Arturo López Pérez, Santiago 7500921, Chile
- https://orcid.org/0000-0003-3133-6706
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Zhang Y, Wu H, Gan C, Rao H, Wang Q, Guo X. BRCA1 and BRCA2 germline mutations in Chinese Hakka breast cancer patients. BMC Med Genomics 2024; 17:3. [PMID: 38167124 PMCID: PMC10763220 DOI: 10.1186/s12920-023-01772-9] [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: 01/05/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
OBJECTIVE To investigate the prevalence of BRCA1/2 gene variants and evaluate the clinical and pathological characteristics associated with these variants in Chinese Hakka breast cancer patients. METHODS A total of 409 breast cancer patients were analyzed based on next-generation sequencing results, with 337 categorized as non-carriers and 72 as carriers of BRCA1/2 variants. Data on the patients' BRCA1/2 gene mutation status, clinical and pathological characteristics, as well as menstrual and reproductive information, were collected, analyzed, compared, and tabulated. Logistic regression analysis was performed to explore the relationship between clinical characteristics and pathogenic variants. RESULTS Among the patients, 72 were identified as carriers of pathogenic or likely pathogenic variants in BRCA1/2, while 337 had likely benign or benign mutations. The BRCA1 c.2635G > T (p. Glu879*) variant was detected at a high frequency, accounting for 12.5% (4/32) of the BRCA1 mutations, while the c.5164_5165del (p.Ser1722Tyrfs*4) variant was common among the BRCA2 mutations, accounting for 17.5% (7/40). It was observed that a higher proportion of BRCA1 carriers had the triple-negative breast cancer subtype, whereas more BRCA2 carriers exhibited estrogen receptor (ER) + and progesterone receptor (PR) + subtypes. Multivariate logistic regression analysis revealed that a family history of cancer (OR = 2.36, 95% CI = 1.00-5.54), bilateral cancer (OR = 4.78, 95% CI 1.61-14.20), human epidermal growth factor receptor 2 (HER2)- (OR = 8.23, 95% CI 3.25-20.84), and Ki67 ≥ 15% (OR = 3.88, 95% CI 1.41-10.65) were associated with BRCA1/2 mutations, with the age at diagnosis, age at menarche, and premenopausal status serving as covariates. CONCLUSIONS The most common pathogenic variant of the BRCA1 and BRCA2 in breast cancer patients was c.2635G > T and c.5164_5165del, respectively. Additionally, a family history of cancer, bilateral cancer, HER2-, and Ki67 ≥ 15% were identified as independent predictors of BRCA1/2 pathogenic variants.
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Affiliation(s)
- Yinmei Zhang
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China
- Guangdong Engineering Technological Research Center of Clinical Molecular Diagnosis and Antibody Drugs, Meizhou, China
| | - Heming Wu
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China
| | - Caiyan Gan
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China
- Guangdong Engineering Technological Research Center of Clinical Molecular Diagnosis and Antibody Drugs, Meizhou, China
| | - Hui Rao
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China
| | - Qiuming Wang
- Department of Medical Oncology, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, People's Republic of China
| | - Xueming Guo
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China.
- Guangdong Engineering Technological Research Center of Clinical Molecular Diagnosis and Antibody Drugs, Meizhou, China.
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5
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Wei B, Zhao J, Li J, Feng J, Sun M, Wang Z, Shi C, Yang K, Qin Y, Zhang J, Ma J, Dong H. Pathogenic germline variants in BRCA1 and TP53 increase lung cancer risk in Chinese. Cancer Med 2023; 12:21219-21228. [PMID: 37930190 PMCID: PMC10726856 DOI: 10.1002/cam4.6692] [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: 06/07/2023] [Revised: 10/07/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUD Multiple studies have identified pathogenic germline variants in cancer susceptibility genes (CSGs) in Chinese lung cancer patients; however, accurate assessment of these variants' contributions to cancer predisposition is always hampered by the absence of data on the prevalence of these variants in the general population. It is necessary to conduct a large-scale case-control study to identify CSGs that significantly increase the risk of lung cancer. MATERIALS AND METHODS We performed targeted sequencing of a CSGs panel in 1117 lung cancer patients and 16,327 controls from the general Chinese population. RESULTS In comparison to controls, lung cancer patients had a considerably higher prevalence of pathogenic and likely pathogenic (P/LP) variations. Among lung cancer patients, 72% of P/LP variants carriers did not have a family cancer history, who would be ignored if germline testing was only provided for patients meeting family history-based criteria. Furthermore, compared to individuals with late-onset lung cancer, patients with early-onset lung cancer had a considerably higher prevalence of P/LP variations. With odds ratios (ORs) ranging from 4-fold (BRCA1: OR, 4.193; 95%CI, 1.382-10.768) to 29-fold (TP53: OR, 29.281; 95%CI, 1.523-1705.506), P/LP variants in the BRCA1 and TP53 genes were discovered to be strongly related to increased lung cancer risk. Additionally, with ORs ranging from 7.322-fold to infinity, we discovered 23 variations previously categorized as non-P/LP variants were highly enriched in lung cancer patients. CONCLUSION Our findings indicated that P/LP variants in BRCA1 and TP53 conferred increased risk of lung cancer in Chinese.
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Affiliation(s)
- Bing Wei
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Jiadong Zhao
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Jun Li
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Junnan Feng
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Manman Sun
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Zhizhong Wang
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Chao Shi
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Ke Yang
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Yue Qin
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Jing Zhang
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Jie Ma
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Hui Dong
- Department of Gastroenterology, Shanghai Key Laboratory of Pancreatic DiseasesShanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
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Xu Y, Liu K, Li C, Li M, Liu F, Zhou X, Sun M, Ranganathan M, Zhang L, Wang S, Hu X, Xu Y. The Largest Chinese Cohort Study Indicates Homologous Recombination Pathway Gene Mutations as Another Major Genetic Risk Factor for Colorectal Cancer with Heterogeneous Clinical Phenotypes. RESEARCH (WASHINGTON, D.C.) 2023; 6:0249. [PMID: 37854294 PMCID: PMC10581333 DOI: 10.34133/research.0249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023]
Abstract
While genetic factors were associated with over 30% of colorectal cancer (CRC) patients, mutations in CRC-susceptibility genes were identified in only 5% to 10% of these patients. Besides, previous studies on hereditary CRC were largely designed to analyze germline mutations in patients with single genetic high-risk factor, which limited understanding of the association between genotype and phenotypes. From January 2015 to December 2018, we retrospectively enrolled 2,181 patients from 8,270 consecutive CRC cases, covering 5 categories of genetic high-risk factors. Leukocyte genomic DNA was analyzed for germline mutations in cancer predisposition genes. The germline mutations under each category were detected and analyzed in association with CRC susceptibility, clinical phenotypes, and prognoses. A total of 462 pathogenic variants were detected in 19.3% of enrolled CRC patients. Mismatch repair gene mutation was identified in 9.1% of patients, most prevalent across all high-risk groups. Homologous recombination (HR) gene mutations were detected in 6.5% of cases, penetrated in early-onset and extra-colonic cancer risk groups. Mutations in HR genes, including BARD1, RAD50, and ATM, were found to increase CRC risk with odds ratios of 2.8-, 3.1-, and 3.1-fold, respectively. CRC patients with distinct germline mutations manifested heterogeneous phenotypes in clinicopathology and long-term prognoses. Thus, germline mutation screenings should be performed for CRC patients with any of those genetic risk factors. This study also reveals that HR gene mutations may be another major driver for increased CRC risk.
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Affiliation(s)
- Yun Xu
- Department of Colorectal Surgery,
Fudan University Shanghai Cancer Center, Shanghai, P.R. China
| | - Kai Liu
- Department of Colorectal Surgery,
Fudan University Shanghai Cancer Center, Shanghai, P.R. China
| | - Cong Li
- Department of Colorectal Surgery,
Fudan University Shanghai Cancer Center, Shanghai, P.R. China
| | - Minghan Li
- Department of Colorectal Surgery,
Fudan University Shanghai Cancer Center, Shanghai, P.R. China
| | - Fangqi Liu
- Department of Colorectal Surgery,
Fudan University Shanghai Cancer Center, Shanghai, P.R. China
| | - Xiaoyan Zhou
- Department of Pathology,
Fudan University Shanghai Cancer Center, Shanghai, P.R. China
| | - Menghong Sun
- Department of Pathology, Tissue Bank,
Fudan University Shanghai Cancer Center, Shanghai, P.R. China
| | - Megha Ranganathan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Liying Zhang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine,
University of California, Los Angeles, CA, USA
| | - Sheng Wang
- Department of Colorectal Surgery,
Fudan University Shanghai Cancer Center, Shanghai, P.R. China
| | - Xin Hu
- Precision Cancer Medical Center,
Fudan University Shanghai Cancer Center, Shanghai, P.R. China
| | - Ye Xu
- Department of Colorectal Surgery,
Fudan University Shanghai Cancer Center, Shanghai, P.R. China
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7
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Chian JS, Li J, Wang SM. Evolutionary Origin of Human PALB2 Germline Pathogenic Variants. Int J Mol Sci 2023; 24:11343. [PMID: 37511102 PMCID: PMC10379391 DOI: 10.3390/ijms241411343] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
PALB2 (Partner and localizer of BRCA2) is crucial for repairing DNA double-stranded breaks (DSBs) through homologous recombination (HR). Germline pathogenic variation in PALB2 disrupts DNA damage repair and increases the risk of Fanconi Anemia, breast cancer, and ovarian cancer. Determination of the evolutionary origin of human PALB2 variants will promote a deeper understanding of the biological basis of PALB2 germline variation and its roles in human diseases. We tested the evolution origin for 1444 human PALB2 germline variants, including 484 pathogenic and 960 benign variants. We performed a phylogenic analysis by tracing the variants in 100 vertebrates. However, we found no evidence to show that cross-species conservation was the origin of PALB2 germline pathogenic variants, but it is indeed a rich source for PALB2 germline benign variants. We performed a paleoanthropological analysis by tracing the variants in over 5000 ancient humans. We identified 50 pathogenic in 71 ancient humans dated from 32,895 to 689 before the present, of which 90.1% were dated within the recent 10,000 years. PALB2 benign variants were also highly shared with ancient humans. Data from our study reveal that human PALB2 pathogenic variants mostly arose in recent human history.
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Affiliation(s)
- Jia Sheng Chian
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
| | - Jiaheng Li
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
| | - San Ming Wang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
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8
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Qin Z, Li J, Tam B, Sinha S, Zhao B, Bhaskaran SP, Huang T, Wu X, Chian JS, Guo M, Kou SH, Lei H, Zhang L, Wang X, Lagniton PNP, Xiao F, Jiang X, Wang SM. Ethnic-specificity, evolution origin and deleteriousness of Asian BRCA variation revealed by over 7500 BRCA variants derived from Asian population. Int J Cancer 2023; 152:1159-1173. [PMID: 36385461 PMCID: PMC10098510 DOI: 10.1002/ijc.34359] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/23/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
Pathogenic variation in BRCA1 and BRCA2 (BRCA) causes high risk of breast and ovarian cancer, and BRCA variation data are important markers for BRCA-related clinical cancer applications. However, comprehensive BRCA variation data are lacking from the Asian population despite its large population size, heterogenous genetic background and diversified living environment across the Asia continent. We performed a systematic study on BRCA variation in Asian population including extensive data mining, standardization, annotation and characterization. We identified 7587 BRCA variants from 685 592 Asian individuals in 40 Asia countries and regions, including 1762 clinically actionable pathogenic variants and 4915 functionally unknown variants (https://genemutation.fhs.um.edu.mo/Asian-BRCA/). We observed the highly ethnic-specific nature of Asian BRCA variants between Asian and non-Asian populations and within Asian populations, highlighting that the current European descendant population-based BRCA data is inadequate to reflect BRCA variation in the Asian population. We also provided archeological evidence for the evolutionary origin and arising time of Asian BRCA variation. We further provided structural-based evidence for the deleterious variants enriched within the functionally unknown Asian BRCA variants. The data from our study provide a current view of BRCA variation in the Asian population and a rich resource to guide clinical applications of BRCA-related cancer for the Asian population.
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Affiliation(s)
- Zixin Qin
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Benjamin Tam
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Siddharth Sinha
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Shanmuga Priya Bhaskaran
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Teng Huang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xiaobing Wu
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Jia Sheng Chian
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Maoni Guo
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Li Zhang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xiaoyu Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Philip Naderev P Lagniton
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xinyang Jiang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
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Wang SM. A global perspective on the ethnic-specific BRCA variation and its implication in clinical application. JOURNAL OF THE NATIONAL CANCER CENTER 2022. [DOI: 10.1016/j.jncc.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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10
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Lei H, Zhang M, Zhang L, Hemminki K, Wang XJ, Chen T. Overview on population screening for carriers with germline BRCA mutation in China. Front Oncol 2022; 12:1002360. [PMID: 36439508 PMCID: PMC9682265 DOI: 10.3389/fonc.2022.1002360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/24/2022] [Indexed: 12/01/2023] Open
Abstract
Carriers with BRCA1/2 germline pathogenic variants are associated with a high risk of breast and ovarian cancers (also pancreatic and prostate cancers). While the spectrum on germline BRCA mutations among the Chinese population shows ethnic specificity, the identification of carriers with germline BRCA mutation before cancer onset is the most effective approach to protect them. This review focused on the current status of BRCA1/2 screening, the surveillance and prevention measures, and discussed the issues and potential impact of BRCA1/2 population screening in China. We conducted literature research on databases PubMed and Google Scholar, as well as Chinese databases CNKI and Wangfang Med Online database (up to 31 March 2022). Latest publications on germline BRCA1/2 prevalence, spectrum, genetic screening as well as carrier counseling, surveillance and prevention were captured where available. While overall 15,256 records were retrieved, 72 publications using germline BRCA1/2 testing were finally retained for further analyses. Germline BRCA1/2 mutations are common in Chinese patients with hereditary breast, ovarian, prostate and pancreatic cancers. Within previous studies, a unique BRCA mutation spectrum in China was revealed. Next-generation sequencing panel was considered as the most common method for BRCA1/2 screening. Regular surveillance and preventive surgeries were tailored to carriers with mutated-BRCA1/2. We recommend that all Chinese diagnosed with breast, ovarian, pancreatic or prostate cancers and also healthy family members, shall undergo BRCA1/2 gene test to provide risk assessment. Subsequently, timely preventive measures for mutation carriers are recommended after authentic genetic counseling.
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Affiliation(s)
- Huijun Lei
- Department of Cancer Prevention/Zhejiang Cancer Institute, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Min Zhang
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Luyao Zhang
- Department of Cancer Epidemiology and Prevention, Henan Engineering Research Center of Cancer Prevention and Control, Henan International Joint Laboratory of Cancer Prevention, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Kari Hemminki
- Biomedical Center, Faculty of Medicine, Charles University in Pilsen, Pilsen, Czechia
- Division of Cancer Epidemiology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany
| | - Xiao-jia Wang
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Tianhui Chen
- Department of Cancer Prevention/Zhejiang Cancer Institute, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
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11
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Wang C, Dai J, Qin N, Fan J, Ma H, Chen C, An M, Zhang J, Yan C, Gu Y, Xie Y, He Y, Jiang Y, Zhu M, Song C, Jiang T, Liu J, Zhou J, Wang N, Hua T, Liang S, Wang L, Xu J, Yin R, Chen L, Xu L, Jin G, Lin D, Hu Z, Shen H. Analyses of rare predisposing variants of lung cancer in 6,004 whole genomes in Chinese. Cancer Cell 2022; 40:1223-1239.e6. [PMID: 36113475 DOI: 10.1016/j.ccell.2022.08.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/08/2022] [Accepted: 08/15/2022] [Indexed: 12/24/2022]
Abstract
We present the largest whole-genome sequencing (WGS) study of non-small cell lung cancer (NSCLC) to date among 6,004 individuals of Chinese ancestry, coupled with 23,049 individuals genotyped by SNP array. We construct a high-quality haplotype reference panel for imputation and identify 20 common and low-frequency loci (minor allele frequency [MAF] ≥ 0.5%), including five loci that have never been reported before. For rare loss-of-function (LoF) variants (MAF < 0.5%), we identify BRCA2 and 18 other cancer predisposition genes that affect 5.29% of individuals with NSCLC, and 98.91% (181 of 183) of LoF variants have not been linked previously to NSCLC risk. Promoter variants of BRCA2 also have a substantial effect on NSCLC risk, and their prevalence is comparable with BRCA2 LoF variants. The associations are validated in an independent case-control study including 4,410 individuals and a prospective cohort study including 23,826 individuals. Our findings not only provide a high-quality reference panel for future array-based association studies but depict the whole picture of rare pathogenic variants for NSCLC.
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Affiliation(s)
- Cheng Wang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Juncheng Dai
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Na Qin
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Jingyi Fan
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Hongxia Ma
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine (Suzhou Centre), Gusu School, Nanjing Medical University, Suzhou 215002, Jiangsu, China; Research Units of Cohort Study on Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Congcong Chen
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Mingxing An
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Jing Zhang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Caiwang Yan
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Yayun Gu
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Yuan Xie
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Yuanlin He
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Yue Jiang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Meng Zhu
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Ci Song
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Tao Jiang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Jia Liu
- Department of Health Promotion & Chronic Non-Communicable Disease Control, Wuxi Center for Disease Control and Prevention, Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi 214145, Jiangsu, China
| | - Jun Zhou
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Nanxi Wang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Tingting Hua
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Shuang Liang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Lu Wang
- Department of Health Promotion & Chronic Non-Communicable Disease Control, Wuxi Center for Disease Control and Prevention, Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi 214145, Jiangsu, China
| | - Jing Xu
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Rong Yin
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210029, Jiangsu, China
| | - Liang Chen
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Lin Xu
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210029, Jiangsu, China
| | - Guangfu Jin
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhibin Hu
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine (Suzhou Centre), Gusu School, Nanjing Medical University, Suzhou 215002, Jiangsu, China.
| | - Hongbing Shen
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine (Suzhou Centre), Gusu School, Nanjing Medical University, Suzhou 215002, Jiangsu, China; Research Units of Cohort Study on Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing 100730, China.
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12
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Panigoro SS, Paramita RI, Siswiandari KM, Fadilah F. Targeted Sequencing of Germline Breast Cancer Susceptibility Genes for Discovering Pathogenic/Likely Pathogenic Variants in the Jakarta Population. Diagnostics (Basel) 2022; 12:diagnostics12092241. [PMID: 36140642 PMCID: PMC9498046 DOI: 10.3390/diagnostics12092241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Germline predisposition plays an important role in breast cancer. Different ethnic populations need respective studies on cancer risks pertinent to germline variants. We aimed to discover the pathogenic and likely pathogenic variants (P/LP-Vs) of germline breast cancer susceptibility genes and to evaluate their correlation with the clinical characteristics in Jakarta populations. The pure DNA was extracted from the blood buffy coat, using reagents from the QIAamp DNA Mini Kit® (Qiagen, Hilden, Germany). The DNA libraries were prepared using the TargetRich™ Hereditary Cancer Panel (Kailos Genetics®, Huntsville, AL, USA). The barcoded DNA libraries were sequenced using the Illumina NextSeq 500 platform. In-house bioinformatics pipelines were used to analyze the gene variants. We identified 35 pathogenic and likely pathogenic (P/LP-Vs) variants (28 frameshift, 5 nonsense, and 2 splice-site variants). The P/LP-Vs group was statistically significantly different in luminal B status (p < 0.05) compared with the non-P/LP-Vs group. The P/LP-Vs found both in BRCA1/2 genes and non-BRCA genes may increase the risk of breast cancer and alter drug responses. The screening of multigene variants is suggested, rather than BRCA testing only. Prior knowledge of the germline variants status is important for optimal breast cancer diagnosis and optimal therapy.
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Affiliation(s)
- Sonar Soni Panigoro
- Surgical Oncology Division, Department of Surgery, Faculty of Medicine, Universitas Indonesia, Central Jakarta 10430, DKI Jakarta, Indonesia
- Correspondence: (S.S.P.); (R.I.P.)
| | - Rafika Indah Paramita
- Doctoral Program in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Central Jakarta 10430, DKI Jakarta, Indonesia
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Central Jakarta 10430, DKI Jakarta, Indonesia
- Bioinformatics Core Facilities—IMERI, Faculty of Medicine, Universitas Indonesia, Central Jakarta 10430, DKI Jakarta, Indonesia
- Correspondence: (S.S.P.); (R.I.P.)
| | - Kristina Maria Siswiandari
- Surgical Oncology Division, Department of Surgery, Faculty of Medicine, Universitas Indonesia, Central Jakarta 10430, DKI Jakarta, Indonesia
| | - Fadilah Fadilah
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Central Jakarta 10430, DKI Jakarta, Indonesia
- Bioinformatics Core Facilities—IMERI, Faculty of Medicine, Universitas Indonesia, Central Jakarta 10430, DKI Jakarta, Indonesia
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13
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Huang G, Lu H, Chen Q, Huang X. Prevalence and Factors Associated with BRCA1/2 Gene Mutation in Chinese Populations with Breast Cancer. Int J Gen Med 2022; 15:6783-6789. [PMID: 36042935 PMCID: PMC9420444 DOI: 10.2147/ijgm.s378706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
Objective We aimed to evaluate the prevalence of BRCA1 and BRCA2 mutations in Chinese populations with breast cancer. Factors associated with BRCA1 and BRCA2 mutations are also evaluated. Methods This was a cross-sectional study, and patients with breast cancer were included. Data on clinical characteristics, information of breast cancer, and BRCA1 and BRCA2 mutations were extracted. Patients were divided into the carrier and noncarrier groups. Results A total of 368 patients were included. Compared to the noncarrier group (n = 240), patients in the carrier group (n = 128) were younger and more likely to have breast cancer at age <40 years. Of the overall 128 patients in the carrier groups, 58 had BRCA1 mutation and 70 had BRCA2 mutation. Among patients with early onset breast cancer, there was no difference in the prevalence of BRCA1 and BRCA2 (20.7% vs 17.1%, P = 0.35). While among patients with a family history of breast/ovarian cancer, BRCA2 mutation was more prevalent than BRCA1 mutation (54.3% vs 44.8%, P = 0.01); and among patients with triple-negative breast cancer, BRCA1 mutation was more prevalent than BRCA2 mutation (34.5% vs 28.6%, P = 0.04). After adjusting for covariates, factors associated with BRCA1 mutation included breast cancer diagnosed <40 years, tumor size >2 cm, and lymph node metastasis; and after adjusting for covariates, factors associated with BRCA2 mutation included age, tumor size >2 cm, and triple-negative breast cancer. Conclusion The prevalence of BRCA1 and BRCA2 mutations varied according to three specific subgroups. Factors associated with BRCA1 and BRCA2 mutations were differential.
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Affiliation(s)
- Guoding Huang
- Department of Oncology, The Central Hospital of Western Area of Hainan, Danzhou, Hainan, People's Republic of China
| | - Hongquan Lu
- Department of Oncology, The Central Hospital of Western Area of Hainan, Danzhou, Hainan, People's Republic of China
| | - Qizhu Chen
- Department of Oncology, The Central Hospital of Western Area of Hainan, Danzhou, Hainan, People's Republic of China
| | - Xinting Huang
- Department of Oncology, The Central Hospital of Western Area of Hainan, Danzhou, Hainan, People's Republic of China
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14
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Zhang Y, Wu H, Yu Z, Li L, Zhang J, Liang X, Huang Q. Germline variants profiling of BRCA1 and BRCA2 in Chinese Hakka breast and ovarian cancer patients. BMC Cancer 2022; 22:842. [PMID: 35918668 PMCID: PMC9347172 DOI: 10.1186/s12885-022-09943-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/25/2022] [Indexed: 12/26/2022] Open
Abstract
Objective To investigate the prevalence and spectrum of BRCA1 and BRCA2 mutations in Chinese Hakka patients with breast and ovarian cancer. Methods A total of 1,664 breast or ovarian cancer patients were enrolled for genetic testing at our hospital. Germline mutations of the BRCA gene were analysed by next-generation sequencing, including the coding regions and exon intron boundary regions. Results The 1,664 patients included 1,415 (85.04%) breast cancer patients and 245 (14.72%) ovarian cancer patients, while four (0.24%) patients had both the breast and ovarian cancers. A total of 151 variants, including 71 BRCA1 variants and 80 BRCA2 variants, were detected in the 234 (14.06%) patients. The 151 variants included 58 pathogenic variants, 8 likely pathogenic variants, and 85 variants of unknown significance (VUS). A total of 56.25% (18/32) and 65.38% (17/26) of pathogenic variants (likely pathogenic variants are not included) were distributed in exon 14 of BRCA1 and exon 11 of BRCA2, respectively. The most common pathogenic variants among this Hakka population are c.2635G > T (p.Glu879*) (n = 7) in the BRCA1 gene and c.5164_5165del (p.Ser1722Tyrfs*4) (n = 7) in the BRCA2 gene among the Hakka population. A hotspot mutation in the Chinese population, the BRCA1 c.5470_5477del variant was not found in this Hakka population. The prevalence and spectrum of variants in the BRCA genes in the Hakka patients are different from that in other ethnic groups. Conclusions The most common pathogenic variant in this population is c.2635G > T in the BRCA1 gene, and c.5164_5165delAG in the BRCA2 gene in this population. The prevalence and spectrum of variants in the BRCA1 and BRCA2 genes in the Hakka patients from southern China are different from those in other ethnic groups. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09943-0.
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Affiliation(s)
- Yunuo Zhang
- Department of Medical Oncology, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China
| | - Heming Wu
- Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Zhikang Yu
- Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Liang Li
- Department of Medical Oncology, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China
| | - Jinhong Zhang
- Department of Medical Oncology, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China
| | - Xinhong Liang
- Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China.,Radiology department, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Qingyan Huang
- Center for Precision Medicine, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China. .,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China. .,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.
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15
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Rweyemamu LP, Gültaşlar BK, Akan G, Dharsee N, Namkinga LA, Lyantagaye SL, Yazıcı H, Atalar F. Breast cancer in East Africa: Prevalence and spectrum of germline SNV/indel and CNVs in BRCA1 and BRCA2 genes among breast cancer patients in Tanzania. Cancer Med 2022; 12:3395-3409. [PMID: 35908255 PMCID: PMC9939169 DOI: 10.1002/cam4.5091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/08/2022] [Accepted: 07/19/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Growing prevalence and aggressiveness of breast cancer (BC) among East African women strongly indicate that the genetic risk factor implicated in the etiology of the disease may have a key role. Germline pathogenic variants in BRCA1 and BRCA2 (BRCA1/2) are known to increase the lifetime risk of BC. This study investigated the prevalence and spectrum of germline single nucleotide variant/insertion and deletion (SNV/indel), and copy number variations (CNVs) in BRCA1/2 among Tanzanian BC patients, and evaluated the associations of identified variants with patient's socio-demographic and histopathological characteristics. METHODS One hundred BC patients were examined for BRCA1/2 variants using next-generation sequencing (NGS). Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA) assay were performed for the confirmation of SNV/indel and CNVs, respectively. RESULTS Six germline SNV/indel pathogenic variants were detected from six unrelated patients. Five of these variants were identified in BRCA1, and one in BRCA2. We also identified, in one patient, one variant of uncertain clinical significance (VUS). CNV was not detected in any of the BC patients. Furthermore, we found that in our cohort, BRCA1/2 variant carriers were triple-negative BC patients (p = 0.019). CONCLUSIONS Our study provides first insight into BC genetic landscape by the use of NGS in the under-represented East African Tanzanian populations. Our findings support the importance of genetic risk factors in BC etiology in Tanzania and showed a relatively high overall prevalence (6%) of germline BRCA1/2 pathogenic variants in BC patients. Therefore, our results indicate that BRCA1/2 pathogenic variants may well contribute to BC incidence in Tanzania. Thus, the identification of frequent variants in BRCA1/2 genes will enable implementation of rapid, inexpensive population-specific BRCA1/2 genetic testing, particularly for triple-negative BC patients known for their high prevalence in Tanzania. This will, in turn, greatly contributes to provide effective therapeutic strategies.
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Affiliation(s)
- Linus P. Rweyemamu
- Department of Molecular Biology and BiotechnologyUniversity of Dar es SalaamDar es SalaamTanzania,Mbeya College of Health and Allied SciencesUniversity of Dar es SalaamMbeyaTanzania
| | - Büşra K. Gültaşlar
- Division of Cancer Genetics, Department of Basic Oncology, Institute of OncologyIstanbul UniversityIstanbulTurkiye
| | - Gokce Akan
- DESAM Research InstituteNear East UniversityNicosiaCyprus,MUHAS Genetic Laboratory, Department of BiochemistryMuhimbili University of Health and Allied SciencesDar es SalaamTanzania
| | - Nazima Dharsee
- Academic, Research and Consultancy UnitOcean Road Cancer InstituteDar es SalaamTanzania
| | - Lucy A. Namkinga
- Department of Molecular Biology and BiotechnologyUniversity of Dar es SalaamDar es SalaamTanzania
| | - Sylvester L. Lyantagaye
- Department of Molecular Biology and BiotechnologyUniversity of Dar es SalaamDar es SalaamTanzania,Mbeya College of Health and Allied SciencesUniversity of Dar es SalaamMbeyaTanzania
| | - Hülya Yazıcı
- Division of Cancer Genetics, Department of Basic Oncology, Institute of OncologyIstanbul UniversityIstanbulTurkiye,Department of Medical Biology and Genetics, Faculty of MedicineIstanbul Arel UniversityIstanbulTurkiye
| | - Fatmahan Atalar
- MUHAS Genetic Laboratory, Department of BiochemistryMuhimbili University of Health and Allied SciencesDar es SalaamTanzania,Department of Rare Diseases, Child Health InstituteIstanbul UniversityIstanbulTurkiye
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16
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Ovarian cancer risk of Chinese women with BRCA1/2 germline pathogenic variants. J Hum Genet 2022; 67:639-642. [PMID: 35864222 DOI: 10.1038/s10038-022-01065-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/16/2022] [Accepted: 07/07/2022] [Indexed: 11/08/2022]
Abstract
Estimating the lifetime risk of ovarian cancer in Chinese women with BRCA1/2 germline pathogenic variants (PVs) is of great importance for the clinical management of BRCA1/2 carriers. This cohort study recruited 9903 unselected Chinese breast cancer patients whose BRCA1/2 status was determined. Of these, 3984 probands completed family history questionnaires, which investigated the health status of their relatives, including 11,997 female first-degree relatives. The ovarian cancer risk of BRCA1/2 germline pathogenic carriers was estimated using the ovarian cancer history of proband first-degree female relatives via the Kin-cohort method. Of the 3984 probands, 126 (3.2%) carried BRCA1 PVs, and 183 (4.6%) carried BRCA2 PVs. The estimated cumulative risks of ovarian cancer by age 70 were 15.3% (95% CI 8.4-18.6%) for BRCA1 carriers, 5.5% (95% CI 2.0-10.2%) for BRCA2 carriers, and 0.4% (95% CI 0.3-0.7%) for noncarriers. The cumulative risks of ovarian cancer were very low before the age of 40 for both BRCA1 and BRCA2 carriers and were an increase up to age 45. The cumulative ovarian cancer risk of BRCA1 carriers was approximately three times higher than that of BRCA2 carriers, and BRCA1 and BRCA2 carriers had 38- and 14-fold higher risks than non-BRCA carriers, respectively. The findings indicate that Chinese women with BRCA1/2 PVs have high risks of ovarian cancer in their lifetime, especially BRCA1 carriers. These results are useful for devising optimal strategies to reduce ovarian cancer risk in BRCA1/2 carriers.
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17
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Qin Z, Huang T, Guo M, Wang SM. Distinct landscapes of deleterious variants in DNA damage repair system in ethnic human populations. Life Sci Alliance 2022; 5:5/9/e202101319. [PMID: 35595529 PMCID: PMC9122833 DOI: 10.26508/lsa.202101319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 12/03/2022] Open
Abstract
Deleterious variants in the DNA damage repair system can cause genome instability and increase cancer risk. The highly ethnic-specific DDR deleterious variation from this study suggests its potential relationship with different disease susceptibility in ethnic human populations. Deleterious variants in DNA damage repair (DDR) system can cause genome instability and increase cancer risk. In this study, we analyzed the deleterious variants in DDR system in 16 ethnic human populations. From the genetic variants in 169 DDR genes involved in nine DDR pathways collected from 158,612 individuals of different ethnic background, we identified 1,781 deleterious variants in 81 DDR genes in eight DDR pathways (https://genemutation.fhs.um.edu.mo/dbddr-global/). Our analysis showed although the quantity of deleterious variants was loaded at a similar level, the landscape of the variants differed substantially among different populations that two-third of the variants were present in single ethnic populations, and the rest was mostly shared between the populations with closer geographic and genetic relationship. The highly ethnic-specific DDR deleterious variation suggests its potential relationship with different disease susceptibility in ethnic human populations.
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Affiliation(s)
- Zixin Qin
- Cancer Centre and Institute of Translational Medicine, Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, China
| | - Teng Huang
- Cancer Centre and Institute of Translational Medicine, Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, China
| | - Maoni Guo
- Cancer Centre and Institute of Translational Medicine, Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, China
| | - San Ming Wang
- Cancer Centre and Institute of Translational Medicine, Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, China
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18
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Li J, Zhao B, Huang T, Qin Z, Wang SM. Human BRCA pathogenic variants were originated during recent human history. Life Sci Alliance 2022; 5:5/5/e202101263. [PMID: 35165121 PMCID: PMC8860097 DOI: 10.26508/lsa.202101263] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/05/2023] Open
Abstract
BRCA1 and BRCA2 (BRCA) play essential roles in maintaining genome stability. BRCA germline pathogenic variants increase cancer risk. However, the evolutionary origin of human BRCA pathogenic variants remains largely elusive. We tested the 2,972 human BRCA1 and 3,652 human BRCA2 pathogenic variants from ClinVar database in 100 vertebrates across eight clades, but failed to find evidence to show cross-species evolution conservation as the origin; we searched the variants in 2,792 ancient human genome data, and identified 28 BRCA1 and 22 BRCA2 pathogenic variants in 44 cases dated from 45,000 to 300 yr ago; we analyzed the haplotype-dated human BRCA pathogenic founder variants, and observed that they were mostly arisen within the past 3,000 yr; we traced ethnic distribution of human BRCA pathogenic variants, and found that the majority were present in single or a few ethnic populations. Based on the data, we propose that human BRCA pathogenic variants were highly likely arisen in recent human history after the latest out-of-Africa migration, and the expansion of modern human population could largely increase the variation spectrum.
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Affiliation(s)
- Jiaheng Li
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Bojin Zhao
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Teng Huang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Zixin Qin
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - San Ming Wang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
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19
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Impact of BRCA mutation on the survival and risk of contralateral breast cancer in Asian breast cancer patients. Breast Cancer Res Treat 2022; 192:629-637. [PMID: 35113257 DOI: 10.1007/s10549-021-06446-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 11/12/2021] [Indexed: 11/02/2022]
Abstract
PURPOSE Breast cancer is increasing around the globe, including Asia. We aimed to examine the survival and risk of contralateral breast cancer (CBC) in Asian breast cancer patients with BRCA mutations. METHODS A total of 128 breast cancer patients with germline BRCA mutations and 4,754 control breast cancer patients were enrolled. Data on clinical-pathologic characteristics, survival, and CBC were collected from the medical record. The rates of survival and CBC were estimated by Kaplan-Meier method. RESULTS The mean age of onset in BRCA mutation carriers was significantly younger than control patients (BRCA vs. Non-BRCA: 43.9 vs. 53.2 years old). BRCA mutation carriers had a higher proportion of triple-negative breast cancer (TNBC) (52%) than control patients (12%, p < 0.001). The risk of CBC was significantly higher in BRCA mutation patients than in control cases (hazard ratio (HR) = 3.95, 95% CI 2.71-5.75); when stratified by genotype, the HRs (95%CI) were 4.84 (3.00-7.82) for BRCA1 and 3.13 (1.78-5.49) for BRCA2 carriers, respectively. Moreover, BRCA1 mutation patients with triple-negative breast cancer (TNBC) as their first breast cancer had the highest risk of CBC (HR = 5.55, 95% CI 3.29-9.34). However, we did not observe any differences in relapse-free survival and overall survival between mutation carriers and control patients. CONCLUSION Our study suggest that BRCA patients had a significantly higher risk of developing CBC, particularly for BRCA1 mutation carriers with TNBC as the first breast cancer.
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20
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Tran VT, Nguyen ST, Pham XD, Phan TH, Nguyen VC, Nguyen HT, Nguyen HP, Doan PTT, Le TA, Nguyen BT, Jasmine TX, Nguyen DS, Nguyen HDL, Nguyen NM, Do DX, Tran VU, Nguyen HHT, Le MP, Nguyen YN, Do TTT, Truong DK, Tang HS, Phan MD, Nguyen HN, Giang H, Tu LN. Pathogenic Variant Profile of Hereditary Cancer Syndromes in a Vietnamese Cohort. Front Oncol 2022; 11:789659. [PMID: 35070997 PMCID: PMC8767154 DOI: 10.3389/fonc.2021.789659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/09/2021] [Indexed: 12/30/2022] Open
Abstract
Background Hereditary cancer syndromes (HCS) are responsible for 5-10% of cancer cases. Genetic testing to identify pathogenic variants associated with cancer predisposition has not been routinely available in Vietnam. Consequently, the prevalence and genetic landscape of HCS remain unknown. Methods 1165 Vietnamese individuals enrolled in genetic testing at our laboratory in 2020. We performed analysis of germline mutations in 17 high- and moderate- penetrance genes associated with HCS by next generation sequencing. Results A total of 41 pathogenic variants in 11 genes were detected in 3.2% individuals. The carrier frequency was 4.2% in people with family or personal history of cancer and 2.6% in those without history. The percentage of mutation carriers for hereditary colorectal cancer syndromes was 1.3% and for hereditary breast and ovarian cancer syndrome was 1.6%. BRCA1 and BRCA2 mutations were the most prevalent with the positive rate of 1.3% in the general cohort and 5.1% in breast or ovarian cancer patients. Most of BRCA1 mutations located at the BRCA C-terminus domains and the top recurrent mutation was NM_007294.3:c.5251C>T (p.Arg1751Ter). One novel variant NM_000038.6(APC):c.6665C>A (p.Pro2222His) was found in a breast cancer patient with a strong family history of cancer. A case study of hereditary cancer syndrome was illustrated to highlight the importance of genetic testing. Conclusion This is the first largest analysis of carrier frequency and mutation spectrum of HCS in Vietnam. The findings demonstrate the clinical significance of multigene panel testing to identify carriers and their at-risk relatives for better cancer surveillance and management strategies.
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Affiliation(s)
| | - Sao Trung Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | - Huu Thinh Nguyen
- University Medical Center Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Huu Phuc Nguyen
- University Medical Center Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Phuong Thao Thi Doan
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | - Duy Sinh Nguyen
- Department of Oncology, Faculty of Medicine, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hong-Dang Luu Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Ngoc Mai Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Duy Xuan Do
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Vu Uyen Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hue Hanh Thi Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Minh Phong Le
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Yen Nhi Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | | | | | - Hung Sang Tang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Minh-Duy Phan
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hoai-Nghia Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Lan N Tu
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
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21
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Impacts of LOC105371267 Variants on Breast Cancer Susceptibility in Northern Chinese Han Females: A Population-Based Case-Control Study. JOURNAL OF ONCOLOGY 2021; 2021:4990695. [PMID: 34475952 PMCID: PMC8407995 DOI: 10.1155/2021/4990695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/18/2021] [Indexed: 11/21/2022]
Abstract
Background LOC105371267, also known as PR-lncRNA1, was reported to be a p53-regulated long noncoding RNA (lncRNA), which played an essential role in the pathogenesis of breast cancer (BC). We aimed to observe the potential association between LOC105371267 polymorphisms and BC risk in Northern Chinese Han females. Methods Totally, 555 healthy individuals and 561 patients with BC were recruited. Five candidate SNPs (rs6499221, rs3931698, rs8044565, rs3852740, and rs111577197) of LOC105371267 were genotyped with the Agena MassARRAY system. Odds ratio (OR) and 95% confidence intervals (CIs) were applied to evaluate the relationship of LOC105371267 genetic polymorphisms with BC susceptibility. Additionally, stratification analysis based on clinical features and haplotype analysis were also conducted. Finally, multifactor dimensionality reduction (MDR) analysis was performed to assess the SNP-SNP interaction among LOC105371267 variants, and false-positive report probability (FPRP) analysis was used to validate the result of this study. Results In this study, rs3931698 was a protective factor of BC in total (GG homozygote: OR = 0.30, 95% CI: 0.11–0.82, p=0.018; recessive model: OR = 0.30, 95% CI: 0.11–0.84, p=0.021). In stratification analysis based on the average age of 52 years and clinical characteristics (PR status, III-IV TNM stage), rs3931698 was also demonstrated to be associated with BC susceptibility. In addition, rs6499221 and rs3852740 were also associated with BC susceptibility among patients at age <52 years and patients with BC in a positive status. Thus, the haplotype analysis had a negative result for the incidence of BC (p > 0.05), and haplotype consisting of rs8044565 and rs111577197 was nonsignificantly associated with the BC risk. Finally, MDR and FPRP analyses also validated the result of this study. Conclusion Polymorphisms rs3931698, rs6499221, and rs3852740 of LOC105371267 were found to be associated with the risk of BC in total, and stratification analysis in the Northern Chinese Han females suggested that LOC105371267 variants might be helpful to predict BC progression.
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22
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Zhang L, Qin Z, Huang T, Tam B, Ruan Y, Guo M, Wu X, Li J, Zhao B, Chian JS, Wang X, Wang L, Wang SM. Prevalence and spectrum of DNA mismatch repair gene variation in the general Chinese population. J Med Genet 2021; 59:652-661. [PMID: 34172528 PMCID: PMC9252855 DOI: 10.1136/jmedgenet-2021-107886] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/06/2021] [Indexed: 01/18/2023]
Abstract
Background Identifying genetic disease-susceptible individuals through population screening is considered as a promising approach for disease prevention. DNA mismatch repair (MMR) genes including MLH1, MSH2, MSH6 and PMS2 play essential roles in maintaining microsatellite stability through DNA mismatch repair, and pathogenic variation in MMR genes causes microsatellite instability and is the genetic predisposition for cancer as represented by the Lynch syndrome. While the prevalence and spectrum of MMR variation has been extensively studied in cancer, it remains largely elusive in the general population. Lack of the knowledge prevents effective prevention for MMR variation–caused cancer. In the current study, we addressed the issue by using the Chinese population as a model. Methods We performed extensive data mining to collect MMR variant data from 18 844 ethnic Chinese individuals and comprehensive analyses for the collected MMR variants to determine its prevalence, spectrum and features of the MMR data in the Chinese population. Results We identified 17 687 distinct MMR variants. We observed substantial differences of MMR variation between the general Chinese population and Chinese patients with cancer, identified highly Chinese-specific MMR variation through comparing MMR data between Chinese and non-Chinese populations, predicted the enrichment of deleterious variants in the unclassified Chinese-specific MMR variants, determined MMR pathogenic prevalence of 0.18% in the general Chinese population and determined that MMR variation in the general Chinese population is evolutionarily neutral. Conclusion Our study provides a comprehensive view of MMR variation in the general Chinese population, a resource for biological study of human MMR variation, and a reference for MMR-related cancer applications.
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Affiliation(s)
- Li Zhang
- University of Macau, Taipa, Macau, China
| | - Zixin Qin
- University of Macau, Taipa, Macau, China
| | - Teng Huang
- University of Macau, Taipa, Macau, China
| | | | | | - Maoni Guo
- University of Macau, Taipa, Macau, China
| | | | - Jiaheng Li
- University of Macau, Taipa, Macau, China
| | - Bojin Zhao
- University of Macau, Taipa, Macau, China
| | | | | | - Lei Wang
- University of Macau, Taipa, Macau, China
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23
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Chian J, Sinha S, Qin Z, Wang SM. BRCA1 and BRCA2 Variation in Taiwanese General Population and the Cancer Cohort. Front Mol Biosci 2021; 8:685174. [PMID: 34235180 PMCID: PMC8256441 DOI: 10.3389/fmolb.2021.685174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/28/2021] [Indexed: 01/08/2023] Open
Abstract
BRCA1 and BRCA2 (BRCA) play essential roles in maintaining genome stability. Rapidly evolving human BRCA generates oncogenic variants causing high cancer risk. BRCA variation is ethnic-specific in reflecting adaptation and/or effects of genetic drift. Taiwanese population of 23.8 million is an admixture of multiple ethnic origins; Taiwan's subtropical and tropical climate and geographically islandic location provide a unique natural environment. Therefore, Taiwanese population provides a unique model to study human BRCA variation. Through collecting, standardizing, annotating, and classifying publicly available BRCA variants derived from Taiwanese general population and the cancer cohort, we identified 335 BRCA variants, of which 164 were from 1,517 non-cancer individuals, 126 from 2,665 cancer individuals, and 45 from both types of individuals. We compared the variant data with those from other ethnic populations such as mainland Chinese, Macau Chinese, Japanese, Korean, Indian, and non-Asians. We observed that the sharing rates with other Asian ethnic populations were correlated with its genetic relationship. Over 60% of the 335 Taiwanese BRCA variants were VUS, unclassified variants, or novel variants, reflecting the ethnic-specific features of Taiwanese BRCA variation. While it remains challenging to classify these variants, our structural and in silico analyses predicted their enrichment of BRCA deleterious variants. We further determined the 3.8% prevalence of BRCA pathogenic variants in the Taiwanese breast cancer cohort, and determined 0.53% prevalence of the BRCA pathogenic variants in Taiwanese general population, with the estimated 126,140 BRCA pathogenic variant carriers. We identified BRCA2 c.5164_5165delAG at BRCA2 BRC6 motif as a potential founder mutation in Taiwanese population. Our study on BRCA variation in Taiwanese and other East Asian populations demonstrates that ethnic specificity is a common phenomenon for BRCA variation in East Asian population; the data generated from the study provide a reference for clinical applications in BRCA-related cancer in Taiwanese population.
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Affiliation(s)
- Jiasheng Chian
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Siddharth Sinha
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Zixin Qin
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - San Ming Wang
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
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24
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Woodward ER, van Veen EM, Evans DG. From BRCA1 to Polygenic Risk Scores: Mutation-Associated Risks in Breast Cancer-Related Genes. Breast Care (Basel) 2021; 16:202-213. [PMID: 34248461 DOI: 10.1159/000515319] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
Background There has been huge progress over the last 30 years in identifying the familial component of breast cancer. Summary Currently around 20% is explained by the high-risk genes BRCA1 and BRCA2, a further 2% by other high-penetrance genes, and around 5% by the moderate risk genes ATM and CHEK2. In contrast, the more than 300 low-penetrance single-nucleotide polymorphisms (SNP) now account for around 28% and they are predicted to account for most of the remaining 45% yet to be found. Even for high-risk genes which confer a 40-90% risk of breast cancer, these SNP can substantially affect the level of breast cancer risk. Indeed, the strength of family history and hormonal and reproductive factors is very important in assessing risk even for a BRCA carrier. The risks of contralateral breast cancer are also affected by SNP as well as by the presence of high or moderate risk genes. Genetic testing using gene panels is now commonplace. Key-Messages There is a need for a more parsimonious approach to panels only testing those genes with a definite 2-fold increased risk and only testing those genes with challenging management implications, such as CDH1 and TP53, when there is strong clinical indication to do so. Testing of SNP alongside genes is likely to provide a more accurate risk assessment.
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Affiliation(s)
- Emma R Woodward
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Elke M van Veen
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom.,PREVENT Breast Cancer Prevention Centre, Nightingale Centre, Manchester Universities Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom.,Manchester Breast Centre, Manchester Cancer Research Centre, The Christie, University of Manchester, Manchester, United Kingdom
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25
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Qin Z, Kuok CN, Dong H, Jiang L, Zhang L, Guo M, Leong HK, Wang L, Meng G, Wang SM. Can population BRCA screening be applied in non-Ashkenazi Jewish populations? Experience in Macau population. J Med Genet 2020; 58:587-591. [DOI: 10.1136/jmedgenet-2020-107181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022]
Abstract
BackgroundPathogenic mutation in BRCA genes causes high cancer risk. Identifying the mutation carriers plays key roles in preventing BRCA mutation-related cancer. Population screening has demonstrated its power for comprehensive identification of the mutation carriers. However, it is only recommended for the Ashkenazi Jewish population with high prevalence of three founder mutations, but not for non-Ashkenazi Jewish populations as the cost-effectiveness could be too low due to their lower mutation prevalence and lack of founder mutation. Population screening would not benefit the majority of the human population for BRCA mutation-related cancer prevention.MethodsWe used population BRCA screening in 6000 residents, 1% of the Macau population, an ethnic Chinese population with unique genetic, linguistic and cultural features, and its BRCA mutation has not been analysed before.ResultsWe called BRCA variants, identified 18 carriers with 14 pathogenic mutations and determined the prevalence of 0.29% in the population (95% CI 0.15% to 0.42%). We compared the testing cost between the Ashkenazi Jewish population, the Sephardi Jewish population and the Macau population, and observed only a few fold differences.ConclusionOur study shows that testing cost is not the most important factor in considering population BRCA screening, at least for the populations in the developed countries/regions, regardless of the status of mutation prevalence and founder mutation.
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