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Sun Z, Chung D, Neelon B, Millar-Wilson A, Ethier SP, Xiao F, Zheng Y, Wallace K, Hardiman G. A Bayesian framework for pathway-guided identification of cancer subgroups by integrating multiple types of genomic data. Stat Med 2023; 42:5266-5284. [PMID: 37715500 DOI: 10.1002/sim.9911] [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: 03/19/2021] [Revised: 07/15/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
In recent years, comprehensive cancer genomics platforms, such as The Cancer Genome Atlas (TCGA), provide access to an enormous amount of high throughput genomic datasets for each patient, including gene expression, DNA copy number alterations, DNA methylation, and somatic mutation. While the integration of these multi-omics datasets has the potential to provide novel insights that can lead to personalized medicine, most existing approaches only focus on gene-level analysis and lack the ability to facilitate biological findings at the pathway-level. In this article, we propose Bayes-InGRiD (Bayesian Integrative Genomics Robust iDentification of cancer subgroups), a novel pathway-guided Bayesian sparse latent factor model for the simultaneous identification of cancer patient subgroups (clustering) and key molecular features (variable selection) within a unified framework, based on the joint analysis of continuous, binary, and count data. By utilizing pathway (gene set) information, Bayes-InGRiD does not only enhance the accuracy and robustness of cancer patient subgroup and key molecular feature identification, but also promotes biological understanding and interpretation. Finally, to facilitate an efficient posterior sampling, an alternative Gibbs sampler for logistic and negative binomial models is proposed using Pólya-Gamma mixtures of normal to represent latent variables for binary and count data, which yields a conditionally Gaussian representation of the posterior. The R package "INGRID" implementing the proposed approach is currently available in our research group GitHub webpage (https://dongjunchung.github.io/INGRID/).
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Affiliation(s)
- Zequn Sun
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | - Dongjun Chung
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Brian Neelon
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | | | - Stephen P Ethier
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Feifei Xiao
- Department of Biostatistics, University of Florida, Gainesville, Florida
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | - Kristin Wallace
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Gary Hardiman
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences and Institute for Global Food Security, Queen's University Belfast, Belfast, UK
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2
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The Role of Immunohistochemistry Markers in Endometrial Cancer with Mismatch Repair Deficiency: A Systematic Review. Cancers (Basel) 2022; 14:cancers14153783. [PMID: 35954447 PMCID: PMC9367287 DOI: 10.3390/cancers14153783] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 02/04/2023] Open
Abstract
The objective of this systematic review was to summarize our current knowledge of the role of immunohistochemistry (IHC) markers for identifying mismatch repair-deficient (MMRd) tumors in endometrial cancer (EC). Identification of MMRd tumors, which occur in 13% to 30% of all ECs, has become critical for patients with colorectal and endometrial cancer for therapeutic management, clinical decision making, and prognosis. This review was conducted by two authors applying the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines using the following terms: “immunohistochemistry and microsatellite instability endometrial cancer” or “immunohistochemistry and mismatch repair endometrial cancer” or “immunohistochemistry and mismatch repair deficient endometrial cancer”. Among 596 retrieved studies, 161 fulfilled the inclusion criteria. Articles were classified and presented according to their interest for the diagnosis, prognosis, and theragnostics for patients with MMRd EC. We identified 10, 18, and 96 articles using IHC expression of two, three, or four proteins of the MMR system (MLH1, MSH2, MHS6, and PMS2), respectively. MLH1 promoter methylation was analyzed in 57 articles. Thirty-four articles classified MMRd tumors with IHC markers according to their prognosis in terms of recurrence-free survival (RFS), overall survival (OS), stage, grade, and lymph node invasion. Theragnostics were studied in eight articles underlying the important concentration of PD-L1 in MMRd EC. Even though the role of IHC has been challenged, it represents the most common, robust, and cheapest method for diagnosing MMRd tumors in EC and is a valuable tool for exploring novel biotherapies and treatment modalities.
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3
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Shah S, Cheung A, Kutka M, Sheriff M, Boussios S. Epithelial Ovarian Cancer: Providing Evidence of Predisposition Genes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19138113. [PMID: 35805770 PMCID: PMC9265838 DOI: 10.3390/ijerph19138113] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 12/19/2022]
Abstract
Epithelial ovarian cancer (EOC) is one of the cancers most influenced by hereditary factors. A fourth to a fifth of unselected EOC patients carry pathogenic variants (PVs) in a number of genes, the majority of which encode for proteins involved in DNA mismatch repair (MMR) pathways. PVs in BRCA1 and BRCA2 genes are responsible for a substantial fraction of hereditary EOC. In addition, PV genes involved in the MMR pathway account for 10–15% of hereditary EOC. The identification of women with homologous recombination (HR)-deficient EOCs has significant clinical implications, concerning chemotherapy regimen planning and development as well as the use of targeted therapies such as poly(ADP-ribose) polymerase (PARP) inhibitors. With several genes involved, the complexity of genetic testing increases. In this context, next-generation sequencing (NGS) allows testing for multiple genes simultaneously with a rapid turnaround time. In this review, we discuss the EOC risk assessment in the era of NGS.
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Affiliation(s)
- Sidrah Shah
- Department of Palliative Care, Guy’s and St Thomas’ Hospital, London SE1 9RT, UK;
| | - Alison Cheung
- Department of Hematology/Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Kent, Gillingham ME7 5NY, UK; (A.C.); (M.K.)
| | - Mikolaj Kutka
- Department of Hematology/Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Kent, Gillingham ME7 5NY, UK; (A.C.); (M.K.)
| | - Matin Sheriff
- Department of Urology, Medway NHS Foundation Trust, Windmill Road, Kent, Gillingham ME7 5NY, UK;
| | - Stergios Boussios
- Department of Palliative Care, Guy’s and St Thomas’ Hospital, London SE1 9RT, UK;
- King’s College London, Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, London SE1 9RT, UK
- AELIA Organization, 9th Km Thessaloniki-Thermi, 57001 Thessaloniki, Greece
- Correspondence: or or
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4
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Ma J, Zhang L, Chen J, Song B, Zang C, Liu H. m 7GDisAI: N7-methylguanosine (m 7G) sites and diseases associations inference based on heterogeneous network. BMC Bioinformatics 2021; 22:152. [PMID: 33761868 PMCID: PMC7992861 DOI: 10.1186/s12859-021-04007-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Background Recent studies have confirmed that N7-methylguanosine (m7G) modification plays an important role in regulating various biological processes and has associations with multiple diseases. Wet-lab experiments are cost and time ineffective for the identification of disease-associated m7G sites. To date, tens of thousands of m7G sites have been identified by high-throughput sequencing approaches and the information is publicly available in bioinformatics databases, which can be leveraged to predict potential disease-associated m7G sites using a computational perspective. Thus, computational methods for m7G-disease association prediction are urgently needed, but none are currently available at present. Results To fill this gap, we collected association information between m7G sites and diseases, genomic information of m7G sites, and phenotypic information of diseases from different databases to build an m7G-disease association dataset. To infer potential disease-associated m7G sites, we then proposed a heterogeneous network-based model, m7G Sites and Diseases Associations Inference (m7GDisAI) model. m7GDisAI predicts the potential disease-associated m7G sites by applying a matrix decomposition method on heterogeneous networks which integrate comprehensive similarity information of m7G sites and diseases. To evaluate the prediction performance, 10 runs of tenfold cross validation were first conducted, and m7GDisAI got the highest AUC of 0.740(± 0.0024). Then global and local leave-one-out cross validation (LOOCV) experiments were implemented to evaluate the model’s accuracy in global and local situations respectively. AUC of 0.769 was achieved in global LOOCV, while 0.635 in local LOOCV. A case study was finally conducted to identify the most promising ovarian cancer-related m7G sites for further functional analysis. Gene Ontology (GO) enrichment analysis was performed to explore the complex associations between host gene of m7G sites and GO terms. The results showed that m7GDisAI identified disease-associated m7G sites and their host genes are consistently related to the pathogenesis of ovarian cancer, which may provide some clues for pathogenesis of diseases. Conclusion The m7GDisAI web server can be accessed at http://180.208.58.66/m7GDisAI/, which provides a user-friendly interface to query disease associated m7G. The list of top 20 m7G sites predicted to be associted with 177 diseases can be achieved. Furthermore, detailed information about specific m7G sites and diseases are also shown. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04007-9.
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Affiliation(s)
- Jiani Ma
- Engineering Research Center of Intelligent Control for Underground Space, Ministry of Education, China University of Mining and Technology, Xuzhou, 221116, China.,School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China
| | - Lin Zhang
- Engineering Research Center of Intelligent Control for Underground Space, Ministry of Education, China University of Mining and Technology, Xuzhou, 221116, China. .,School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China.
| | - Jin Chen
- Engineering Research Center of Intelligent Control for Underground Space, Ministry of Education, China University of Mining and Technology, Xuzhou, 221116, China.,School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China
| | - Bowen Song
- Department of Biological Sciences, AI University Research Center, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Chenxuan Zang
- Department of Biological Sciences, AI University Research Center, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Hui Liu
- Engineering Research Center of Intelligent Control for Underground Space, Ministry of Education, China University of Mining and Technology, Xuzhou, 221116, China.,School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China
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5
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Deshpande M, Romanski PA, Rosenwaks Z, Gerhardt J. Gynecological Cancers Caused by Deficient Mismatch Repair and Microsatellite Instability. Cancers (Basel) 2020; 12:E3319. [PMID: 33182707 PMCID: PMC7697596 DOI: 10.3390/cancers12113319] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/30/2020] [Accepted: 11/07/2020] [Indexed: 01/05/2023] Open
Abstract
Mutations in mismatch repair genes leading to mismatch repair (MMR) deficiency (dMMR) and microsatellite instability (MSI) have been implicated in multiple types of gynecologic malignancies. Endometrial carcinoma represents the largest group, with approximately 30% of these cancers caused by dMMR/MSI. Thus, testing for dMMR is now routine for endometrial cancer. Somatic mutations leading to dMMR account for approximately 90% of these cancers. However, in 5-10% of cases, MMR protein deficiency is due to a germline mutation in the mismatch repair genes MLH1, MSH2, MSH6, PMS2, or EPCAM. These germline mutations, known as Lynch syndrome, are associated with an increased risk of both endometrial and ovarian cancer, in addition to colorectal, gastric, urinary tract, and brain malignancies. So far, gynecological cancers with dMMR/MSI are not well characterized and markers for detection of MSI in gynecological cancers are not well defined. In addition, currently advanced endometrial cancers have a poor prognosis and are treated without regard to MSI status. Elucidation of the mechanism causing dMMR/MSI gynecological cancers would aid in diagnosis and therapeutic intervention. Recently, a new immunotherapy was approved for the treatment of solid tumors with MSI that have recurred or progressed after failing traditional treatment strategies. In this review, we summarize the MMR defects and MSI observed in gynecological cancers, their prognostic value, and advances in therapeutic strategies to treat these cancers.
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Affiliation(s)
- Madhura Deshpande
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA; (M.D.); (P.A.R.); (Z.R.)
| | - Phillip A. Romanski
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA; (M.D.); (P.A.R.); (Z.R.)
| | - Zev Rosenwaks
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA; (M.D.); (P.A.R.); (Z.R.)
| | - Jeannine Gerhardt
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA; (M.D.); (P.A.R.); (Z.R.)
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY 10021, USA
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Zhang L, Bhaskaran SP, Huang T, Dong H, Chandratre K, Wu X, Qin Z, Wang X, Cao W, Chen T, Lynch H, Wang SM. Variants of DNA mismatch repair genes derived from 33,998 Chinese individuals with and without cancer reveal their highly ethnic-specific nature. Eur J Cancer 2020; 125:12-21. [DOI: 10.1016/j.ejca.2019.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/21/2019] [Accepted: 11/01/2019] [Indexed: 01/01/2023]
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7
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Flaum N, Crosbie EJ, Edmondson RJ, Smith MJ, Evans DG. Epithelial ovarian cancer risk: A review of the current genetic landscape. Clin Genet 2019; 97:54-63. [PMID: 31099061 PMCID: PMC7017781 DOI: 10.1111/cge.13566] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/18/2019] [Accepted: 05/14/2019] [Indexed: 12/11/2022]
Abstract
Ovarian cancer is the fourth most common cause of cancer-related death in women in the developed world, and one of the most heritable cancers. One of the most significant risk factors for epithelial ovarian cancer (EOC) is a family history of breast and/or ovarian cancer. Combined risk factors can be used in models to stratify risk of EOC, and aid in decisions regarding risk-reduction strategies. Germline pathogenic variants in EOC susceptibility genes including those involved in homologous recombination and mismatch repair pathways are present in approximately 22% to 25% of EOC. These genes are associated with an estimated lifetime risk of EOC of 13% to 60% for BRCA1 variants and 10% to 25% for BRCA2 variants, with lower risks associated with remaining genes. Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) thought to explain an additional 6.4% of the familial risk of ovarian cancer, with 34 susceptibility loci identified to date. However, an unknown proportion of the genetic component of EOC risk remains unexplained. This review comprises an overview of individual genes and SNPs suspected to contribute to risk of EOC, and discusses use of a polygenic risk score to predict individual cancer risk more accurately.
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Affiliation(s)
- Nicola Flaum
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Emma J Crosbie
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,Department of Gynaecology, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Richard J Edmondson
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,Department of Gynaecology, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Miriam J Smith
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Dafydd G Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.,Prevention Breast Cancer Centre and Nightingale Breast Screening Centre, University Hospital of South Manchester, Manchester, UK.,Department of Cancer Genetics, The Christie NHS Foundation Trust, Manchester, UK.,Manchester Breast Centre, Manchester Cancer Research Centre, University of Manchester, Manchester, UK
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8
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Abstract
Lynch syndrome (LS) predisposes to a spectrum of cancers and increases the lifetime risk of developing colorectal- or endometrial cancer to over 50%. Lynch syndrome is dominantly inherited and is caused by defects in DNA mismatch-repair genes MLH1, MSH2, MSH6 or PMS2, with the vast majority detected in MLH1 and MSH2. Recurrent LS-associated variants observed in apparently unrelated individuals, have either arisen de novo in different families due to mutation hotspots, or are inherited from a founder (a common ancestor) that lived several generations back. There are variants that recur in some populations while also acting as founders in other ethnic groups. Testing for founder mutations can facilitate molecular diagnosis of Lynch Syndrome more efficiently and more cost effective than screening for all possible mutations. Here we report a study of the missense mutation MLH1 c.2059C > T (p.Arg687Trp), a potential founder mutation identified in eight Swedish families and one Finnish family with Swedish ancestors. Haplotype analysis confirmed that the Finnish and Swedish families shared a haplotype of between 0.9 and 2.8 Mb. While MLH1 c.2059C > T exists worldwide, the Swedish haplotype was not found among mutation carriers from Germany or France, which indicates a common founder in the Swedish population. The geographic distribution of MLH1 c.2059C > T in Sweden suggests a single, ancient mutational event in the northern part of Sweden.
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9
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Ponti G, Castellsagué E, Ruini C, Percesepe A, Tomasi A. Mismatch repair genes founder mutations and cancer susceptibility in Lynch syndrome. Clin Genet 2014; 87:507-16. [PMID: 25345868 DOI: 10.1111/cge.12529] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/03/2014] [Accepted: 10/17/2014] [Indexed: 12/18/2022]
Abstract
Founder mutations in specific populations are common in several Mendelian disorders. They are shared by apparently unrelated families that inherited them from a common ancestor that existed hundreds to thousands of years ago. They have been proven to impact in molecular diagnostics strategies in specific populations, where they can be assessed as the first screening step and, if positive, avoid further expensive gene scanning. In Lynch syndrome (LS), a dominantly inherited colorectal cancer disease, more than 50 founder pathogenic mutations have been described so far in the mismatch repair (MMR) genes (MLH1, MSH2, MSH6 and PMS2). We here provide a comprehensive summary of the founder mutations found in the MMR genes and an overview of their main characteristics. At a time when high-throughput strategies are being introduced in the molecular diagnostics of cancer, genetic testing for founder mutations can complement next generation sequencing (NGS) technologies to most efficiently identify MMR gene mutations in any given population. Additionally, special attention is paid to MMR founder mutations with interesting anthropological significance.
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Affiliation(s)
- G Ponti
- Department of Diagnostic and Clinical Medicine and Public Health, University of Modena and Reggio Emilia, Modena, Italy
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10
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Castellsagué E, Liu J, Volenik A, Giroux S, Gagné R, Maranda B, Roussel-Jobin A, Latreille J, Laframboise R, Palma L, Kasprzak L, Marcus VA, Breguet M, Nolet S, El-Haffaf Z, Australie K, Gologan A, Aleynikova O, Oros-Klein K, Greenwood C, Mes-Masson AM, Provencher D, Tischkowitz M, Chong G, Rousseau F, Foulkes WD. Characterization of a novel founder MSH6 mutation causing Lynch syndrome in the French Canadian population. Clin Genet 2014; 87:536-42. [PMID: 25318681 DOI: 10.1111/cge.12526] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/07/2014] [Accepted: 10/08/2014] [Indexed: 01/12/2023]
Abstract
We identified an MSH6 mutation (c.10C>T, p.Gln4*) causing Lynch syndrome (LS) in 11 French Canadian (FC) families from the Canadian province of Quebec. We aimed to investigate the molecular and clinical implications of this mutation among FC carriers and to assess its putative founder origin. We studied 11 probands and 27 family members. Additionally 6433 newborns, 187 colorectal cancer (CRC) cases, 381 endometrial cancer (EC) cases and 179 additional controls, all of them from Quebec, were used. Found in approximately 1 of 400 newborns, the mutation is one of the most common LS mutations described. We have found that this mutation confers a greater risk for EC than for CRC, both in the 11 studied families and in the unselected cases: EC [odds ratio (OR) = 7.5, p < 0.0001] and CRC (OR = 2.2, p = 0.46). Haplotype analyses showed that the mutation arose in a common ancestor, probably around 430-656 years ago, coinciding with the arrival of the first French settlers. Application of the results of this study could significantly improve the molecular testing and clinical management of LS families in Quebec.
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Affiliation(s)
- E Castellsagué
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada; Department of Medical Genetics, The Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada; Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, Barcelona, Spain
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11
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Zhang T, Boswell EL, McCall SJ, Hsu DS. Mismatch repair gone awry: Management of Lynch syndrome. Crit Rev Oncol Hematol 2014; 93:170-9. [PMID: 25459670 DOI: 10.1016/j.critrevonc.2014.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 08/22/2014] [Accepted: 10/01/2014] [Indexed: 12/16/2022] Open
Abstract
The hallmark of Lynch syndrome involves germline mutations of genes important in DNA mismatch repair. Affected family kindreds will have multiple associated malignancies, the most common of which is colorectal adenocarcinoma. Recently, evidence has shown that clinical diagnostic criteria provided by the Amsterdam Criteria and the Bethesda Guidelines must be linked with microsatellite instability testing to correctly diagnose Lynch syndrome. We present a case of metachronous colorectal adenocarcinomas in a patient less than 50 years of age, followed by a discussion of Lynch syndrome, with an emphasis on surveillance and prevention of malignancies.
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Affiliation(s)
- Tian Zhang
- Hematology and Medical Oncology, Duke Cancer Institute, Department of Medicine, Duke University Medical Center, DUMC 3841, Durham, NC 27710, United States.
| | - Elizabeth L Boswell
- Pathology and Laboratory Medicine Service, Durham VA Medical Center, 508 Fulton St., Durham, NC 27705, United States.
| | - Shannon J McCall
- Duke Cancer Institute, Department of Pathology, Duke University Medical Center, DUMC 3712, Durham, NC 27710, United States.
| | - David S Hsu
- Duke Cancer Institute, Department of Medicine, Division of Medical Oncology, Duke University Medical Center, DUMC 3233, Durham, NC 27710, United States.
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12
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Nakamura K, Banno K, Yanokura M, Iida M, Adachi M, Masuda K, Ueki A, Kobayashi Y, Nomura H, Hirasawa A, Tominaga E, Aoki D. Features of ovarian cancer in Lynch syndrome (Review). Mol Clin Oncol 2014; 2:909-916. [PMID: 25279173 DOI: 10.3892/mco.2014.397] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 05/30/2014] [Indexed: 01/03/2023] Open
Abstract
Lynch syndrome is a hereditary ovarian cancer with a prevalence of 0.9-2.7%. Lynch syndrome accounts for 10-15% of hereditary ovarian cancers, while hereditary breast and ovarian cancer syndrome accounts for 65-75% of these cancers. The lifetime risk for ovarian cancer in families with Lynch syndrome is ~8%, which is lower than colorectal and endometrial cancers, and ovarian cancer is not listed in the Amsterdam Criteria II. More than half of sporadic ovarian cancers are diagnosed in stage III or IV, but ≥80% of ovarian cancers in Lynch syndrome are diagnosed in stage I or II. Ovarian cancers in Lynch syndrome mostly have non-serous histology and different properties from those of sporadic ovarian cancers. A screening method for ovarian cancers in Lynch syndrome has yet to be established and clinical studies of prophylactic administration of oral contraceptives are not available. However, molecular profiles at the genetic level indicate that ovarian cancer in Lynch syndrome has a more favorable prognosis than sporadic ovarian cancer. Inhibitors of the phosphatidylinositol 3-kinase/mammalian target of the rapamycin pathway and anti-epidermal growth factor antibodies may have efficacy for the disease. To the best of our knowledge, this is the first review focusing on ovarian cancer in Lynch syndrome.
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Affiliation(s)
- Kanako Nakamura
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo 160-8582, Japan
| | - Kouji Banno
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo 160-8582, Japan
| | - Megumi Yanokura
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo 160-8582, Japan
| | - Miho Iida
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo 160-8582, Japan
| | - Masataka Adachi
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo 160-8582, Japan
| | - Kenta Masuda
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo 160-8582, Japan
| | - Arisa Ueki
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo 160-8582, Japan
| | - Yusuke Kobayashi
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo 160-8582, Japan
| | - Hiroyuki Nomura
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo 160-8582, Japan
| | - Akira Hirasawa
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo 160-8582, Japan
| | - Eiichiro Tominaga
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo 160-8582, Japan
| | - Daisuke Aoki
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo 160-8582, Japan
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Association between MSH6 G39E polymorphism and cancer susceptibility: a meta-analysis of 7,046 cases and 34,554 controls. Tumour Biol 2014; 35:6029-37. [DOI: 10.1007/s13277-014-1798-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 02/25/2014] [Indexed: 10/25/2022] Open
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Terui H, Akagi K, Kawame H, Yura K. CoDP: predicting the impact of unclassified genetic variants in MSH6 by the combination of different properties of the protein. J Biomed Sci 2013; 20:25. [PMID: 23621914 PMCID: PMC3651391 DOI: 10.1186/1423-0127-20-25] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 04/15/2013] [Indexed: 02/06/2023] Open
Abstract
Background Lynch syndrome is a hereditary cancer predisposition syndrome caused by a mutation in one of the DNA mismatch repair (MMR) genes. About 24% of the mutations identified in Lynch syndrome are missense substitutions and the frequency of missense variants in MSH6 is the highest amongst these MMR genes. Because of this high frequency, the genetic testing was not effectively used in MSH6 so far. We, therefore, developed CoDP (Combination of the Different Properties), a bioinformatics tool to predict the impact of missense variants in MSH6. Methods We integrated the prediction results of three methods, namely MAPP, PolyPhen-2 and SIFT. Two other structural properties, namely solvent accessibility and the change in the number of heavy atoms of amino acids in the MSH6 protein, were further combined explicitly. MSH6 germline missense variants classified by their associated clinical and molecular data were used to fit the parameters for the logistic regression model and to assess the prediction. The performance of CoDP was compared with those of other conventional tools, namely MAPP, SIFT, PolyPhen-2 and PON-MMR. Results A total of 294 germline missense variants were collected from the variant databases and literature. Of them, 34 variants were available for the parameter training and the prediction performance test. We integrated the prediction results of MAPP, PolyPhen-2 and SIFT, and two other structural properties, namely solvent accessibility and the change in the number of heavy atoms of amino acids in the MSH6 protein, were further combined explicitly. Variants data classified by their associated clinical and molecular data were used to fit the parameters for the logistic regression model and to assess the prediction. The values of the positive predictive value (PPV), the negative predictive value (NPV), sensitivity, specificity and accuracy of the tools were compared on the whole data set. PPV of CoDP was 93.3% (14/15), NPV was 94.7% (18/19), specificity was 94.7% (18/19), sensitivity was 93.3% (14/15) and accuracy was 94.1% (32/34). Area under the curve of CoDP was 0.954, that of MAPP for MSH6 was 0.919, of SIFT was 0.864 and of PolyPhen-2 HumVar was 0.819. The power to distinguish between pathogenic and non-pathogenic variants of these methods was tested by Wilcoxon rank sum test (p < 8.9 × 10-6 for CoDP, p < 3.3 × 10-5 for MAPP, p < 3.1 × 10-4 for SIFT and p < 1.2 × 10-3 for PolyPhen-2 HumVar), and CoDP was shown to outperform other conventional methods. Conclusion In this paper, we provide a human curated data set for MSH6 missense variants, and CoDP, the prediction tool, which achieved better accuracy for predicting the impact of missense variants in MSH6 than any other known tools. CoDP is available at http://cib.cf.ocha.ac.jp/CoDP/.
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Affiliation(s)
- Hiroko Terui
- The Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan
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Therkildsen C, Isinger-Ekstrand A, Ladelund S, Nissen A, Rambech E, Bernstein I, Nilbert M. Cancer risks and immunohistochemical profiles linked to the Danish MLH1 Lynch syndrome founder mutation. Fam Cancer 2013; 11:579-85. [PMID: 22864660 DOI: 10.1007/s10689-012-9552-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Founder mutations with a large impact in distinct populations have been described in Lynch syndrome. In Denmark, the MLH1 c.1667+2_1667_+8TAAATCAdelinsATTT mutation accounts for 25 % of the MLH1 mutant families. We used the national Danish hereditary nonpolyposis colorectal cancer register to estimate the cumulative lifetime risks for Lynch syndrome-associated cancer in 16 founder mutation families with comparison to 47 other MLH1 mutant families. The founder mutation conferred comparable risks for colorectal cancer (relative risks, RR, of 0.99 for males and 0.79 for females) and lower risks for extracolonic cancer (RR of 0.69 for endometrial cancer and 0.39 for all other extracolonic cancers). We also characterized expression of key Wnt-signaling proteins in colorectal cancers with the founder mutation. Aberrant staining affected β-catenin in 59 %, E-cadherin in 68 %, TCF-4 in 94 % and Cyclin D1 in 68 % with extensive inter-tumor variability despite the same underlying germline mutation. In conclusion, the Danish MLH1 founder mutation that accounts for a significant proportion of Lynch syndrome and is associated with a lower risk for extracolonic cancers.
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Affiliation(s)
- Christina Therkildsen
- HNPCC Register, Clinical Research Centre, Copenhagen University Hospital, Kettegård Alle 30, Hvidovre, Denmark.
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16
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Rosenthal AN, Fraser L, Manchanda R, Badman P, Philpott S, Mozersky J, Hadwin R, Cafferty FH, Benjamin E, Singh N, Evans DG, Eccles DM, Skates SJ, Mackay J, Menon U, Jacobs IJ. Results of annual screening in phase I of the United Kingdom familial ovarian cancer screening study highlight the need for strict adherence to screening schedule. J Clin Oncol 2012; 31:49-57. [PMID: 23213100 DOI: 10.1200/jco.2011.39.7638] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE To establish the performance characteristics of annual transvaginal ultrasound and serum CA125 screening for women at high risk of ovarian/fallopian tube cancer (OC/FTC) and to investigate the impact of delayed screening interval and surgical intervention. PATIENTS AND METHODS Between May 6, 2002, and January 5, 2008, 3,563 women at an estimated ≥ 10% lifetime risk of OC/FTC were recruited and screened by 37 centers in the United Kingdom. Participants were observed prospectively by centers, questionnaire, and national cancer registries. RESULTS Sensitivity for detection of incident OC/FTC at 1 year after last annual screen was 81.3% (95% CI, 54.3% to 96.0%) if occult cancers were classified as false negatives and 87.5% (95% CI, 61.7% to 98.5%) if they were classified as true positives. Positive and negative predictive values of incident screening were 25.5% (95% CI, 14.3 to 40.0) and 99.9% (95% CI, 99.8 to 100) respectively. Four (30.8%) of 13 incident screen-detected OC/FTCs were stage I or II. Compared with women screened in the year before diagnosis, those not screened in the year before diagnosis were more likely to have ≥ stage IIIc disease (85.7% v 26.1%; P = .009). Screening interval was delayed by a median of 88 days before detection of incident OC/FTC. Median interval from detection screen to surgical intervention was 79 days in prevalent and incident OC/FTC. CONCLUSION These results in the high-risk population highlight the need for strict adherence to screening schedule. Screening more frequently than annually with prompt surgical intervention seems to offer a better chance of early-stage detection.
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Affiliation(s)
- Adam N Rosenthal
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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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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Mukherjee B, Rennert G, Ahn J, Dishon S, Lejbkowicz F, Rennert H, Shiovitz S, Moreno V, Gruber SB. High risk of colorectal and endometrial cancer in Ashkenazi families with the MSH2 A636P founder mutation. Gastroenterology 2011; 140:1919-26. [PMID: 21419771 PMCID: PMC4835182 DOI: 10.1053/j.gastro.2011.02.071] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 02/08/2011] [Accepted: 02/23/2011] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS The MSH2 A636P mutation is a founder mutation in Ashkenazi Jews that causes Lynch syndrome, with a prevalence of 0.4%-0.7%. Estimates of age-specific cumulative risk and lifetime risk for colorectal cancer (CRC) and endometrial cancer (EC) specific to carriers of this mutation are not available. METHODS We studied 27 families with MSH2 A636P gene mutations identified in Israel; 13 were identified via a population-based, case-control study and 14 were identified from a clinical genetics service. Age-specific cumulative risks (penetrance) and hazard ratio (HR) estimates of CRC and EC risks were calculated and compared with the general Ashkenazi population using modified segregation analysis. An ascertainment-corrected likelihood that combined population-based and clinic-based sampling provided a powerful analysis for estimating penetrance. We analyzed 74 cases of CRC (40 in the clinic series and 34 in the population-based series), diagnosed at median ages of 50 years (men) and 49 years (women) in the combined sample. RESULTS The cumulative risk of CRC at age 70 was 61.62% for men (95% confidence interval [CI], 37.49%-76.45%) and 61.08% for women (95% CI, 39.39%-75.14%), with overall HRs of 31.8 (19.9-51.0) and 41.8 (27.4-64.0), respectively. There were 28 cases of EC, diagnosed at a median age of 53.0 years. The cumulative risk of EC was 55.64% (95% CI, 33.07%-70.58%) with an overall HR of 66.7 (41.7-106.7). CONCLUSIONS Lifetime risks of CRC and EC in MSH2 A636P carriers are high even after adjusting for ascertainment. These estimates are valuable for patients and providers; specialized cancer screening is necessary for carriers of this mutation.
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Affiliation(s)
- Bhramar Mukherjee
- Department of Biostatistics, University of Michigan Medical School and School of Public Health
| | - Gad Rennert
- Clalit National Israeli Cancer Control Center, Carmel Medical Center and Technion, Haifa, Israel
| | - Jaeil Ahn
- Department of Biostatistics, University of Michigan Medical School and School of Public Health
| | - Sara Dishon
- Clalit National Israeli Cancer Control Center, Carmel Medical Center and Technion, Haifa, Israel
| | - Flavio Lejbkowicz
- Clalit National Israeli Cancer Control Center, Carmel Medical Center and Technion, Haifa, Israel
| | - Hedy Rennert
- Clalit National Israeli Cancer Control Center, Carmel Medical Center and Technion, Haifa, Israel
| | - Stacey Shiovitz
- Department of Internal Medicine, University of Michigan Medical School
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology, IDIBELL,Department of Clinical Sciences, School of Medicine, University of Barcelona
| | - Stephen B. Gruber
- Department of Internal Medicine, University of Michigan Medical School,Department of Human Genetics, University of Michigan Medical School,Department of Epidemiology, University of Michigan School of Public Health
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19
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Borràs E, Pineda M, Blanco I, Jewett EM, Wang F, Teulé A, Caldés T, Urioste M, Martínez-Bouzas C, Brunet J, Balmaña J, Torres A, Ramón y Cajal T, Sanz J, Pérez-Cabornero L, Castellví-Bel S, Alonso A, Lanas A, González S, Moreno V, Gruber SB, Rosenberg NA, Mukherjee B, Lázaro C, Capellá G. MLH1 founder mutations with moderate penetrance in Spanish Lynch syndrome families. Cancer Res 2010; 70:7379-91. [PMID: 20858721 DOI: 10.1158/0008-5472.can-10-0570] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The variants c.306+5G>A and c.1865T>A (p.Leu622His) of the DNA repair gene MLH1 occur frequently in Spanish Lynch syndrome families. To understand their ancestral history and clinical effect, we performed functional assays and a penetrance analysis and studied their genetic and geographic origins. Detailed family histories were taken from 29 carrier families. Functional analysis included in silico and in vitro assays at the RNA and protein levels. Penetrance was calculated using a modified segregation analysis adjusted for ascertainment. Founder effects were evaluated by haplotype analysis. The identified MLH1 c.306+5G>A and c.1865T>A (p.Leu622His) variants are absent in control populations and segregate with the disease. Tumors from carriers of both variants show microsatellite instability and loss of expression of the MLH1 protein. The c.306+5G>A variant is a pathogenic mutation affecting mRNA processing. The c.1865T>A (p.Leu622His) variant causes defects in MLH1 expression and stability. For both mutations, the estimated penetrance is moderate (age-cumulative colorectal cancer risk by age 70 of 20.1% and 14.1% for c.306+5G>A and of 6.8% and 7.3% for c.1865T>A in men and women carriers, respectively) in the lower range of variability estimated for other pathogenic Spanish MLH1 mutations. A common haplotype was associated with each of the identified mutations, confirming their founder origin. The ages of c.306+5G>A and c.1865T>A mutations were estimated to be 53 to 122 and 12 to 22 generations, respectively. Our results confirm the pathogenicity, moderate penetrance, and founder origin of the MLH1 c.306+5G>A and c.1865T>A mutations. These findings have important implications for genetic counseling and molecular diagnosis of Lynch syndrome.
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Affiliation(s)
- Ester Borràs
- Laboratori de Recerca Translacional, Institut Català d'Oncologia, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
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20
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Shulman LP. Hereditary breast and ovarian cancer (HBOC): clinical features and counseling for BRCA1 and BRCA2, Lynch syndrome, Cowden syndrome, and Li-Fraumeni syndrome. Obstet Gynecol Clin North Am 2010; 37:109-33, Table of Contents. [PMID: 20494261 DOI: 10.1016/j.ogc.2010.03.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This article provides an overview of the molecular changes associated with inherited gynecologic malignancies and the incorporation of this information in the counseling of individuals at increased risk for developing malignancies, as well as conventional and emerging approaches to the screening of the general population. Cancer genetic counseling and its role in women's health care is examined. The focus is hereditary breast and ovarian cancer; however, cancer predisposition caused by genes other than BRCA1 and BRCA2 is also considered. The aim is to provide a foundation for counseling based on fundamental knowledge of the genes and their clinical consequences. The reader is then guided through the mechanics of risk assessment for individual patients, concluding with the psychosocial implications of counseling.
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Affiliation(s)
- Lee P Shulman
- Division of Clinical Genetics, Feinberg School of Medicine of Northwestern University, Chicago, IL, USA.
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21
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Walsh MD, Buchanan DD, Cummings MC, Pearson SA, Arnold ST, Clendenning M, Walters R, McKeone DM, Spurdle AB, Hopper JL, Jenkins MA, Phillips KD, Suthers GK, George J, Goldblatt J, Muir A, Tucker K, Pelzer E, Gattas MR, Woodall S, Parry S, Macrae FA, Haile RW, Baron JA, Potter JD, Le Marchand L, Bapat B, Thibodeau SN, Lindor NM, McGuckin MA, Young JP. Lynch syndrome-associated breast cancers: clinicopathologic characteristics of a case series from the colon cancer family registry. Clin Cancer Res 2010; 16:2214-24. [PMID: 20215533 PMCID: PMC2848890 DOI: 10.1158/1078-0432.ccr-09-3058] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PURPOSE The recognition of breast cancer as a spectrum tumor in Lynch syndrome remains controversial. The aim of this study was to explore features of breast cancers arising in Lynch syndrome families. EXPERIMENTAL DESIGN This observational study involved 107 cases of breast cancer identified from the Colorectal Cancer Family Registry (Colon CFR) from 90 families in which (a) both breast and colon cancer co-occurred, (b) families met either modified Amsterdam criteria, or had at least one early-onset (<50 years) colorectal cancer, and (c) breast tissue was available within the biospecimen repository for mismatch repair (MMR) testing. Eligibility criteria for enrollment in the Colon CFR are available online. Breast cancers were reviewed by one pathologist. Tumor sections were stained for MLH1, PMS2, MSH2, and MSH6, and underwent microsatellite instability testing. RESULTS Breast cancer arose in 35 mutation carriers, and of these, 18 (51%) showed immunohistochemical absence of MMR protein corresponding to the MMR gene mutation segregating the family. MMR-deficient breast cancers were more likely to be poorly differentiated (P = 0.005) with a high mitotic index (P = 0.002), steroid hormone receptor-negative (estrogen receptor, P = 0.031; progesterone receptor, P = 0.022), and to have peritumoral lymphocytes (P = 0.015), confluent necrosis (P = 0.002), and growth in solid sheets (P < 0.001) similar to their colorectal counterparts. No difference in age of onset was noted between the MMR-deficient and MMR-intact groups. CONCLUSIONS MMR deficiency was identified in 51% of breast cancers arising in known mutation carriers. Breast cancer therefore may represent a valid tissue option for the detection of MMR deficiency in which spectrum tumors are lacking.
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Affiliation(s)
- Michael D Walsh
- Familial Cancer Laboratory, I Floor, Bancroft Centre, Queensland Institute of Medical Research, Herston Road, Herston, Queensland 4006, Australia.
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22
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Baglietto L, Lindor NM, Dowty JG, White DM, Wagner A, Gomez Garcia EB, Vriends AHJT, Cartwright NR, Barnetson RA, Farrington SM, Tenesa A, Hampel H, Buchanan D, Arnold S, Young J, Walsh MD, Jass J, Macrae F, Antill Y, Winship IM, Giles GG, Goldblatt J, Parry S, Suthers G, Leggett B, Butz M, Aronson M, Poynter JN, Baron JA, Le Marchand L, Haile R, Gallinger S, Hopper JL, Potter J, de la Chapelle A, Vasen HF, Dunlop MG, Thibodeau SN, Jenkins MA. Risks of Lynch syndrome cancers for MSH6 mutation carriers. J Natl Cancer Inst 2010; 102:193-201. [PMID: 20028993 PMCID: PMC2815724 DOI: 10.1093/jnci/djp473] [Citation(s) in RCA: 263] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 11/10/2009] [Accepted: 11/17/2009] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Germline mutations in MSH6 account for 10%-20% of Lynch syndrome colorectal cancers caused by hereditary DNA mismatch repair gene mutations. Because there have been only a few studies of mutation carriers, their cancer risks are uncertain. METHODS We identified 113 families of MSH6 mutation carriers from five countries that we ascertained through family cancer clinics and population-based cancer registries. Mutation status, sex, age, and histories of cancer, polypectomy, and hysterectomy were sought from 3104 of their relatives. Age-specific cumulative risks for carriers and hazard ratios (HRs) for cancer risks of carriers, compared with those of the general population of the same country, were estimated by use of a modified segregation analysis with appropriate conditioning depending on ascertainment. RESULTS For MSH6 mutation carriers, the estimated cumulative risks to ages 70 and 80 years, respectively, were as follows: for colorectal cancer, 22% (95% confidence interval [CI] = 14% to 32%) and 44% (95% CI = 28% to 62%) for men and 10% (95% CI = 5% to 17%) and 20% (95% CI = 11% to 35%) for women; for endometrial cancer, 26% (95% CI = 18% to 36%) and 44% (95% CI = 30% to 58%); and for any cancer associated with Lynch syndrome, 24% (95% CI = 16% to 37%) and 47% (95% CI = 32% to 66%) for men and 40% (95% CI = 32% to 52%) and 65% (95% CI = 53% to 78%) for women. Compared with incidence for the general population, MSH6 mutation carriers had an eightfold increased incidence of colorectal cancer (HR = 7.6, 95% CI = 5.4 to 10.8), which was independent of sex and age. Women who were MSH6 mutation carriers had a 26-fold increased incidence of endometrial cancer (HR = 25.5, 95% CI = 16.8 to 38.7) and a sixfold increased incidence of other cancers associated with Lynch syndrome (HR = 6.0, 95% CI = 3.4 to 10.7). CONCLUSION We have obtained precise and accurate estimates of both absolute and relative cancer risks for MSH6 mutation carriers.
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Affiliation(s)
- Laura Baglietto
- Cancer Epidemiology Centre, Victorian Cancer Registry, Carlton, Victoria, Australia
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Shulman LP, Dungan JS. Cancer genetics: risks and mechanisms of cancer in women with inherited susceptibility to epithelial ovarian cancer. Cancer Treat Res 2010; 156:69-85. [PMID: 20811826 PMCID: PMC3086477 DOI: 10.1007/978-1-4419-6518-9_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Lee P Shulman
- Division of Reproductive Genetics, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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Abstract
In comparison with the mismatch repair genes MLH1 and MSH2, the genes MSH6 and PMS2 are relatively understudied with respect to cancer risk. However, some recent large studies of data combined from several sources, using analytic methods that appropriately condition on the varying methods of ascertainment, are producing reasonably precise estimates, which can be used for risk estimation in patients. To identify modifiers for risk in such carriers, a goal for epidemiologists to improve the health of carriers, such collaborative studies need to continue and expand to include additional mutation carriers in which lifestyle factors and DNA samples are available for analysis.
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Affiliation(s)
- Mark A Jenkins
- Centre for MEGA Epidemiology, School of Population Health, The University of Melbourne, Victoria 3010, Australia.
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25
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Tang R, Hsiung C, Wang JY, Lai CH, Chien HT, Chiu LL, Liu CT, Chen HH, Wang HM, Chen SX, Hsieh LL. Germ line MLH1 and MSH2 mutations in Taiwanese Lynch syndrome families: characterization of a founder genomic mutation in the MLH1 gene. Clin Genet 2009; 75:334-45. [PMID: 19419416 DOI: 10.1111/j.1399-0004.2009.01162.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This multicenter study evaluated the mutation spectrum and frequencies of the MLH1 and MSH2 genes and determined the occurrence of large genomic deletions in 93 unrelated Taiwanese families that fulfilled the Amsterdam criteria II by denaturing high-performance liquid chromatography analysis, DNA sequencing for aberrant chromatograms, and multiplex ligation-dependent probe amplification analysis. In total, 38 pathogenic mutations (10 large deletions and 28 point mutations or small deletion/insertions) in the MSH2 or MLH1 gene were identified in 61 of the 93 families (66%). Three of the 10 large deletions and 14 of the 28 point mutations or small insertions/deletions have not been reported elsewhere. Three mutations in the MLH1 gene, the MLH1c.1846_1848delAAG (5 families), deletion exons 11-15 (4 unrelated families), and MLH1c.793C>T (13 unrelated families), accounted for 35% of all cases with pathogenic mutations. Haplotype analysis indicated that mutant c.793C>T alleles were derived from two distinct common founders that might be inherited from a single ancestor of presumably Chinese origin. As a mutation detection strategy for Taiwanese Lynch syndrome patients, we recommend that diagnosis starts with screening for large genomic deletions and continues by screening for common mutations in exons 10 and 16 of the MLH1 gene prior to searching for small mutations in the remaining exons.
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Affiliation(s)
- R Tang
- Department of Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
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Hereditary non-polyposis colorectal cancer or Lynch syndrome: the gynaecological perspective. Curr Opin Obstet Gynecol 2009; 21:31-8. [PMID: 19125001 DOI: 10.1097/gco.0b013e32831c844d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Hereditary non-polyposis colorectal cancer (HNPCC) or Lynch syndrome is characterized by a number of other cancers including colorectal, endometrial and ovarian cancer. This review covers the gynaecological aspects of managing women with HNPCC: diagnostic criteria, molecular tests for diagnosis, cancer risks and different strategies for surveillance and prevention. RECENT FINDINGS Studies correcting for ascertainment bias found slightly lower penetrance estimates than those obtained from high-risk families. HNPCC linked ovarian cancer presents at an earlier age and stage and has similar survival rates as sporadic cancer. In endometrial tumours, microsatellite instability or immunohistochemistry has limited effectiveness in selecting individuals for genetic testing, due to molecular differences. Population-based data indicate that a significant proportion of mismatch repair gene carriers would be missed by current clinical criteria. Effective risk prediction models complement clinical risk assessment. Effectiveness of screening is unproven and prophylactic surgery is the best preventive option for women who have completed their families. Multimodal screening protocols from the age of 30-35 years are being evaluated. SUMMARY Risk of endometrial cancer in women with Lynch syndrome is as high as the risk of colorectal cancer. Further research is needed to identify the appropriate strategy for clinical risk assessment and optimize screening. A multidisciplinary approach is necessary to manage these women.
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Permuth-Wey J, Boulware D, Valkov N, Livingston S, Nicosia S, Lee JH, Sutphen R, Schildkraut J, Narod S, Parker A, Coppola D, Sellers T, Pal T. Sampling strategies for tissue microarrays to evaluate biomarkers in ovarian cancer. Cancer Epidemiol Biomarkers Prev 2009; 18:28-34. [PMID: 19124477 DOI: 10.1158/1055-9965.epi-08-0713] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
INTRODUCTION Tissue microarrays (TMA) enable rapid analysis of biomarkers in large-scale studies involving archival tumor specimens, however, their utility in heterogeneous tumors such as ovarian cancer is limited. METHODS In this study, immunohistochemical analysis was done on TMAs comprised of epithelial ovarian cancer (EOC) to estimate the prevalence of loss of expression of three mismatch repair proteins. TMAs were initially created using cores sampled from the center of donor tissue blocks from 59 EOC cases. Full sections were subsequently created and levels of expression were compared between tissues sampled from the central portion versus the periphery. Follow-up analyses were done by obtaining cores from the periphery of up to five additional donor blocks per case. A linear mixed model for each protein was used to investigate differences between results from the initial and follow-up blocks. RESULTS In the original TMAs created using centrally sampled cores, loss of mismatch repair expression was noted in 17 (29%) of the 59 cases. By comparison, analyses from peripherally sampled cores revealed loss of expression in only 6 of these 17 cases. For each protein, significant differences (P < 0.05) were detected between results from the initial donor block and the majority of the follow-up blocks. CONCLUSIONS Our investigations, based on EOC, suggest that sampling variability in protein expression may result when TMAs are used. Thus, at least for EOC, it is important to preferentially sample from the periphery of tumor blocks where exposure to tissue fixatives is optimal.
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Pal T, Permuth-Wey J, Sellers TA. A review of the clinical relevance of mismatch-repair deficiency in ovarian cancer. Cancer 2008; 113:733-42. [PMID: 18543306 DOI: 10.1002/cncr.23601] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Ovarian cancer ranks fifth in both cancer incidence and mortality among women in the United States. Defects in the mismatch-repair (MMR) pathway that arise through genetic and/or epigenetic mechanisms may be important etiologically in a reasonable proportion of ovarian cancers. Genetic mechanisms of MMR dysfunction include germline and somatic mutations in the MMR proteins. Germline mutations cause hereditary nonpolyposis colorectal cancer (HNPCC), which is the third most common cause of inherited ovarian cancer after BRCA1 and BRCA2 mutations. An epigenetic mechanism known to cause inactivation of the MMR system is promoter hypermethylation of 1 of the MMR genes, mutL homolog 1 (MLH1). Various laboratory methods, in addition to clinical and histopathologic criteria, can be used to identify MMR-deficient ovarian cancers. Such methods include microsatellite instability analysis, immunohistochemistry, MLH1 promoter hypermethylation testing, and germline mutation analysis. In this review, the authors describe the existing literature regarding the molecular, clinical, and histologic characteristics of MMR-deficient ovarian cancers along with the possible effect on survival and treatment response. By further defining the profile of MMR-deficient ovarian cancers and their associated etiologic mechanisms, there may be a greater potential to distinguish between those of hereditary and sporadic etiology. The ability to make such distinctions may be of diagnostic, prognostic, and therapeutic utility.
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Affiliation(s)
- Tuya Pal
- Department of Cancer Epidemiology and Genetics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.
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Abstract
Single-gene germline mutations conferring a high lifetime risk of colorectal cancer (CRC) account for up to 6% of all CRC cases. The most widely studied monogenic colorectal cancer syndromes include familial adenomatous polyposis (FAP) and Lynch syndrome. However, additional syndromes continue to be defined and new predisposition genes are continuing to be identified. Most recently, MYH-associated polyposis (MAP) and an "atypical Lynch syndrome" related to the presence of MSH6 mutations have been linked to an increased risk of CRC. In this review, we summarize basic information related to these newly recognized gene mutations, including the accumulating data on the prevalence and penetrance of deleterious mutations, as well as the management options for identified carriers and their families. Recognizing these heritable syndromes is essential and predictive genetic testing will continue to transform the field of cancer risk assessment by offering the opportunity to focus on more precise risk management and cancer prevention.
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Affiliation(s)
- Fay Kastrinos
- Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
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Abstract
The impact of predictive genetic testing on cancer care can be measured by the increased demand for and utilization of genetic services as well as in the progress made in reducing cancer risks in known mutation carriers. Nonetheless, differential access to and utilization of genetic counseling and cancer predisposition testing among underserved racial and ethnic minorities compared with the white population has led to growing health care disparities in clinical cancer genetics that are only beginning to be addressed. Furthermore, deficiencies in the utility of genetic testing in underserved populations as a result of limited testing experience and in the effectiveness of risk-reducing interventions compound access and knowledge-base disparities. The recent literature on racial/ethnic health care disparities is briefly reviewed, and is followed by a discussion of the current limitations of risk assessment and genetic testing outside of white populations. The importance of expanded testing in underserved populations is emphasized.
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Affiliation(s)
- Michael J Hall
- Department of Medicine, Mailman School of Public Health, Columbia University, New York, NY, USA
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Gruber SB. New developments in Lynch syndrome (hereditary nonpolyposis colorectal cancer) and mismatch repair gene testing. Gastroenterology 2006; 130:577-87. [PMID: 16472609 DOI: 10.1053/j.gastro.2006.01.031] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Stephen B Gruber
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, 48109, USA.
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Malander S, Rambech E, Kristoffersson U, Halvarsson B, Ridderheim M, Borg A, Nilbert M. The contribution of the hereditary nonpolyposis colorectal cancer syndrome to the development of ovarian cancer. Gynecol Oncol 2005; 101:238-43. [PMID: 16360201 DOI: 10.1016/j.ygyno.2005.10.029] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 09/30/2005] [Accepted: 10/14/2005] [Indexed: 02/05/2023]
Abstract
OBJECTIVE Ovarian cancer has one of the highest fractions of hereditary cases. The hereditary breast and ovarian cancer syndrome, primarily due to mutations in BRCA1 and BRCA2, is the main cause of heredity, but also the hereditary nonpolyposis colorectal cancer (HNPCC) syndrome confers an increased risk of ovarian cancer. In order to clarify the contribution of HNPCC to the development of ovarian cancer, we collected data on family history of cancer and characterized MMR function in a consecutive series of 128 tumors unselected for age at diagnosis and previously characterized for BRCA gene mutations. METHODS Expression of the MMR proteins MLH1, PMS2, MSH2, and MSH6 was analyzed by immunohistochemistry using tissue microarray sections. Tumors with reduced staining or loss of staining were also analyzed for microsatellite instability (MSI). RESULTS Loss of MMR protein expression was identified in 3 ovarian cancers, all of which had a MSI-high phenotype. DNA sequence analysis revealed disease-causing germline mutations (deletions of exons 4-6 in MLH1 and a 1-nucleotide deletion in exon 5 of MSH6) in two patients diagnosed at ages 40 and 49 years, both of whom had family histories suggestive of HNPCC. The genetic defect in the third case, which was a 47-year old woman without knowledge about her family history with loss of MLH1/PMS2 expression in the tumor tissue, remains elusive. A family history suggestive of HNPCC was identified in an additional case, but this tumor showed normal, retained MMR protein expression and a microsatellite stable phenotype. CONCLUSIONS About 2% of ovarian cancer is caused by germline mutations in the MMR-genes, a minor proportion as compared to the contribution of the BRCA-genes (11% in the present series). However, identification of HNPCC patients is important since it allows inclusion of high-risk individuals into control programs aimed at preventing the more frequent colorectal and endometrial cancers. Tumors within the HNPCC-spectrum should therefore be included when recording a family history of cancer among patients diagnosed with ovarian cancer.
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Affiliation(s)
- Susanne Malander
- Department of Oncology, Institute of Clinical Sciences, Lund University Hospital, SE-221 85 Lund, Sweden.
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