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Ferreyra Y, Rosas G, Cock-Rada AM, Araujo J, Bravo L, Doimi F, Casas J, Clavo MDLÁ, Pinto JA, Belmar-López C. Landscape of germline BRCA1/BRCA2 variants in breast and ovarian cancer in Peru. Front Oncol 2023; 13:1227864. [PMID: 37664050 PMCID: PMC10470619 DOI: 10.3389/fonc.2023.1227864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/27/2023] [Indexed: 09/05/2023] Open
Abstract
Background There is an increasing amount of data from Latin America on the characterization of BRCA variants; however, there is limited information from Peru. We conducted a retrospective study to describe germline pathogenic/likely pathogenic(P/LP) variants and variants of uncertain/unknown significance (VUS) in the BRCA1 and BRCA2 genes in Peru, in patients with breast and ovarian cancer, candidates for treatment with poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitors. Methods The patients were evaluated during the period 2019-2021. Genomic DNA was isolated from peripheral blood samples and targeted sequencing was performed using the Ampliseq BRCA panel. Genetic variant interpretation was carried out in accordance with the recommendations of the American College of Medical Genetics and ClinVar. During this period, 525 patients (143 with breast cancer and 382 with ovarian cancer) were studied. Results We found that 14.7% (21/143) of breast cancer patients and 20.7% (79/382) of ovarian cancer patients were carriers of P/LP variants in BRCA1/2. The most frequent pathogenic variants detected in BRCA1 were c.2105dupT (BIC: 2224insT, n=12, 18.75%), c.68_69delAG (BIC: 185delAG, n=6, 9.38%), c.140G>T and c.815_824dupAGCCATGTGG (n=5, 7.81%), while in BRCA2 were c.8023A>G (n=6, 16.67%), c.6024dupG (BIC: 6252insG, n=4, 11.11%), and c.9235delG (BIC: 9463delG, n=3, 8.33%). Regarding VUS, we found that 6.99% (10/143) of breast cancer patients and 7.33% (28/382) of ovarian cancer patients were carriers of a VUS in BRCA1/2. For BRCA1, the most frequent VUS was c.93C>G (n=2), and for BRCA2, c.5465A>T (n=4), c.3101T>C (n=3), c.205C>A and c.437T>C (n=2). Conclusion We found a frequency of 14.7% germline mutations in breast cancer patients and 20.7% in ovarian cancer patients. The most recurrent mutations were BRCA1 c.2105dupT and BRCA2 c.8023A>G. We found that BRCA2 c.8023A>G, c.6024dupG, and c.9235delG were not previously reported in Peruvian patients. BRCA1 c.2344dupA is a novel mutation that has not been previously reported in any database. The frequency of VUS in our cohort was 7.2%.
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Affiliation(s)
- Yomali Ferreyra
- Departamento de Bioingeniería, Universidad de Ingenieria y Tecnología, Lima, Peru
| | - Gina Rosas
- Departamento de Patología, Insituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Alicia M. Cock-Rada
- Departmento de Oncología Médica, Instituto de Cancerología Las Américas - Auna, Medellín, Colombia
| | - Jhajaira Araujo
- Centro de Investigación Básicas y traslacional, Auna Ideas, Lima, Peru
| | - Leny Bravo
- Escuela Profesional de Medicina Humana-Filial Ica, Universidad Privada San Juan Bautista, Ica, Peru
| | | | | | | | - Joseph A. Pinto
- Centro de Investigación Básicas y traslacional, Auna Ideas, Lima, Peru
| | - Carolina Belmar-López
- Escuela Profesional de Medicina Humana-Filial Ica, Universidad Privada San Juan Bautista, Ica, Peru
- Oncogenomics, Auna, Lima, Peru
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Guo W, Ji Y, Guo L, Che S, Huai Q, Yang K, Tan F, Xue Q, Gao S, He J. Severe hypoglycemia and finger clubbing in a patient with a BRCA1 mutation in a solitary fibrous tumor: a case report. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1093. [PMID: 34423005 PMCID: PMC8339833 DOI: 10.21037/atm-21-914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/31/2021] [Indexed: 12/17/2022]
Abstract
Solitary fibrous tumors (SFTs) are rare tumors that stem from mesenchymal cells of submesothelial tissues belonging to the pleura. They can occur in many places such as the spinal canal, intracranial, neck, kidney, liver, pelvis, limbs and other places, most commonly in the chest and abdomen. Pleural SFTs are one of the most common types, and are common in middle-aged people. Pleural SFTs can have an insidious expression, such that the illness can progress for years before diagnosis. SFTs can induce paraneoplastic syndromes, such as reactive hypoglycemia [Doege-Potter syndrome (DPS)] or hypertrophic osteoarthropathy [Pierre-Marie-Bamberger syndrome (PMBS)]. In this article, we report a case study of a 51-year-old man with pleural SFTs. Preoperative imaging examinations, including chest X-ray, computed tomography (CT), and magnetic resonance imaging (MRI), showed a huge mass in the right thoracic cavity, compressing surrounding tissues and organs and may invade other tissues. In addition, he suffers from severe hypoglycemia and finger clubbing, and has successfully undergone a complete resection, and now attends regular follow-up appointments. The paraneoplastic syndromes have resolved, and no recurrence has been found. Importantly, we used next-generation sequencing (NGS) to explore the molecular characteristics of the patient’s pathological tissue at the DNA level and mRNA level, and found that breast cancer gene 1 (BRAC1) mutations may be an important pathogenic factor.
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Affiliation(s)
- Wei Guo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Ji
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shunan Che
- Department of Radiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qilin Huai
- Department of Graduate School, Zunyi Medical University, Zunyi, China
| | - Kun Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fengwei Tan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Xue
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Malhotra H, Kowtal P, Mehra N, Pramank R, Sarin R, Rajkumar T, Gupta S, Bapna A, Bhattacharyya GS, Gupta S, Maheshwari A, Mannan AU, Reddy Kundur R, Sekhon R, Singhal M, Smruti B, SP S, Suryavanshi M, Verma A. Genetic Counseling, Testing, and Management of HBOC in India: An Expert Consensus Document from Indian Society of Medical and Pediatric Oncology. JCO Glob Oncol 2020; 6:991-1008. [PMID: 32628584 PMCID: PMC7392772 DOI: 10.1200/jgo.19.00381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Hereditary breast and ovarian cancer (HBOC) syndrome is primarily characterized by mutations in the BRCA1/2 genes. There are several barriers to the implementation of genetic testing and counseling in India that may affect clinical decisions. These consensus recommendations were therefore convened as a collaborative effort to improve testing and management of HBOC in India. DESIGN Recommendations were developed by a multidisciplinary group of experts from the Indian Society of Medical and Pediatric Oncology and some invited experts on the basis of graded evidence from the literature and using a formal Delphi process to help reach consensus. PubMed and Google Scholar databases were searched to source relevant articles. RESULTS This consensus statement provides practical insight into identifying patients who should undergo genetic counseling and testing on the basis of assessments of family and ancestry and personal history of HBOC. It discusses the need and significance of genetic counselors and medical professionals who have the necessary expertise in genetic counseling and testing. Recommendations elucidate requirements of pretest counseling, including discussions on genetic variants of uncertain significance and risk reduction options. The group of experts recommended single-site mutation testing in families with a known mutation and next-generation sequencing coupled with multiplex ligation probe amplification for the detection of large genomic rearrangements for unknown mutations. Recommendations for surgical and lifestyle-related risk reduction approaches and management using poly (ADP-ribose) polymerase inhibitors are also detailed. CONCLUSION With rapid strides being made in the field of genetic testing/counseling in India, more oncologists are expected to include genetic testing/counseling as part of their clinical practice. These consensus recommendations are anticipated to help homogenize genetic testing and management of HBOC in India for improved patient care.
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Affiliation(s)
- Hemant Malhotra
- Department of Medical Oncology, Sri Ram Cancer Center, Mahatma Gandhi Medical College Hospital, Jaipur, India
| | - Pradnya Kowtal
- Sarin Laboratory and OIC Sanger Sequencing Facility, Advanced Centre for Treatment Research, and Education in Cancer, Navi Mumbai, India
| | - Nikita Mehra
- Department of Medical Oncology, Cancer Institute (WIA), Chennai, India
| | - Raja Pramank
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Rajiv Sarin
- Radiation Oncology, Cancer Genetics Unit, Tata Memorial Centre and PI Sarin Laboratory, Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
| | | | - Sudeep Gupta
- Tata Memorial Centre Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, India
| | - Ajay Bapna
- Department of Medical Oncology, Bhagwan Mahavir Cancer Hospital Research Center, Jaipur, India
| | | | - Sabhyata Gupta
- Department of Gynae Oncology, Medanta-The Medicity, Gurgaon, India
| | - Amita Maheshwari
- Department of Gynecologic Oncology, Tata Memorial Centre, Mumbai, India
| | - Ashraf U. Mannan
- Clinical Diagnostics, Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | | | - Rupinder Sekhon
- Gynae Oncology, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | | | - B.K. Smruti
- Bombay Hospital and Medical Research Centre, Mumbai, India
| | - Somashekhar SP
- Manipal Comprehensive Cancer Center, Manipal Hospital, Bengaluru, India
| | - Moushumi Suryavanshi
- Molecular Diagnostics, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Amit Verma
- Molecular Oncology and Cancer Genetics, Max Hospital, New Delhi, India
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Ow SGW, Ong PY, Lee SC. Discoveries beyond BRCA1/2: Multigene testing in an Asian multi-ethnic cohort suspected of hereditary breast cancer syndrome in the real world. PLoS One 2019; 14:e0213746. [PMID: 30875412 PMCID: PMC6420039 DOI: 10.1371/journal.pone.0213746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 02/27/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Due to historically low uptake of genetic testing, the mutational spectrum of Asians with Hereditary Breast Cancer (HBC) is not well understood. This study sought to understand the incidence and spectrum of germline mutations in Asian patients with suspected HBC in a clinic setting. METHODS 1056 patients with suspected HBC were seen in our Cancer (CA) Genetics Clinic from 2000-2017, of which 460 underwent genetic testing. RESULTS Of 460 probands tested, 93% were female, 61% Chinese, 90% had prior CA, with 19% (77/414) having ≥2 primary CA. Median age at CA-diagnosis was 43y (17-83); 70% had Breast CA (BC) and 25% Ovarian CA (OC). 34% had young-onset BC, 8% bilateral BC, and 4% BC/OC. Majority had family history of BC (53%) or OC (20%). 57% underwent multigene testing (14-49 genes), 34% targeted testing, and 8% predictive testing. 30% were found to have a pathogenic mutation: 80% in BRCA1/2 (8 novel mutations noted). Of 33 non-BRCA1/2 pathogenic mutations detected, 61% were in 11 BC genes while 39% were in non-BC genes suggestive of alternative CA syndromes. Testing beyond BRCA1/2 impacted management for 15.9% (22/138) of carriers, but extensive testing identified variants of uncertain significance (VUS) in up to 44.5% of probands. Restricting multigene panel testing to a guideline-based 20-gene panel including Lynch Syndrome genes was found to be most optimal, detecting 94.6% of mutation carriers while reducing VUS rate to 21.5%. CONCLUSIONS Evolution of CA Genetics testing strategy to a multigene approach facilitated detection of pathogenic mutations in non-BRCA1/2 genes and aided management. Guideline-based panel testing is feasible and can be offered in Asians with suspected HBC.
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Affiliation(s)
- Samuel Guan Wei Ow
- Department of Hematology-Oncology, National University Cancer Institute, Singapore, Singapore
| | - Pei Yi Ong
- Department of Hematology-Oncology, National University Cancer Institute, Singapore, Singapore
| | - Soo-Chin Lee
- Department of Hematology-Oncology, National University Cancer Institute, Singapore, Singapore
- Cancer Science Institute, National University of Singapore, Singapore, Singapore
- * E-mail:
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Abbas S, Siddique A, Shahid N, Khan RT, Fatima W. Breast cancer risk associated with BRCA1/2 variants in the Pakistani population. Breast Cancer 2018; 26:365-372. [PMID: 30430339 DOI: 10.1007/s12282-018-0932-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/04/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Majority of the BRCA1 and BRCA2 mutations are associated with the risk of sporadic and familial breast cancer. Since these genes are significant in DNA repair mechanisms, we focused homology-directed DNA repair (HDDR) and BRCA complex. METHODS We selected BRCA1 variant (rs80356932, 4491C/T) and BRCA2 variant (rs80359182, 319T/C) from the interaction region of BRCA complex and studied in 100 breast cancer patients and 100 controls using tetra-ARMS-PCR. RESULTS Here we show that BRCA1 and BRCA2 variants are significantly associated with high breast cancer risk (BRCA1 rs80356932; Genotype T/T OR 8.66, 95% CI 3.16-23.71, p < 0.0001; Allele-T, OR 2.48, 95% CI 1.62-3.81, p < 0.0001 and BRCA2 rs80359182; Genotype C/C OR 4.32, 95% CI 1.95-9.53, p = 0.0001; Allele-C, OR 2.19, 95% CI 1.43-3.34, p = 0.0002). Additionally, bioinformatics analysis showed that BRCA2-tryptophan > arginine substitutions result in altered interaction of BRCA1/PALB2/BRCA2/protein complex and impaired HDDR pathway. We also observed that breast cancer risk was significantly increased in over-weighted and obese women. CONCLUSIONS Our results indicate that high risk of breast cancer is significantly associated with BRCA1 and BRCA2 variants, and mutations may alter the protein interactions of BRCA complex that results in tumor genesis.
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Affiliation(s)
- Saba Abbas
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-azam Campus, Lahore, Pakistan
| | - Ayesha Siddique
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-azam Campus, Lahore, Pakistan.
| | - Naeem Shahid
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari Campus, Pakistan
| | - Rabbia Tariq Khan
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-azam Campus, Lahore, Pakistan
| | - Warda Fatima
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-azam Campus, Lahore, Pakistan.
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Wang T, Wang H, Yang S, Guo H, Zhang B, Guo H, Wang L, Zhu G, Zhang Y, Zhou H, Zhang X, Li H, Su H. Association of APEX1 and OGG1 gene polymorphisms with breast cancer risk among Han women in the Gansu Province of China. BMC MEDICAL GENETICS 2018; 19:67. [PMID: 29720094 PMCID: PMC5930440 DOI: 10.1186/s12881-018-0578-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 04/18/2018] [Indexed: 11/17/2022]
Abstract
Background Genetic variations in key DNA repair genes may influence DNA repair capacity, DNA damage and breast carcinogenesis. The current study aimed to estimate the association of APEX1 and OGG1 polymorphisms with the risk of breast cancer development. Methods A total of 518 patients with histopathologically confirmed breast cancer and 921 region- and age-matched cancer-free controls were genotyped for the APEX1 polymorphisms rs3136817 and rs1130409 and the OGG1 polymorphisms rs1052133 and rs2072668 using a QuantStudio™ 12 K Flex Real-Time PCR System. Results The rs3136817 heterozygous TC genotype along with the rs3136817 dominant model (TC + CC) was strongly associated with breast cancer susceptibility (odds ratio [OR] = 0.670, 95% confidence interval [95% CI]: 0.513 - 0.873, P = 0.003; OR = 0.682, 95% CI: 0.526 - 0.883, P = 0.004, respectively). No significant associations were observed among rs1130409, rs1052133, rs2072668 and breast cancer risk. Furthermore, an allele combination analysis revealed that APEX1 haplotypes containing C-T (alleles rs3136817 and rs1130409) conferred a significantly lower risk (corrected P < 0.001). Conclusion This research is the latest report showing that an APEX1 rs3136817 heterozygous genotype may have a positive influence on DNA repair capacity in patients with breast cancer and thus may have a potential protective effect for Chinese Han women. Electronic supplementary material The online version of this article (10.1186/s12881-018-0578-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tao Wang
- Research Center of Translational Medicine, Gansu Provincial Academic Institute for Medical Research, NO. 2 Xiaoxihu East Street, Lanzhou, Gansu, 730050, People's Republic of China
| | - Haitao Wang
- Research Center of Translational Medicine, Gansu Provincial Academic Institute for Medical Research, NO. 2 Xiaoxihu East Street, Lanzhou, Gansu, 730050, People's Republic of China
| | - Suisheng Yang
- Department of Breast Surgery, Gansu Provincial Cancer Hospital, Lanzhou, Gansu, 730050, People's Republic of China
| | - Hongyun Guo
- Research Center of Translational Medicine, Gansu Provincial Academic Institute for Medical Research, NO. 2 Xiaoxihu East Street, Lanzhou, Gansu, 730050, People's Republic of China
| | - Binming Zhang
- Department of Breast Surgery, Gansu Provincial Cancer Hospital, Lanzhou, Gansu, 730050, People's Republic of China
| | - Huan Guo
- Research Center of Translational Medicine, Gansu Provincial Academic Institute for Medical Research, NO. 2 Xiaoxihu East Street, Lanzhou, Gansu, 730050, People's Republic of China
| | - Lan Wang
- Research Center of Translational Medicine, Gansu Provincial Academic Institute for Medical Research, NO. 2 Xiaoxihu East Street, Lanzhou, Gansu, 730050, People's Republic of China
| | - Gongjian Zhu
- Research Center of Translational Medicine, Gansu Provincial Academic Institute for Medical Research, NO. 2 Xiaoxihu East Street, Lanzhou, Gansu, 730050, People's Republic of China
| | - Yongdong Zhang
- Research Center of Translational Medicine, Gansu Provincial Academic Institute for Medical Research, NO. 2 Xiaoxihu East Street, Lanzhou, Gansu, 730050, People's Republic of China
| | - Haihong Zhou
- Research Center of Translational Medicine, Gansu Provincial Academic Institute for Medical Research, NO. 2 Xiaoxihu East Street, Lanzhou, Gansu, 730050, People's Republic of China
| | - Xiuli Zhang
- Research Center of Translational Medicine, Gansu Provincial Academic Institute for Medical Research, NO. 2 Xiaoxihu East Street, Lanzhou, Gansu, 730050, People's Republic of China
| | - Haining Li
- Research Center of Translational Medicine, Gansu Provincial Academic Institute for Medical Research, NO. 2 Xiaoxihu East Street, Lanzhou, Gansu, 730050, People's Republic of China
| | - Haixiang Su
- Research Center of Translational Medicine, Gansu Provincial Academic Institute for Medical Research, NO. 2 Xiaoxihu East Street, Lanzhou, Gansu, 730050, People's Republic of China.
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Lai KN, Ho WK, Kang IN, Kang PCE, Phuah SY, Mariapun S, Yip CH, Mohd Taib NA, Teo SH. Characterization of BRCA1 and BRCA2 variants in multi-ethnic Asian cohort from a Malaysian case-control study. BMC Cancer 2017; 17:149. [PMID: 28222693 PMCID: PMC5320733 DOI: 10.1186/s12885-017-3099-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/31/2017] [Indexed: 11/18/2022] Open
Abstract
Background Genetic testing for BRCA1 and BRCA2 has led to the accurate identification of individuals at higher risk of cancer and the development of new therapies. Approximately 10-20% of the genetic testing for BRCA1 and BRCA2 leads to the identification of variants of uncertain significance (VUS), with higher proportions in Asians. We investigated the functional significance of 7 BRCA1 and 25 BRCA2 variants in a multi-ethnic Asian cohort using a case-control approach. Methods The MassARRAY genotyping was conducted in 1,394 Chinese, 406 Malay and 310 Indian breast cancer cases and 1,071 Chinese, 167 Malay and 255 Indian healthy controls. The association of individual variant with breast cancer risk was analyzed using logistic regression model adjusted for ethnicity, age and family history. Results Our study confirmed BRCA2 p.Ile3412Val is presented in >2% of unaffected women and is likely benign, and BRCA2 p.Ala1996Thr which is predicted to be likely pathogenic by in-silico models is presented in 2% of healthy Indian women suggesting that it may not be associated with breast cancer risk. Single-variant analysis suggests that BRCA1 p.Arg762Ser may be associated with breast cancer risk (OR = 7.4; 95% CI, 0.9–62.3; p = 0.06). Conclusions Our study shows that BRCA2 p.Ile3412Val and p.Ala1996Thr are likely benign and highlights the need for population-specific studies to determine the likely functional significance of population-specific variants. Our study also suggests that BRCA1 p.Arg762Ser may be associated with increased risk of breast cancer but other methods or larger studies are required to determine a more precise estimate of breast cancer risk. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3099-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kah Nyin Lai
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Weang Kee Ho
- Department of Applied Mathematics, Faculty of Engineering, The University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor, Malaysia
| | - In Nee Kang
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Peter Choon Eng Kang
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Sze Yee Phuah
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Shivaani Mariapun
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Cheng-Har Yip
- Subang Jaya Medical Centre, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Nur Aishah Mohd Taib
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, 50603, Kuala Lumpur, Malaysia.,Department of Surgery, Faculty of Medicine, University Malaya Medical Centre, 50603, Kuala Lumpur, Malaysia
| | - Soo-Hwang Teo
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia. .,Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, 50603, Kuala Lumpur, Malaysia. .,Department of Surgery, Faculty of Medicine, University Malaya Medical Centre, 50603, Kuala Lumpur, Malaysia.
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8
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Kang HP, Maguire JR, Chu CS, Haque IS, Lai H, Mar-Heyming R, Ready K, Vysotskaia VS, Evans EA. Design and validation of a next generation sequencing assay for hereditary BRCA1 and BRCA2 mutation testing. PeerJ 2016; 4:e2162. [PMID: 27375968 PMCID: PMC4928470 DOI: 10.7717/peerj.2162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 06/01/2016] [Indexed: 12/02/2022] Open
Abstract
Hereditary breast and ovarian cancer syndrome, caused by a germline pathogenic variant in the BRCA1 or BRCA2 (BRCA1/2) genes, is characterized by an increased risk for breast, ovarian, pancreatic and other cancers. Identification of those who have a BRCA1/2 mutation is important so that they can take advantage of genetic counseling, screening, and potentially life-saving prevention strategies. We describe the design and analytic validation of the Counsyl Inherited Cancer Screen, a next-generation-sequencing-based test to detect pathogenic variation in the BRCA1 and BRCA2 genes. We demonstrate that the test is capable of detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy-number variants (CNVs, also known as large rearrangements) with zero errors over a 114-sample validation set consisting of samples from cell lines and deidentified patient samples, including 36 samples with BRCA1/2pathogenic germline mutations.
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Affiliation(s)
| | | | - Clement S Chu
- Counsyl Inc. , South San Francisco , CA , United States
| | - Imran S Haque
- Counsyl Inc. , South San Francisco , CA , United States
| | - Henry Lai
- Counsyl Inc. , South San Francisco , CA , United States
| | | | - Kaylene Ready
- Counsyl Inc. , South San Francisco , CA , United States
| | | | - Eric A Evans
- Counsyl Inc. , South San Francisco , CA , United States
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9
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Ng PS, Wen WX, Fadlullah MZH, Yoon SY, Lee SY, Thong MK, Yip CH, Mohd Taib NA, Teo SH. Identification of germline alterations in breast cancer predisposition genes among Malaysian breast cancer patients using panel testing. Clin Genet 2016; 90:315-23. [PMID: 26757417 DOI: 10.1111/cge.12735] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 12/23/2022]
Abstract
Although an association between protein-truncating variants and breast cancer risk has been established for 11 genes, only alterations in BRCA1, BRCA2, TP53 and PALB2 have been reported in Asian populations. Given that the age of onset of breast cancer is lower in Asians, it is estimated that inherited predisposition to breast cancer may be more significant. To determine the potential utility of panel testing, we investigated the prevalence of germline alterations in 11 established and 4 likely breast cancer genes in a cross-sectional hospital-based cohort of 108 moderate to high-risk breast cancer patients using targeted next generation sequencing. Twenty patients (19%) were identified to carry deleterious mutations, of whom 13 (12%) were in the BRCA1 or BRCA2, 6 (6%) were in five other known breast cancer predisposition genes and 1 patient had a mutation in both BRCA2 and BARD1. Our study shows that BRCA1 and BRCA2 account for the majority of genetic predisposition to breast cancer in our cohort of Asian women. Although mutations in other known breast cancer genes are found, the functional significance and breast cancer risk have not yet been determined, thus limiting the clinical utility of panel testing in Asian populations.
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Affiliation(s)
- P S Ng
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia.,University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - W X Wen
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia.,University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | | | - S Y Yoon
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - S Y Lee
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - M K Thong
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - C H Yip
- Subang Jaya Medical Centre, Subang Jaya, Selangor, Malaysia
| | - N A Mohd Taib
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia.,Department of Surgery, Faculty of Medicine, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - S H Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia. .,University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia. .,Department of Surgery, Faculty of Medicine, University Malaya Medical Centre, Kuala Lumpur, Malaysia.
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Abstract
Purpose The National Comprehensive Cancer Network (NCCN) has proposed guidelines for the genetic testing of the BRCA1 and BRCA2 genes, based on studies in western populations. This current study assessed potential predictive factors for BRCA mutation probability, in an Asian population. Methods A total of 359 breast cancer patients, who presented with either a family history (FH) of breast and/or ovarian cancer or early onset breast cancer, were accrued at the National Cancer Center Singapore (NCCS). The relationships between clinico-pathological features and mutational status were calculated using the Chi-squared test and binary logistic regression analysis. Results Of 359 patients, 45 (12.5%) had deleterious or damaging missense mutations in BRCA1 and/or BRCA2. BRCA1 mutations were more likely to be found in ER-negative than ER-positive breast cancer patients (P=0.01). Moreover, ER-negative patients with BRCA mutations were diagnosed at an earlier age (40 vs. 48 years, P=0.008). Similarly, triple-negative breast cancer (TNBC) patients were more likely to have BRCA1 mutations (P=0.001) and that these patients were diagnosed at a relatively younger age than non-TNBC patients (38 vs. 46 years, P=0.028). Our analysis has confirmed that ER-negative status, TNBC status and a FH of hereditary breast and ovarian cancer (HBOC) are strong factors predicting the likelihood of having BRCA mutations. Conclusions Our study provides evidence that TNBC or ER-negative patients may benefit from BRCA genetic testing, particularly younger patients (<40 years) or those with a strong FH of HBOC, in Asian patients.
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11
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Mohamad S, Isa NM, Muhammad R, Emran NA, Kitan NM, Kang P, Kang IN, Taib NAM, Teo SH, Akmal SN. Low prevalence of CHEK2 gene mutations in multiethnic cohorts of breast cancer patients in Malaysia. PLoS One 2015; 10:e0117104. [PMID: 25629968 PMCID: PMC4309602 DOI: 10.1371/journal.pone.0117104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/18/2014] [Indexed: 12/20/2022] Open
Abstract
CHEK2 is a protein kinase that is involved in cell-cycle checkpoint control after DNA damage. Germline mutations in CHEK2 gene have been associated with increase in breast cancer risk. The aim of this study is to identify the CHEK2 gene germline mutations among high-risk breast cancer patients and its contribution to the multiethnic population in Malaysia. We screened the entire coding region of CHEK2 gene on 59 high-risk breast cancer patients who tested negative for BRCA1/2 germline mutations from UKM Medical Centre (UKMMC), Hospital Kuala Lumpur (HKL) and Hospital Putrajaya (HPJ). Sequence variants identified were screened further in case-control cohorts consisting of 878 unselected invasive breast cancer patients (180 Malays, 526 Chinese and 172 Indian) and 270 healthy individuals (90 Malays, 90 Chinese and 90 Indian). By screening the entire coding region of the CHEK2 gene, two missense mutations, c.480A>G (p.I160M) and c.538C>T (p.R180C) were identified in two unrelated patients (3.4%). Further screening of these missense mutations on the case-control cohorts unveiled the variant p.I160M in 2/172 (1.1%) Indian cases and 1/90 (1.1%) Indian control, variant p.R180C in 2/526 (0.38%) Chinese cases and 0/90 Chinese control, and in 2/180 (1.1%) of Malay cases and 1/90 (1.1%) of Malay control. The results of this study suggest that CHEK2 mutations are rare among high-risk breast cancer patients and may play a minor contributing role in breast carcinogenesis among Malaysian population.
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Affiliation(s)
- Suriati Mohamad
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Cheras, Kuala Lumpur, Malaysia
| | - Nurismah Md Isa
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Cheras, Kuala Lumpur, Malaysia
| | - Rohaizak Muhammad
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Cheras, Kuala Lumpur, Malaysia
| | - Nor Aina Emran
- Department of General Surgery, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Nor Mayah Kitan
- Department of Endocrine Surgery, Hospital Putrajaya, Putrajaya, Malaysia
| | - Peter Kang
- Cancer Research Initiative Foundation (CARIF), Subang Jaya, Selangor, Malaysia
| | - In Nee Kang
- Cancer Research Initiative Foundation (CARIF), Subang Jaya, Selangor, Malaysia
| | - Nur Aishah Mohd Taib
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Soo Hwang Teo
- Cancer Research Initiative Foundation (CARIF), Subang Jaya, Selangor, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Sharifah Noor Akmal
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Cheras, Kuala Lumpur, Malaysia
- * E-mail:
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