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Singh S, Sharma S, Baranwal M. Identification of SNPs in hMSH3/MSH6 interaction domain affecting the structure and function of MSH2 protein. Biotechnol Appl Biochem 2022; 69:2454-2465. [PMID: 34837403 DOI: 10.1002/bab.2295] [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: 05/24/2021] [Accepted: 11/23/2021] [Indexed: 12/27/2022]
Abstract
MutS homolog 2 (MSH2) is a mismatch repair gene that plays a critical role in DNA repair pathways, and its mutations are associated with different cancers. The present study aimed to find out the single nucleotide polymorphisms (SNPs) of MSH2 protein associated with causing structural and functional changes leading to the development of cancer with the help of computational tools. Four different tools for predicting deleterious SNPs (SIFT, PROVEAN, PANTHER, and PolyPhen), two tools each for identifying disease association (PhD-SNP and SNP&GO) and estimating stability (I-mutant and MUPro) were employed. Homology modeling, energy minimization, and root mean square deviation calculation were used to estimate structural variations. Twenty-seven SNPs and five SNPs (double amino acid change) were identified based on a consensus approach that might be associated with the structural and functional change in MSH2 protein. Molecular docking reveals that six SNPs affect the interaction of MSH2 and MSH6. Twelve identified SNPs were reported to be linked with hereditary nonpolyposis, colorectal cancer, and Lynch syndrome. Further, selected SNPs need to be validated in an in vitro system for their precise association with cancer predisposition.
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Affiliation(s)
- Sidhartha Singh
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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Jalkh N, Chouery E, Haidar Z, Khater C, Atallah D, Ali H, Marafie MJ, Al-Mulla MR, Al-Mulla F, Megarbane A. Next-generation sequencing in familial breast cancer patients from Lebanon. BMC Med Genomics 2017; 10:8. [PMID: 28202063 PMCID: PMC5312584 DOI: 10.1186/s12920-017-0244-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 02/02/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Familial breast cancer (BC) represents 5 to 10% of all BC cases. Mutations in two high susceptibility BRCA1 and BRCA2 genes explain 16-40% of familial BC, while other high, moderate and low susceptibility genes explain up to 20% more of BC families. The Lebanese reported prevalence of BRCA1 and BRCA2 deleterious mutations (5.6% and 12.5%) were lower than those reported in the literature. METHODS In the presented study, 45 Lebanese patients with a reported family history of BC were tested using Whole Exome Sequencing (WES) technique followed by Sanger sequencing validation. RESULTS Nineteen pathogenic mutations were identified in this study. These 19 mutations were found in 13 different genes such as: ABCC12, APC, ATM, BRCA1, BRCA2, CDH1, ERCC6, MSH2, POLH, PRF1, SLX4, STK11 and TP53. CONCLUSIONS In this first application of WES on BC in Lebanon, we detected six BRCA1 and BRCA2 deleterious mutations in seven patients, with a total prevalence of 15.5%, a figure that is lower than those reported in the Western literature. The p.C44F mutation in the BRCA1 gene appeared twice in this study, suggesting a founder effect. Importantly, the overall mutation prevalence was equal to 40%, justifying the urgent need to deploy WES for the identification of genetic variants responsible for familial BC in the Lebanese population.
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Affiliation(s)
- Nadine Jalkh
- Unité de Génétique Médicale, Pôle Technologie Santé, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Eliane Chouery
- Unité de Génétique Médicale, Pôle Technologie Santé, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Zahraa Haidar
- Unité de Génétique Médicale, Pôle Technologie Santé, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | | | - David Atallah
- Department of Gynecology and Obstetrics, Hôtel-Dieu de France University Hospital, Saint Joseph University, Beirut, Lebanon
| | - Hamad Ali
- Department of Medical Laboratory Sciences (MLS), Faculty of Allied Health Sciences, Health Sciences Center (HSC), Kuwait University, Safat, Kuwait.,Dasman Diabetes Institute (DDI), P.O Box 1180, Dasman, 15462, Kuwait
| | - Makia J Marafie
- Kuwait Medical Genetics Center, Maternity Hospital, Safat, Kuwait
| | - Mohamed R Al-Mulla
- Department of Computing Sciences and Engineering, Kuwait University, P.O. Box 5969, Safat, 13060, Kuwait
| | - Fahd Al-Mulla
- Dasman Diabetes Institute (DDI), P.O Box 1180, Dasman, 15462, Kuwait. .,Health Sciences Center, Faculty of Medicine, Department of Pathology, Kuwait University, P.O.Box 24923, Safat, 13110, Kuwait.
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Wang P, Wang X, Fang M, Vander Weele TJ. Factors influencing the decision to participate in medical premarital examinations in Hubei Province, Mid-China. BMC Public Health 2013; 13:217. [PMID: 23497086 PMCID: PMC3606626 DOI: 10.1186/1471-2458-13-217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 11/21/2012] [Indexed: 11/24/2022] Open
Abstract
Background To investigate the attitudes of premarital couples towards the premarital screening program after the abolition of compulsory screening in China and to study the factors influencing participation. Methods Between July 1st 2010 to August 31st 2010, 650 people who registered for marriage at the civil affairs bureau of Wuhan, Suizhou, Zaoyang in Hubei province were studied using questionnaires. Logistic regression was used to examine the factors influencing participation in the premarital screening program. Results The premarital screening rate was 34.8% (95% Confidence Interval: 31.0% to 38.5%). Several demographic factors (age, residence, profession), awareness, knowledge, and attitudes towards premarital screening all had significant influence on participation in the premarital screening program. Conclusions Promotion activities and health education to improve knowledge and attitudes to premarital screening will help increase the rate of voluntary premarital screening.
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Affiliation(s)
- Peigang Wang
- School of public health, Wuhan University, Wuhan 430071, China
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Patrinos GP, Smith TD, Howard H, Al-Mulla F, Chouchane L, Hadjisavvas A, Hamed SA, Li XT, Marafie M, Ramesar RS, Ramos FJ, de Ravel T, El-Ruby MO, Shrestha TR, Sobrido MJ, Tadmouri G, Witsch-Baumgartner M, Zilfalil BA, Auerbach AD, Carpenter K, Cutting GR, Dung VC, Grody W, Hasler J, Jorde L, Kaput J, Macek M, Matsubara Y, Padilla C, Robinson H, Rojas-Martinez A, Taylor GR, Vihinen M, Weber T, Burn J, Qi M, Cotton RGH, Rimoin D. Human Variome Project country nodes: documenting genetic information within a country. Hum Mutat 2012; 33:1513-9. [PMID: 22753370 DOI: 10.1002/humu.22147] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 06/04/2012] [Indexed: 11/09/2022]
Abstract
The Human Variome Project (http://www.humanvariomeproject.org) is an international effort aiming to systematically collect and share information on all human genetic variation. The two main pillars of this effort are gene/disease-specific databases and a network of Human Variome Project Country Nodes. The latter are nationwide efforts to document the genomic variation reported within a specific population. The development and successful operation of the Human Variome Project Country Nodes are of utmost importance to the success of Human Variome Project's aims and goals because they not only allow the genetic burden of disease to be quantified in different countries, but also provide diagnosticians and researchers access to an up-to-date resource that will assist them in their daily clinical practice and biomedical research, respectively. Here, we report the discussions and recommendations that resulted from the inaugural meeting of the International Confederation of Countries Advisory Council, held on 12th December 2011, during the 2011 Human Variome Project Beijing Meeting. We discuss the steps necessary to maximize the impact of the Country Node effort for developing regional and country-specific clinical genetics resources and summarize a few well-coordinated genetic data collection initiatives that would serve as paradigms for similar projects.
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Affiliation(s)
- George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.
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WEI WENQIAN, LIU LEI, CHEN JIAN, JIN KE, JIANG FAN, LIU FANGQI, FAN RONG, CHENG ZHE, SHEN MENG, XUE CHENYI, CAI SANJUN, XU YE, NAN PENG. RACIAL DIFFERENCES IN MLH1 AND MSH2 MUTATION: AN ANALYSIS OF YELLOW RACE AND WHITE RACE BASED ON THE INSIGHT DATABASE. J Bioinform Comput Biol 2011; 8 Suppl 1:111-25. [DOI: 10.1142/s0219720010005154] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 08/25/2010] [Accepted: 09/10/2010] [Indexed: 11/18/2022]
Abstract
MLH1 and MSH2 mutations underlie 90% of hereditary nonpolyposis colorectal cancer (HNPCC) mutations. The International Society of Gastrointestinal Hereditary Tumors (InSiGHT) has established an international database of mutations associated with HNPCC. Based on the InSiGHT database and the original references that reported the mutations, we analyzed the distributions of MLH1 and MSH2 mutations in yellow race and white race respectively and compared them subsequently. We found: (1) the distributions of mutation individuals in exon 1, 17 and 19 of MLH1 gene and in exon 2 of MSH2 gene showed significant differences between the two race groups (p < 0.05); (2) the distributions of mutation types in exon 2, 7 and 18 of MLH1 and exon 10 and 16 of MSH2 showed significant differences (p < 0.05); and (3) three mutations (c.649C > T, c.1625A > T and c.1721T > C) in MLH1 and five mutations (c.23C > T, c.187dupG, c.505A > G, c.1168C > T and c.2211-6T > C) in MSH2 have much higher frequency in yellow race than those in white race. Furthermore, three mutations (c.1453G > C, c.1742C > T and c.1758dupC) in MLH1 and two mutations (c.1255C > A and c.1886A > G) in MSH2 were only found in yellow race, which implies that specific mutations in yellow race need more attention when screening mutations in these two genes.
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Affiliation(s)
- WENQIAN WEI
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, P. R. China
| | - LEI LIU
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, P. R. China
- The Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, P. R. China
| | - JIAN CHEN
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, P. R. China
| | - KE JIN
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, P. R. China
| | - FAN JIANG
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, P. R. China
| | - FANGQI LIU
- Shanghai Cancer Hospital of Fudan University, Shanghai 200032, P. R. China
| | - RONG FAN
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, P. R. China
| | - ZHE CHENG
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, P. R. China
| | - MENG SHEN
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, P. R. China
| | - CHENYI XUE
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, P. R. China
| | - SANJUN CAI
- Shanghai Cancer Hospital of Fudan University, Shanghai 200032, P. R. China
| | - YE XU
- Shanghai Cancer Hospital of Fudan University, Shanghai 200032, P. R. China
| | - PENG NAN
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, P. R. China
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Herkert JC, Niessen RC, Olderode-Berends MJW, Veenstra-Knol HE, Vos YJ, van der Klift HM, Scheenstra R, Tops CMJ, Karrenbeld A, Peters FTM, Hofstra RMW, Kleibeuker JH, Sijmons RH. Paediatric intestinal cancer and polyposis due to bi-allelic PMS2 mutations: case series, review and follow-up guidelines. Eur J Cancer 2011; 47:965-82. [PMID: 21376568 DOI: 10.1016/j.ejca.2011.01.013] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 01/20/2011] [Indexed: 11/30/2022]
Abstract
BACKGROUND Bi-allelic germline mutations of one of the DNA mismatch repair genes, so far predominantly found in PMS2, cause constitutional MMR-deficiency syndrome. This rare disorder is characterised by paediatric intestinal cancer and other malignancies. We report the clinical, immunohistochemical and genetic characterisation of four families with bi-allelic germline PMS2 mutations. We present an overview of the published gastrointestinal manifestations of CMMR-D syndrome and propose recommendations for gastro-intestinal screening. METHODS AND RESULTS The first proband developed a cerebral angiosarcoma at age 2 and two colorectal adenomas at age 7. Genetic testing identified a complete PMS2 gene deletion and a frameshift c.736_741delinsTGTGTGTGAAG (p.Pro246CysfsX3) mutation. In the second family, both the proband and her brother had multiple intestinal adenomas, initially wrongly diagnosed as familial adenomatous polyposis. A splice site c.2174+1G>A, and a missense c.137G>T (p.Ser46Ile) mutation in PMS2 were identified. The third patient was diagnosed with multiple colorectal adenomas at age 11; he developed a high-grade dysplastic colorectal adenocarcinoma at age 21. Two intragenic PMS2 deletions were found. The fourth proband developed a cerebral anaplastic ganglioma at age 9 and a high-grade colerectal dysplastic adenoma at age 10 and carries a homozygous c.2174+1G>A mutation. Tumours of all patients showed microsatellite instability and/or loss of PMS2 expression. CONCLUSIONS Our findings show the association between bi-allelic germline PMS2 mutations and severe childhood-onset gastrointestinal manifestations, and support the notion that patients with early-onset gastrointestinal adenomas and cancer should be investigated for CMMR-D syndrome. We recommend yearly follow-up with colonoscopy from age 6 and simultaneous video-capsule small bowel enteroscopy from age 8.
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Affiliation(s)
- Johanna C Herkert
- Department of Genetics, University Medical Center Groningen, University of Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands.
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