1
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Lin YJ, Menon AS, Hu Z, Brenner SE. Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors. Hum Genomics 2024; 18:90. [PMID: 39198917 PMCID: PMC11360829 DOI: 10.1186/s40246-024-00663-z] [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: 06/22/2024] [Accepted: 08/19/2024] [Indexed: 09/01/2024] Open
Abstract
BACKGROUND Variant interpretation is essential for identifying patients' disease-causing genetic variants amongst the millions detected in their genomes. Hundreds of Variant Impact Predictors (VIPs), also known as Variant Effect Predictors (VEPs), have been developed for this purpose, with a variety of methodologies and goals. To facilitate the exploration of available VIP options, we have created the Variant Impact Predictor database (VIPdb). RESULTS The Variant Impact Predictor database (VIPdb) version 2 presents a collection of VIPs developed over the past three decades, summarizing their characteristics, ClinGen calibrated scores, CAGI assessment results, publication details, access information, and citation patterns. We previously summarized 217 VIPs and their features in VIPdb in 2019. Building upon this foundation, we identified and categorized an additional 190 VIPs, resulting in a total of 407 VIPs in VIPdb version 2. The majority of the VIPs have the capacity to predict the impacts of single nucleotide variants and nonsynonymous variants. More VIPs tailored to predict the impacts of insertions and deletions have been developed since the 2010s. In contrast, relatively few VIPs are dedicated to the prediction of splicing, structural, synonymous, and regulatory variants. The increasing rate of citations to VIPs reflects the ongoing growth in their use, and the evolving trends in citations reveal development in the field and individual methods. CONCLUSIONS VIPdb version 2 summarizes 407 VIPs and their features, potentially facilitating VIP exploration for various variant interpretation applications. VIPdb is available at https://genomeinterpretation.org/vipdb.
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Affiliation(s)
- Yu-Jen Lin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA, 94720, USA
| | - Arul S Menon
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
- College of Computing, Data Science, and Society, University of California, Berkeley, CA, 94720, USA
| | - Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall #3102, Berkeley, CA, 94720-3102, USA
- Illumina, Foster City, CA, 94404, USA
| | - Steven E Brenner
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
- Center for Computational Biology, University of California, Berkeley, CA, 94720, USA.
- College of Computing, Data Science, and Society, University of California, Berkeley, CA, 94720, USA.
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall #3102, Berkeley, CA, 94720-3102, USA.
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2
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Tezuka K, Yamakawa M, Murakami R, Hirai I, Toya R, Suzuki A, Kawamura H, Miyano Y, Sato H, Motoi F. Familial Intraductal Papillary Mucinous Neoplasm Associated With the Germline MSH6 Missense Variant and Progression of Pancreatic cancer. Pancreas 2024; 53:e476-e486. [PMID: 38416847 DOI: 10.1097/mpa.0000000000002313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
OBJECTIVES Intraductal papillary mucinous neoplasm (IPMN) in individuals with at least one first-degree relative with IPMN is defined as familial IPMN. However, few studies have reported on familial IPMN, its clinical characteristics, or the associated genetic factors. MATERIALS AND METHODS We report the case of a 58-year-old woman with multifocal IPMN and a mural nodule in the pancreatic body. The patient underwent a distal pancreatectomy and developed pancreatic head cancer 1 year and 6 months postoperatively. The patient had a family history of multifocal IPMN in her father. Therefore, a genetic predisposition to IPMN and pancreatic cancer was suspected. The patient was analyzed for germline variants, and the resected IPMN was subjected to immunohistochemical and somatic variant analyses. RESULTS Next-generation sequencing revealed a heterozygous germline missense variant in exon 5 of MSH6 (c.3197A>G; Tyr1066Cys). The pathogenicity of this variant of uncertain significance was suspected based on multiple in silico analyses, and the same MSH6 variant was identified in the patient's father's colonic adenoma. The mural nodule in the pancreatic body was pathologically diagnosed as a high-grade IPMN with ossification and somatic KRAS and PIK3CA variants. CONCLUSIONS This case revealed a possible genetic factor for familial IPMN development and presented interesting clinicopathological findings.
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Affiliation(s)
| | | | - Ryoko Murakami
- Genome Informatics Unit, Institution for Promotion of Medical Science Research, Yamagata University Faculty of Medicine
| | | | | | | | | | - Yuki Miyano
- Genome Informatics Unit, Institution for Promotion of Medical Science Research, Yamagata University Faculty of Medicine
| | - Hidenori Sato
- Genome Informatics Unit, Institution for Promotion of Medical Science Research, Yamagata University Faculty of Medicine
| | - Fuyuhiko Motoi
- First Department of Surgery, Yamagata University Faculty of Medicine, Yamagata, Japan
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3
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Lin YJ, Menon AS, Hu Z, Brenner SE. Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600283. [PMID: 38979289 PMCID: PMC11230257 DOI: 10.1101/2024.06.25.600283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Background Variant interpretation is essential for identifying patients' disease-causing genetic variants amongst the millions detected in their genomes. Hundreds of Variant Impact Predictors (VIPs), also known as Variant Effect Predictors (VEPs), have been developed for this purpose, with a variety of methodologies and goals. To facilitate the exploration of available VIP options, we have created the Variant Impact Predictor database (VIPdb). Results The Variant Impact Predictor database (VIPdb) version 2 presents a collection of VIPs developed over the past 25 years, summarizing their characteristics, ClinGen calibrated scores, CAGI assessment results, publication details, access information, and citation patterns. We previously summarized 217 VIPs and their features in VIPdb in 2019. Building upon this foundation, we identified and categorized an additional 186 VIPs, resulting in a total of 403 VIPs in VIPdb version 2. The majority of the VIPs have the capacity to predict the impacts of single nucleotide variants and nonsynonymous variants. More VIPs tailored to predict the impacts of insertions and deletions have been developed since the 2010s. In contrast, relatively few VIPs are dedicated to the prediction of splicing, structural, synonymous, and regulatory variants. The increasing rate of citations to VIPs reflects the ongoing growth in their use, and the evolving trends in citations reveal development in the field and individual methods. Conclusions VIPdb version 2 summarizes 403 VIPs and their features, potentially facilitating VIP exploration for various variant interpretation applications. Availability VIPdb version 2 is available at https://genomeinterpretation.org/vipdb.
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Affiliation(s)
- Yu-Jen Lin
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Center for Computational Biology, University of California, Berkeley, California 94720, USA
| | - Arul S. Menon
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- College of Computing, Data Science, and Society, University of California, Berkeley, California 94720, USA
| | - Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Currently at: Illumina, Foster City, California 94404, USA
| | - Steven E. Brenner
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Center for Computational Biology, University of California, Berkeley, California 94720, USA
- College of Computing, Data Science, and Society, University of California, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
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4
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Song Y, Guo J, Zhou Y, Wei X, Li J, Zhang G, Wang H. A loss-of-function variant in ZCWPW1 causes human male infertility with sperm head defect and high DNA fragmentation. Reprod Health 2024; 21:18. [PMID: 38310235 PMCID: PMC10837985 DOI: 10.1186/s12978-024-01746-9] [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: 09/18/2023] [Accepted: 01/23/2024] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND Male infertility is a global health issue. The more causative genes related to human male infertility should be further explored. The essential role of Zcwpw1 in male mouse fertility has been established and the role of ZCWPW1 in human reproduction needs further investigation to verify. METHODS An infertile man with oligoasthenoteratozoospermia phenotype and his parents were recruited from West China Second University Hospital, Sichuan University. A total of 200 healthy Han Chinese volunteers without any evidence of infertility were recruited as normal controls, while an additional 150 infertile individuals were included to assess the prevalence of ZCWPW1 variants in a sporadic male sterile population. The causative gene variant was identified by Whole-exome sequencing and Sanger sequencing. The phenotype of the oligoasthenoteratozoospermia was determined by Papanicolaou staining, immunofluorescence staining and electron microscope. In-vitro experiments, western blot and in-silicon analysis were applied to assess the pathogenicity of the identified variant. Additionally, we examined the influence of the variant on the DNA fragmentation and DNA repair capability by Sperm Chromatin Dispersion and Neutral Comet Assay. RESULTS The proband exhibits a phenotype of oligoasthenoteratozoospermia, his spermatozoa show head defects by semen examination, Papanicolaou staining and electron microscope assays. Whole-exome sequencing and Sanger sequencing found the proband carries a homozygous ZCWPW1 variant (c.1064C > T, p. P355L). Immunofluorescence analysis shows a significant decrease in ZCWPW1 expression in the proband's sperm. By exogenous expression with ZCWPW1 mutant plasmid in vitro, the obvious declined expression of ZCWPW1 with the mutation is validated in HEK293T. After being treated by hydroxyurea, MUT-ZCWPW1 transfected cells and empty vector transfected cells have a higher level of γ-H2AX, increased tail DNA and reduced H3K9ac level than WT-ZCWPW1 transfected cells. Furthermore, the Sperm Chromatin Dispersion assay revealed the proband's spermatozoa have high DNA fragmentation. CONCLUSIONS It is the first report that a novel homozygous missense mutation in ZCWPW1 caused human male infertility with sperm head defects and high DNA fragmentation. This finding enriches the gene variant spectrum and etiology of oligoasthenoteratozoospermia.
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Affiliation(s)
- Yuelin Song
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Juncen Guo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yanling Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xingjian Wei
- Department of Obstetrics and Gynaecology, Southwest Medical University, Luzhou, 646000, China
| | - Jianlan Li
- Child Healthcare Department, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610000, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Guohui Zhang
- Key Laboratory of Reproductive Medicine, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610000, China.
| | - Hongjing Wang
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
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5
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Liu Y, Yeung WSB, Chiu PCN, Cao D. Computational approaches for predicting variant impact: An overview from resources, principles to applications. Front Genet 2022; 13:981005. [PMID: 36246661 PMCID: PMC9559863 DOI: 10.3389/fgene.2022.981005] [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: 06/29/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
One objective of human genetics is to unveil the variants that contribute to human diseases. With the rapid development and wide use of next-generation sequencing (NGS), massive genomic sequence data have been created, making personal genetic information available. Conventional experimental evidence is critical in establishing the relationship between sequence variants and phenotype but with low efficiency. Due to the lack of comprehensive databases and resources which present clinical and experimental evidence on genotype-phenotype relationship, as well as accumulating variants found from NGS, different computational tools that can predict the impact of the variants on phenotype have been greatly developed to bridge the gap. In this review, we present a brief introduction and discussion about the computational approaches for variant impact prediction. Following an innovative manner, we mainly focus on approaches for non-synonymous variants (nsSNVs) impact prediction and categorize them into six classes. Their underlying rationale and constraints, together with the concerns and remedies raised from comparative studies are discussed. We also present how the predictive approaches employed in different research. Although diverse constraints exist, the computational predictive approaches are indispensable in exploring genotype-phenotype relationship.
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Affiliation(s)
- Ye Liu
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - William S. B. Yeung
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Philip C. N. Chiu
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Dandan Cao
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
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6
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Duong HTT, Suzuki H, Katagiri S, Shibata M, Arai M, Yura K. Computational study of the impact of nucleotide variations on highly conserved proteins: In the case of actin. Biophys Physicobiol 2022; 19:e190025. [PMID: 36160324 PMCID: PMC9465404 DOI: 10.2142/biophysico.bppb-v19.0025] [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: 06/13/2022] [Accepted: 07/27/2022] [Indexed: 12/01/2022] Open
Abstract
Sequencing of individual human genomes enables studying relationship among nucleotide variations, amino acid substitutions, effect on protein structures and diseases. Many studies have found general tendencies, for instance, that pathogenic variations tend to be found in the buried regions of the protein structures, that benign variations tend to be found on the surface of the proteins, and that variations on evolutionary conserved residues tend to be pathogenic. These tendencies were deduced from globular proteins with standard evolutionary changes in amino acid sequences. In this study, we investigated the variation distribution on actin, one of the highly conserved proteins. Many nucleotide variations and three-dimensional structures of actin have been registered in databases. By combining those data, we found that variations buried inside the protein were rather benign and variations on the surface of the protein were pathogenic. This idiosyncratic distribution of the variation impact is likely ascribed to the extensive use of the surface of the protein for protein-protein interactions in actin.
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Affiliation(s)
- Ha T. T. Duong
- Graduate School of Humanities and Sciences, Ochanomizu University
| | - Hirofumi Suzuki
- Graduate School of Advanced Science and Engineering, Waseda University
| | - Saki Katagiri
- Graduate School of Humanities and Sciences, Ochanomizu University
| | - Mayu Shibata
- Graduate School of Humanities and Sciences, Ochanomizu University
| | - Misae Arai
- Graduate School of Humanities and Sciences, Ochanomizu University
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University
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7
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Schaettler MO, Richters MM, Wang AZ, Skidmore ZL, Fisk B, Miller KE, Vickery TL, Kim AH, Chicoine MR, Osbun JW, Leuthardt EC, Dowling JL, Zipfel GJ, Dacey RG, Lu HC, Johanns TM, Griffith OL, Mardis ER, Griffith M, Dunn GP. Characterization of the Genomic and Immunological Diversity of Malignant Brain Tumors Through Multi-Sector Analysis. Cancer Discov 2021; 12:154-171. [PMID: 34610950 DOI: 10.1158/2159-8290.cd-21-0291] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/19/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022]
Abstract
Despite some success in secondary brain metastases, targeted or immune-based therapies have shown limited efficacy against primary brain malignancies such as glioblastoma (GBM). While the intratumoral heterogeneity of GBM is implicated in treatment resistance, it remains unclear whether this diversity is observed within brain metastases and to what extent cancer-cell intrinsic heterogeneity sculpts the local immune microenvironment. Here, we profiled the immunogenomic state of 93 spatially distinct regions from 30 malignant brain tumors through whole exome, RNA, and TCR-sequencing. Our analyses identified differences between primary and secondary malignancies with gliomas displaying more spatial heterogeneity at the genomic and neoantigen level. Additionally, this spatial diversity was recapitulated in the distribution of T cell clones where some gliomas harbored highly expanded but spatially restricted clonotypes. This study defines the immunogenomic landscape across a cohort of malignant brain tumors and contains implications for the design of targeted and immune-based therapies against intracranial malignancies.
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Affiliation(s)
| | - Megan M Richters
- Department of Medicine, McDonnell Genome Institute, Washington University in St. Louis School of Medicine
| | - Anthony Z Wang
- Department of Neurological Surgery, Washington University in St. Louis School of Medicine
| | - Zachary L Skidmore
- The Genome Institute, Washington University in St. Louis School of Medicine
| | - Bryan Fisk
- McDonnell Genome Institute, Washington University in St. Louis School of Medicine
| | | | - Tammi L Vickery
- Center for Human Immunology and Immunotherapy Programs, Washington University in St. Louis School of Medicine
| | - Albert H Kim
- Neurosurgery, Washington University in St. Louis School of Medicine
| | - Michael R Chicoine
- Department of Neurological Surgery, Washington University in St. Louis School of Medicine
| | - Joshua W Osbun
- Neurological Surgery, Washington University in St. Louis
| | - Eric C Leuthardt
- Department of Neurological Surgery, Washington University in St. Louis School of Medicine
| | - Joshua L Dowling
- Department of Neurological Surgery, Washington University in St. Louis School of Medicine
| | - Gregory J Zipfel
- Department of Neurological Surgery, Washington University in St. Louis School of Medicine
| | - Ralph G Dacey
- Department of Neurological Surgery, Washington University in St. Louis School of Medicine
| | - Hsiang-Chih Lu
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine
| | - Tanner M Johanns
- Division of Oncology, Washington University in St. Louis School of Medicine
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University in St. Louis School of Medicine
| | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children's Hospital
| | - Malachi Griffith
- Department of Medicine, McDonnell Genome Institute, Washington University in St. Louis School of Medicine
| | - Gavin P Dunn
- Department of Neurological Surgery, Washington University in St. Louis School of Medicine
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8
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Hu Z, Yu C, Furutsuki M, Andreoletti G, Ly M, Hoskins R, Adhikari AN, Brenner SE. VIPdb, a genetic Variant Impact Predictor Database. Hum Mutat 2019; 40:1202-1214. [PMID: 31283070 PMCID: PMC7288905 DOI: 10.1002/humu.23858] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 06/27/2019] [Indexed: 12/30/2022]
Abstract
Genome sequencing identifies vast number of genetic variants. Predicting these variants' molecular and clinical effects is one of the preeminent challenges in human genetics. Accurate prediction of the impact of genetic variants improves our understanding of how genetic information is conveyed to molecular and cellular functions, and is an essential step towards precision medicine. Over one hundred tools/resources have been developed specifically for this purpose. We summarize these tools as well as their characteristics, in the genetic Variant Impact Predictor Database (VIPdb). This database will help researchers and clinicians explore appropriate tools, and inform the development of improved methods. VIPdb can be browsed and downloaded at https://genomeinterpretation.org/vipdb.
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Affiliation(s)
- Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Changhua Yu
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
| | - Mabel Furutsuki
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA
| | - Gaia Andreoletti
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Melissa Ly
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Division of Data Sciences, University of California, Berkeley, California 94720, USA
| | - Roger Hoskins
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Aashish N. Adhikari
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Steven E. Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
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9
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A portrait of germline mutation in Brazilian at-risk for hereditary breast cancer. Breast Cancer Res Treat 2018; 172:637-646. [PMID: 30159786 DOI: 10.1007/s10549-018-4938-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 08/22/2018] [Indexed: 12/12/2022]
Abstract
PURPOSE Knowledge about the germline mutational spectrum among Brazilian with hereditary breast and ovarian cancer (HBOC) is limited. Only five studies have performed comprehensive BRCA sequencing, corresponding to 1041 individuals among a Brazilian population of over 207 million people. Herein we aimed to determine the clinical and molecular characteristics of Brazilian patients who underwent oncogenetic counseling and genetic testing of a panel of high-risk and moderate-risk genes from 2009 to 2017. METHODS Massively parallel sequencing was applied in 157 individuals (132 breast cancer-affected and 25 breast cancer-unaffected individuals) selected according NCCN criteria for hereditary breast cancer. Analysis of mutation segregation in family members was performed by capillary bidirectional sequencing, clinical response after treament and survival analysis was estimated by Kaplan-Meier. RESULTS Nineteen germline variants were identified,15 pathogenic and 4 VUS (Variants of Uncertain Significance) in 27 individuals (27/157; 17% P < 0.0001) distributed among 7 genes. Sixty-eight percent of patients (13/19) harbor mutation in BRCA genes and 32% (6/19) in moderate risk genes. This is the first study reporting ATR deleterious germline mutation in association with hereditary breast cancer. Cancer-affected patients with moderate- risk mutation present a more aggressive phenotype, with bilateral cancer (25% vs. 13%, P = 0.0305), high-grade tumors (79.2% vs. 46.3%, P = 0.0001) and triple-negative (50% vs. 22.4%, P < 0.0001). However, no difference in the 5 years overall survival was observed between BRCA and moderate risk groups. CONCLUSIONS This work highlights the benefits of large-scale sequencing for oncogenetic counseling and extends our understanding about the genetics of hereditary breast cancer in the multi-ethnic Brazilian population.
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10
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Duan FX, Gu GL, Yang HR, Yu PF, Zhang Z. Must Peutz-Jeghers syndrome patients have the LKB1/STK11 gene mutation? A case report and review of the literature. World J Clin Cases 2018; 6:224-232. [PMID: 30148152 PMCID: PMC6107527 DOI: 10.12998/wjcc.v6.i8.224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/23/2018] [Accepted: 05/13/2018] [Indexed: 02/05/2023] Open
Abstract
Peutz-Jeghers syndrome (PJS) is an autosomal dominant inherited disease, which is characterized by mucocutaneous pigmentation and multiple gastrointestinal hamartoma polyps. The germline mutation of LKB1/STK11 gene on chromosome 19p13.3 is considered to be the hereditary cause of PJS. However, must a patient with PJS have the LKB1/STK11 gene mutation? We here report a case of a male patient who had typical manifestations of PJS and a definite family history, but did not have LKB1/STK11 gene mutation. By means of high-throughput sequencing technology, only mutations in APC gene (c.6662T > C: p.Met2221Thr) and MSH6 gene (c.3488A > T: p.Glu1163Val) were detected. The missense mutations in APC and MSH6 gene may lead to abnormalities in structure and function of their expression products, and may result in the occurrence of PJS. This study suggests that some other genetic disorders may cause PJS besides LKB1/STK11 gene mutation.
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Affiliation(s)
- Fu-Xiao Duan
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
| | - Guo-Li Gu
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
| | - Hai-Rui Yang
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
| | - Peng-Fei Yu
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
| | - Zhi Zhang
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
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11
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Gray PN, Tsai P, Chen D, Wu S, Hoo J, Mu W, Li B, Vuong H, Lu HM, Batth N, Willett S, Uyeda L, Shah S, Gau CL, Umali M, Espenschied C, Janicek M, Brown S, Margileth D, Dobrea L, Wagman L, Rana H, Hall MJ, Ross T, Terdiman J, Cullinane C, Ries S, Totten E, Elliott AM. TumorNext-Lynch-MMR: a comprehensive next generation sequencing assay for the detection of germline and somatic mutations in genes associated with mismatch repair deficiency and Lynch syndrome. Oncotarget 2018; 9:20304-20322. [PMID: 29755653 PMCID: PMC5945525 DOI: 10.18632/oncotarget.24854] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/06/2018] [Indexed: 12/12/2022] Open
Abstract
The current algorithm for Lynch syndrome diagnosis is highly complex with multiple steps which can result in an extended time to diagnosis while depleting precious tumor specimens. Here we describe the analytical validation of a custom probe-based NGS tumor panel, TumorNext-Lynch-MMR, which generates a comprehensive genetic profile of both germline and somatic mutations that can accelerate and streamline the time to diagnosis and preserve specimen. TumorNext-Lynch-MMR can detect single nucleotide variants, small insertions and deletions in 39 genes that are frequently mutated in Lynch syndrome and colorectal cancer. Moreover, the panel provides microsatellite instability status and detects loss of heterozygosity in the five Lynch genes; MSH2, MSH6, MLH1, PMS2 and EPCAM. Clinical cases are described that highlight the assays ability to differentiate between somatic and germline mutations, precisely classify variants and resolve discordant cases.
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Affiliation(s)
- Phillip N Gray
- Advanced Genomic Services, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Pei Tsai
- Advanced Genomic Services, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Daniel Chen
- Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sitao Wu
- Bioinformatics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Jayne Hoo
- Bioinformatics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Wenbo Mu
- Bioinformatics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Bing Li
- Bioinformatics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Huy Vuong
- Bioinformatics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Hsiao-Mei Lu
- Bioinformatics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Navanjot Batth
- Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sara Willett
- Advanced Genomic Services, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Lisa Uyeda
- Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Swati Shah
- Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Chia-Ling Gau
- Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Monalyn Umali
- Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Carin Espenschied
- Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Mike Janicek
- Cancer Genetic Risk Assessment Program, Arizona Oncology, Scottsdale, AZ 85258, USA
| | - Sandra Brown
- Cancer Genetics Program, Saint Joseph of Orange, Orange, CA 92868, USA
| | - David Margileth
- Cancer Genetics Program, Saint Joseph of Orange, Orange, CA 92868, USA
| | - Lavinia Dobrea
- Oncology Research and Biospecimen Program, Saint Joseph of Orange, Orange, CA 92868, USA
| | - Lawrence Wagman
- The Center for Cancer Prevention and Treatment, Saint Joseph of Orange, Orange, CA 92868, USA
| | - Huma Rana
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02461, USA
| | - Michael J Hall
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia PA 19111, USA
| | - Theodora Ross
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jonathan Terdiman
- Department of Medicine - Gastroenterology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Carey Cullinane
- Department of Pathology, Long Beach Memorial Medical Center, Long Beach, CA 90801, USA
| | - Savita Ries
- Department of Pathology, Long Beach Memorial Medical Center, Long Beach, CA 90801, USA
| | - Ellen Totten
- Advocate Medical Group, Park Ridge, Illinois 60068, USA
| | - Aaron M Elliott
- Advanced Genomic Services, Ambry Genetics, Aliso Viejo, CA 92656, USA
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12
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Houlleberghs H, Goverde A, Lusseveld J, Dekker M, Bruno MJ, Menko FH, Mensenkamp AR, Spaander MCW, Wagner A, Hofstra RMW, te Riele H. Suspected Lynch syndrome associated MSH6 variants: A functional assay to determine their pathogenicity. PLoS Genet 2017; 13:e1006765. [PMID: 28531214 PMCID: PMC5460888 DOI: 10.1371/journal.pgen.1006765] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 06/06/2017] [Accepted: 04/18/2017] [Indexed: 12/14/2022] Open
Abstract
Lynch syndrome (LS) is a hereditary cancer predisposition caused by inactivating mutations in DNA mismatch repair (MMR) genes. Mutations in the MSH6 DNA MMR gene account for approximately 18% of LS cases. Many LS-associated sequence variants are nonsense and frameshift mutations that clearly abrogate MMR activity. However, missense mutations whose functional implications are unclear are also frequently seen in suspected-LS patients. To conclusively diagnose LS and enroll patients in appropriate surveillance programs to reduce morbidity as well as mortality, the functional consequences of these variants of uncertain clinical significance (VUS) must be defined. We present an oligonucleotide-directed mutagenesis screen for the identification of pathogenic MSH6 VUS. In the screen, the MSH6 variant of interest is introduced into mouse embryonic stem cells by site-directed mutagenesis. Subsequent selection for MMR-deficient cells using the DNA damaging agent 6-thioguanine (6TG) allows the identification of MMR abrogating VUS because solely MMR-deficient cells survive 6TG exposure. We demonstrate the efficacy of the genetic screen, investigate the phenotype of 26 MSH6 VUS and compare our screening results to clinical data from suspected-LS patients carrying these variant alleles. The colorectal and endometrial cancer predisposition Lynch syndrome (LS) is caused by an inherited heterozygous defect in one of four DNA mismatch repair (MMR) genes. Deleterious mutations (e.g., protein-deleting or -truncating) in DNA MMR genes unambiguously allow for the clinical diagnosis LS and hence enable appropriate surveillance measures to be taken to reduce cancer risk and ensure early detection of tumors. However, currently about one-third of detected MMR gene variants are subtle with less clear functional consequences: missense mutations affecting a single amino acid may be innocuous, hence not causing LS, or partially or fully destroy protein function. As long as uncertainty exists about their pathogenicity, such mutations are labeled ‘variants of uncertain (clinical) significance’ (VUS). VUS hamper genetic counseling and therefore the need for functional testing of VUS is widely recognized. To functionally annotate MMR gene VUS, we have developed a high content cellular assay in which the VUS is introduced in a cell culture by oligonucleotide-directed gene modification. Should the VUS be deleterious for MMR, the modified cells survive exposure to the guanine analog 6-thioguanine (6TG) and 6TG-resistant colonies appear. Should the mutation not affect MMR, no colonies appear. Here we present the adaptation and application of this protocol to the functional annotation of variants of the MMR gene MSH6. Implementation of our assay in clinical genetics laboratories will provide clinicians with information for proper counseling of mutation carriers and treatment of their of tumors.
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Affiliation(s)
- Hellen Houlleberghs
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anne Goverde
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jarnick Lusseveld
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marleen Dekker
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marco J. Bruno
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Fred H. Menko
- Family Cancer Clinic, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arjen R. Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Manon C. W. Spaander
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert M. W. Hofstra
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hein te Riele
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- * E-mail:
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13
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Arora S, Huwe PJ, Sikder R, Shah M, Browne AJ, Lesh R, Nicolas E, Deshpande S, Hall MJ, Dunbrack RL, Golemis EA. Functional analysis of rare variants in mismatch repair proteins augments results from computation-based predictive methods. Cancer Biol Ther 2017; 18:519-533. [PMID: 28494185 DOI: 10.1080/15384047.2017.1326439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The cancer-predisposing Lynch Syndrome (LS) arises from germline mutations in DNA mismatch repair (MMR) genes, predominantly MLH1, MSH2, MSH6, and PMS2. A major challenge for clinical diagnosis of LS is the frequent identification of variants of uncertain significance (VUS) in these genes, as it is often difficult to determine variant pathogenicity, particularly for missense variants. Generic programs such as SIFT and PolyPhen-2, and MMR gene-specific programs such as PON-MMR and MAPP-MMR, are often used to predict deleterious or neutral effects of VUS in MMR genes. We evaluated the performance of multiple predictive programs in the context of functional biologic data for 15 VUS in MLH1, MSH2, and PMS2. Using cell line models, we characterized VUS predicted to range from neutral to pathogenic on mRNA and protein expression, basal cellular viability, viability following treatment with a panel of DNA-damaging agents, and functionality in DNA damage response (DDR) signaling, benchmarking to wild-type MMR proteins. Our results suggest that the MMR gene-specific classifiers do not always align with the experimental phenotypes related to DDR. Our study highlights the importance of complementary experimental and computational assessment to develop future predictors for the assessment of VUS.
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Affiliation(s)
- Sanjeevani Arora
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Peter J Huwe
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Rahmat Sikder
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Manali Shah
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Amanda J Browne
- b Immersion Science Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Randy Lesh
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Emmanuelle Nicolas
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Sanat Deshpande
- b Immersion Science Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Michael J Hall
- c Department of Clinical Genetics , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Roland L Dunbrack
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Erica A Golemis
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
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14
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De Lellis L, Aceto GM, Curia MC, Catalano T, Mammarella S, Veschi S, Fantini F, Battista P, Stigliano V, Messerini L, Mareni C, Sala P, Bertario L, Radice P, Cama A. Integrative analysis of hereditary nonpolyposis colorectal cancer: the contribution of allele-specific expression and other assays to diagnostic algorithms. PLoS One 2013; 8:e81194. [PMID: 24278394 PMCID: PMC3835792 DOI: 10.1371/journal.pone.0081194] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 10/09/2013] [Indexed: 01/27/2023] Open
Abstract
The identification of germline variants predisposing to hereditary nonpolyposis colorectal cancer (HNPCC) is crucial for clinical management of carriers, but several probands remain negative for such variants or bear variants of uncertain significance (VUS). Here we describe the results of integrative molecular analyses in 132 HNPCC patients providing evidences for improved genetic testing of HNPCC with traditional or next generation methods. Patients were screened for: germline allele-specific expression (ASE), nucleotide variants, rearrangements and promoter methylation of mismatch repair (MMR) genes; germline EPCAM rearrangements; tumor microsatellite instability (MSI) and immunohistochemical (IHC) MMR protein expression. Probands negative for pathogenic variants of MMR genes were screened for germline APC and MUTYH sequence variants. Most germline defects identified were sequence variants and rearrangements of MMR genes. Remarkably, altered germline ASE of MMR genes was detected in 8/22 (36.5%) probands analyzed, including 3 cases negative at other screenings. Moreover, ASE provided evidence for the pathogenic role and guided the characterization of a VUS shared by 2 additional probands. No germline MMR gene promoter methylation was observed and only one EPCAM rearrangement was detected. In several cases, tumor IHC and MSI diverged from germline screening results. Notably, APC or biallelic MUTYH germline defects were identified in 2/19 probands negative for pathogenic variants of MMR genes. Our results show that ASE complements gDNA-based analyses in the identification of MMR defects and in the characterization of VUS affecting gene expression, increasing the number of germline alterations detected. An appreciable fraction of probands negative for MMR gene variants harbors APC or MUTYH variants. These results indicate that germline ASE analysis and screening for APC and MUTYH defects should be included in HNPCC diagnostic algorithms.
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Affiliation(s)
- Laura De Lellis
- Department of Pharmacy, “G. d’Annunzio” University, Chieti, Italy
| | - Gitana Maria Aceto
- Department of Experimental and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
- Unit of Molecular Pathology and Genomics, Aging Research Center, “G. d’Annunzio” University Foundation, Chieti, Italy
| | - Maria Cristina Curia
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University, Chieti, Italy
- Unit of Molecular Pathology and Genomics, Aging Research Center, “G. d’Annunzio” University Foundation, Chieti, Italy
| | - Teresa Catalano
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | | | - Serena Veschi
- Unit of Molecular Pathology and Genomics, Aging Research Center, “G. d’Annunzio” University Foundation, Chieti, Italy
| | - Fabiana Fantini
- Department of Experimental and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
| | - Pasquale Battista
- Department of Experimental and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
| | - Vittoria Stigliano
- Department of Gastroenterology, Unit of Hereditary Colorectal Cancer, National Cancer Institute, Regina Elena (IRE), Rome, Italy
| | - Luca Messerini
- Section of Pathological Anatomy, Department of Medical and Surgical Critical Care, University of Florence, Florence, Italy
| | - Cristina Mareni
- Department of Internal Medicine, University of Genova, Genova, Italy
| | - Paola Sala
- Unit of Hereditary Digestive Tract Tumors, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Lucio Bertario
- Unit of Hereditary Digestive Tract Tumors, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Radice
- Unit of Molecular bases of genetic risk and genetic testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Alessandro Cama
- Department of Pharmacy, “G. d’Annunzio” University, Chieti, Italy
- * E-mail:
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15
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Terui H, Tachikawa T, Kakuta M, Nishimura Y, Yatsuoka T, Yamaguchi K, Yura K, Akagi K. Molecular and clinical characteristics of MSH6 germline variants detected in colorectal cancer patients. Oncol Rep 2013; 30:2909-16. [PMID: 24100870 DOI: 10.3892/or.2013.2781] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/16/2013] [Indexed: 11/06/2022] Open
Abstract
The MSH6 gene is one of the mismatch repair genes involved in Lynch syndrome and its mutations account for 10-20% of Lynch syndrome. Although previous studies suggested that the difference of the geographical region affects the clinical phenotype of Lynch syndrome, there has been no report on the detailed features of Japanese Lynch syndrome patients carrying an MSH6 mutation. The aim of the present study was to investigate the clinical and molecular features of MSH6 mutation carriers in Japan. Surgically resected 1720 colorectal carcinoma specimens were screened by microsatellite instability (MSI) testing and the MSI-high cases were subjected to a germline mutation analysis of the mismatch repair genes MLH1, MSH2 and MSH6. We investigated the clinical and molecular features of the MSH6 variants, such as the family cancer history, pathological findings, immunohistochemistry, methylation status of the MLH1 promoter and BRAF mutation in the colorectal tumor. Furthermore, the impact of the missense variants on MSH6 protein was predicted by using in silico tools. We identified nine novel pathogenic mutations and eight unclassified missense variants. Among the eight missense variants, three were suspected pathogenic by in silico analysis. We also found that most colorectal cancers in the MSH6 mutation carrier were diagnosed after the age of 50 and were localized distally. Furthermore, the mean age at diagnosis of endometrial cancer in Japanese MSH6 mutation carriers (49.2 years) was earlier than previous reports from Western countries (56.5 years). These results may improve the surveillance program for Japanese MSH6 mutation carriers.
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Affiliation(s)
- Hiroko Terui
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362-0806, Japan
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