International Society For Gastrointestinal Hereditary Tumours Research Articles

Position statement of the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) on APC I1307K and cancer risk

While constitutional pathogenic variants in the APC gene cause familial adenomatous polyposis, APC c.3920T>A; p.Ile1307Lys (I1307K) has been associated with a moderate increased risk of colorectal cancer (CRC), particularly in...

A novel heterozygous large deletion of MSH6 gene in a Chinese family with Lynch syndrome

Lynch syndrome (LS) is a common cancer syndrome that is inherited in an autosomal dominant manner. Its pathogenesis is thought to be closely related to germline mutations of mismatch repair (MMR) genes such as the MLH1, MSH2, PMS2 and MSH6 genes. This study identifies a Chinese family with LS clinically diagnosed according to the Amsterdam II criteria. In these patients, immuno-histochemical staining showed negative MSH6 expressions but positive MLH1, MSH2, and PMS2 expressions. In order to further explore the molecular biology of this LS family, we used targeted next-generation sequencing (NGS) and Multiplex ligation dependent probe amplification (MLPA) to identify the mutation and verify the authenticity of the mutation in 15 family members. For NGS, two panels have been used, one is of MLH1, MSH2, PMS2 and MSH6 genes, the other one is of 139 cancer genetic susceptibility genes. And for the large deletions/duplications can also be identified by NGS panel, an adjusted data analysis strategy of NGS has been used. As a result, we identified a novel heterozygous large deletion in MSH6 gene that was found to be co-segregated among affected family members. This deletion results in the loss of a 3246 bp-sized fragment in MSH6 gene exons 5–9 which represents the coding regions of the MSH6 ATPase domain. This novel mutation has yet to be documented in the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) database. This mutation resulted in MSH6 protein losing gene mismatch repair function, and further caused the microsatellite instable. We speculate that this mutation may significantly impact MMR function through impaired ATP domain function. Theoretically, this proband would likely benefit from PD-1 immune check-point blockade therapy, but conversely, we observed that tumors appeared to rapidly progress after 4 sessions of anti-PD-1 treatment. Further studies to validate the effectiveness of anti-PD-1 treatments in carriers of this mutation are necessary.

Assessment of the InSiGHT Interpretation Criteria for the Clinical Classification of 24 MLH1 and MSH2 Gene Variants.

Pathogenicity assessment of DNA variants in disease genes to explain their clinical consequences is an integral component of diagnostic molecular testing. The International Society for Gastrointestinal Hereditary Tumors (InSiGHT) has developed specific criteria for the interpretation of mismatch repair (MMR) gene variants. Here, we performed a systematic investigation of 24 MLH1 and MSH2 variants. The assessments were done by analyzing population frequency, segregation, tumor molecular characteristics, RNA effects, protein expression levels, and in vitro MMR activity. Classifications were confirmed for 15 variants and changed for three, and for the first time determined for six novel variants. Overall, based on our results, we propose the introduction of some refinements to the InSiGHT classification rules. The proposed changes have the advantage of homogenizing the InSIGHT interpretation criteria with those set out by the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium for the BRCA1/BRCA2 genes. We also observed that the addition of only few clinical data was sufficient to obtain a more stable classification for variants considered as "likely pathogenic" or "likely nonpathogenic." This shows the importance of obtaining as many as possible points of evidence for variant interpretation, especially from the clinical setting.

Update on Lynch syndrome genomics.

Four main DNA mismatch repair (MMR) genes have been identified, MLH1, MSH2, MSH6, and PMS2, which when mutated cause susceptibility to Lynch syndrome (LS). LS is one of the most prevalent hereditary cancer syndromes in man and accounts for 1–3 % of unselected colorectal carcinomas and some 15 % of those with microsatellite instability and/or absent MMR protein. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) maintains a database for LS-associated mutations since 1996. The database was recently reorganized to efficiently gather published and unpublished data and to classify the variants according to a five-tiered scheme linked to clinical recommendations. This review provides an update of germline mutations causing susceptibility to LS based on information available in the InSiGHT database and the latest literature. MMR gene mutation profiles, correlations between genotype and phenotype, and possible mechanisms leading to the characteristic spectrum of tumors in LS are discussed in light of the different functions of MMR proteins, many of which directly serve cancer avoidance.

A proposed staging system and stage-specific interventions for familial adenomatous polyposis

It is not possible to accurately count adenomas in many patients with familial adenomatous polyposis (FAP). Nevertheless, polyp counts are critical in evaluating each patient's response to interventions. However, the U.S. Food and Drug Administration no longer recognizes the decrease in polyp burden as a sufficient chemoprevention trial treatment endpoint requiring a measure of "clinical benefit." To develop endpoints for future industry-sponsored chemopreventive trials, the International Society for Gastrointestinal Hereditary Tumors (InSIGHT) developed an FAP staging and intervention classification scheme for lower-GI tract polyposis. Twenty-four colonoscopy or sigmoidoscopy videos were reviewed by 26 clinicians familiar with diagnosis and treatment of FAP. The reviewers independently assigned a stage to a case by using the proposed system and chose a stage-specific intervention for each case. Our endpoint was the degree of concordance among reviewers staging and intervention assessments. The staging and intervention ratings of the 26 reviewers were highly concordant (ρ= 0.710; 95% credible interval, 0.651-0.759). Sixty-two percent of reviewers agreed on the FAP stage, and 90% of scores were within ±1 stage of the mode. Sixty percent of reviewers agreed on the intervention, and 86% chose an intervention within ±1 level of the mode. The proposed FAP colon polyposis staging system and stage-specific intervention are based on a high degree of agreement on the part of experts in the review of individual cases of polyposis. Therefore, reliable and clinically relevant means for measuring trial outcomes can be developed. Outlier cases showing wide scatter in stage assignment call for individualized attention and may be inappropriate for enrollment in clinical trials for this reason.

Literature mining of genetic variants for curation: quantifying the importance of supplementary material

A major focus of modern biological research is the understanding of how genomic variation relates to disease. Although there are significant ongoing efforts to capture this understanding in curated resources, much of the information remains locked in unstructured sources, in particular, the scientific literature. Thus, there have been several text mining systems developed to target extraction of mutations and other genetic variation from the literature. We have performed the first study of the use of text mining for the recovery of genetic variants curated directly from the literature. We consider two curated databases, COSMIC (Catalogue Of Somatic Mutations In Cancer) and InSiGHT (International Society for Gastro-intestinal Hereditary Tumours), that contain explicit links to the source literature for each included mutation. Our analysis shows that the recall of the mutations catalogued in the databases using a text mining tool is very low, despite the well-established good performance of the tool and even when the full text of the associated article is available for processing. We demonstrate that this discrepancy can be explained by considering the supplementary material linked to the published articles, not previously considered by text mining tools. Although it is anecdotally known that supplementary material contains ‘all of the information’, and some researchers have speculated about the role of supplementary material (Schenck et al. Extraction of genetic mutations associated with cancer from public literature. J Health Med Inform 2012;S2:2.), our analysis substantiates the significant extent to which this material is critical. Our results highlight the need for literature mining tools to consider not only the narrative content of a publication but also the full set of material related to a publication.

Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database

The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases.

Annotating the biomedical literature for the human variome

This article introduces the Variome Annotation Schema, a schema that aims to capture the core concepts and relations relevant to cataloguing and interpreting human genetic variation and its relationship to disease, as described in the published literature. The schema was inspired by the needs of the database curators of the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) database, but is intended to have application to genetic variation information in a range of diseases. The schema has been applied to a small corpus of full text journal publications on the subject of inherited colorectal cancer. We show that the inter-annotator agreement on annotation of this corpus ranges from 0.78 to 0.95 F-score across different entity types when exact matching is measured, and improves to a minimum F-score of 0.87 when boundary matching is relaxed. Relations show more variability in agreement, but several are reliable, with the highest, cohort-has-size, reaching 0.90 F-score. We also explore the relevance of the schema to the InSiGHT database curation process. The schema and the corpus represent an important new resource for the development of text mining solutions that address relationships among patient cohorts, disease and genetic variation, and therefore, we also discuss the role text mining might play in the curation of information related to the human variome. The corpus is available at http://opennicta.com/home/health/variome.

The InSiGHT approach to classification of mismatch repair gene variants

The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) is committed to the sharing of MMR variant information through the publicly accessible InSiGHT database. This amalgamation of various types of data related to MMR variants and Lynch Syndrome encompasses family history, tumour pathology, genotype, RNA, in silico and in vitro information sourced from published literature and submissions from various centers. InSiGHT is collaborating with organisations including those with national MMR data-sets, in order to centralise and make public the full extent of Lynch Syndrome associated variants. It is also InSiGHT’s goal to increase the number of submissions from individual labs, and encourages scientists from around the world to participate in this effort. To understand the clinical impact of these variants, InSiGHT is bringing together an international group of experts to develop qualitative classification rules and apply them to variants of uncertain significance. The application of these classification rules to variants is a work in progress, with input from specialists in a diverse range of fields, and will enable thorough analysis of the available data. This process will culminate in regular teleconferences of a panel of experts who will discuss each variant and reach consensus on the clinical significance. Subsequent publication of the outcome will be of particular relevance to the medical genetics community.

Deciphering the colon cancer genes—report of the InSiGHT‐Human Variome Project Workshop, UNESCO, Paris 2010

The Human Variome Project (HVP) has established a pilot program with the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) to compile all inherited variation affecting colon cancer susceptibility genes. An HVP-InSiGHT Workshop was held on May 10, 2010, prior to the HVP Integration and Implementation Meeting at UNESCO in Paris, to review the progress of this pilot program. A wide range of topics were covered, including issues relating to genotype-phenotype data submission to the InSiGHT Colon Cancer Gene Variant Databases (chromium.liacs.nl/LOVD2/colon_cancer/home.php). The meeting also canvassed the recent exciting developments in models to evaluate the pathogenicity of unclassified variants using in silico data, tumor pathology information, and functional assays, and made further plans for the future progress and sustainability of the pilot program.

The Human Variome Project – Pilot project and progress

AbstractCotton R.G.H. and Collaborators Convenor, Human Variome Project; Head, Genomic Disorders Research Centre, Howard Florey Institute; Department of Medicine, the University of Melbourne, Melbourne, Australia The Human Variome Project (Cotton et al 2007) ("www.humanvariomeproject.org":http://www.humanvariomeproject.org) was initiated in June 2006 (Ring H.Z. et al. 2006) drawing attention to the importance of collection of variation and its phenotype and to develop programs to put this into effect.The project builds on work and concepts of the HGVS and others over many years ("www.hgvs.org":http://www.hgvs.org) to focus on all variation associated with disease. The project will include those discovering mutations and their effects and then collecting the data making it instantly available for those who need it to inform clinical decisions, therapy, and research.A high level meeting in Spain (Kaput et al. 2009) developed plans to implement the recommendations of the HVP Melbourne meeting (Cotton et al. 2007). The HVP was featured recently in relation to Neurogenetic databases in Science (Cotton et al. 2008) and a HVP Neurogenetic Database Initiative is being formed after an HVP Neurogenetics forum in Hawaii October 2009. The Nutrigenomics community is establishing protocols in partnership with HVP. This activity culminated in the third HVP meeting hosted by and under the patronage of UNESCO in Paris ("www.humanvariomeproject.org":http://www.humanvariomeproject.org). A manuscript on the Paris meeting is in preparation (Maija Kohonen Corish et al).The HVP and InSiGHT (International Society for Gastrointestinal Hereditary Tumours) ("www.insight-group.org":http://www.insight-group.org) has developed a major pilot study to develop procedures and systems to allow effortless flow of de-identified data for the colon cancer genes from the patient/clinic/diagnostic laboratory via curated locus or gene specific databases to central databases/genome browsers such as NCBI, UCSC and EBI. The system will be easily adaptable to other genes and to multiple laboratories, states and countries worldwide.A country specific collection pilot is underway in Australia and an International Confederation of these countries has been initiated with Malaysia, Korea, China, Australia and Saudi Arabia in the application process.Other pilot studies developed include specific ethical studies related to mutation collection, loading of LSDB content to NCBI databases, funding of curation of LSDBs, a system of Microattribution/reward for mutation submission.

The Human Variome Project – Pilot project and progress

Cotton R.G.H. and Collaborators Convenor, Human Variome Project; Head, Genomic Disorders Research Centre, Howard Florey Institute; Department of Medicine, the University of Melbourne, Melbourne, Australia The Human Variome Project (Cotton et al 2007) ("www.humanvariomeproject.org":http://www.humanvariomeproject.org) was initiated in June 2006 (Ring H.Z. et al. 2006) drawing attention to the importance of collection of variation and its phenotype and to develop programs to put this into effect.The project builds on work and concepts of the HGVS and others over many years ("www.hgvs.org":http://www.hgvs.org) to focus on all variation associated with disease. The project will include those discovering mutations and their effects and then collecting the data making it instantly available for those who need it to inform clinical decisions, therapy, and research.A high level meeting in Spain (Kaput et al. 2009) developed plans to implement the recommendations of the HVP Melbourne meeting (Cotton et al. 2007). The HVP was featured recently in relation to Neurogenetic databases in Science (Cotton et al. 2008) and a HVP Neurogenetic Database Initiative is being formed after an HVP Neurogenetics forum in Hawaii October 2009. The Nutrigenomics community is establishing protocols in partnership with HVP. This activity culminated in the third HVP meeting hosted by and under the patronage of UNESCO in Paris ("www.humanvariomeproject.org":http://www.humanvariomeproject.org). A manuscript on the Paris meeting is in preparation (Maija Kohonen Corish et al).The HVP and InSiGHT (International Society for Gastrointestinal Hereditary Tumours) ("www.insight-group.org":http://www.insight-group.org) has developed a major pilot study to develop procedures and systems to allow effortless flow of de-identified data for the colon cancer genes from the patient/clinic/diagnostic laboratory via curated locus or gene specific databases to central databases/genome browsers such as NCBI, UCSC and EBI. The system will be easily adaptable to other genes and to multiple laboratories, states and countries worldwide.A country specific collection pilot is underway in Australia and an International Confederation of these countries has been initiated with Malaysia, Korea, China, Australia and Saudi Arabia in the application process.Other pilot studies developed include specific ethical studies related to mutation collection, loading of LSDB content to NCBI databases, funding of curation of LSDBs, a system of Microattribution/reward for mutation submission.

Report of the Combined Meeting of the International Society for Gastrointestinal Hereditary Tumours, the Human Variome Project and the National Cancer Institute Colon Cancer Family Registry, Duesseldorf, Germany, 24 June 2009

This report provides a summary of the first combined meeting of the International Society for Gastrointestinal Hereditary Tumours (InSiGHT), the NCI Colon Cancer Family Registry (C-CFR) Steering Committee and the Human Variome Project (HVP), held as a daylong premeeting of the 2009 Biennial Meeting of InSiGHT in Duesseldorf Germany. The meeting was attended by over 100 registrants representing over 40 countries including 26 members of the CFR Steering Committee. The meeting organizer Finlay Macrae (Melbourne, Australia), Secretary of InSiGHT, opened the meeting and explained that the purpose of the meeting was to bring together the collective expertise of the NCI CFR leadership, the HVP and InSiGHT in order to share knowledge and foster future substantive research collaboration. InSiGHT President Gabriela Moeslein (Duesseldorf, Germany) presented a brief history of the successful merger of the Leeds Castle Polyposis Group and the International Collaborative Group on HNPCC to form InSiGHT, with its first formal meeting in Newcastle UK in 2005. Altogether 25 active countries are represented in InSiGHT from Europe, North and South America, Middle East, Africa, Asia and Oceania. Gabriela Moeslein stressed the clinical relevance of the many areas of translational research being conducted by InSiGHT members including the detailed analysis of genotype-phenotype relationships in hereditary gastrointestinal malignancy. With the advances of molecular genetics, focus is now shifting from ascertainment of hereditary cancer through the disease phenotype to the interpretation of the entire range of molecular variants of the susceptibility genes. The chair of NCI C-CFR Steve Gallinger (Toronto, Canada) described the C-CFR as a platform for research on the genetics of colorectal cancer including gene and environment interactions. A major goal of the C-CFR is to provide resources for interdisciplinary studies designed to understand the etiology and prognosis of colon cancer. He described the Phase 1 and 2 accomplishments of the C-CFR efforts since 1998, including clinic-based and population-based studies. About 7,400 probands, 30,871 family members and 5,050 controls have been enrolled in six centres in the US, Canada and Australasia. The goals of Phase 3, initiated in 2008, were also reviewed including expansion of the number of families enrolled through clinic-based recruitment. Steve Gallinger stressed the extensive biospecimen resources, consisting of blood, paraffin-embedded and frozen tissue and transformed cell This study is conducted for the InSiGHT, HVP and NCI-CCFR Meeting Participants: G. Moeslein, S. Gallinger, R. Cotton, M. Genuardi, S. Tavtigian, G. Byrnes, A. Spurdle, I. Bernstein, N. de Wind, M. Nystrom, R. Hofstra, M. Woods, J. den Dunnen, B. Bhapat, M. Qi, P. Propping, H. Vasen, S. Povey, R. Sijmons, H. Thomas, J. Baron, S. Thibodeau, A. Boussioutas, J. Young, M. Jenkins, M. Dunlop, R. Houlston, I. Tomlinson, U. Peters, D. Ahnen, S. Parry, B. Parry, R. Scott, G. Hannan.

Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue

BackgroundHereditary non-polyposis colon cancer (HNPCC) is an autosomal dominant syndrome predisposing to the early development of various cancers including those of colon, rectum, endometrium, ovarium, small bowel, stomach and urinary tract. HNPCC is caused by germline mutations in the DNA mismatch repair genes, mostly hMSH2 or hMLH1.In this study, we report the analysis for genetic counseling of three first-degree relatives (the mother and two sisters) of a male who died of colorectal adenocarcinoma at the age of 23. The family fulfilled strict Amsterdam-I criteria (AC-I) with the presence of extracolonic tumors in the extended pedigree. We overcame the difficulty of having a proband post-mortem non-tumor tissue sample for MSI testing by studying the alleles carried by his progenitors.MethodsTumor MSI testing is described as initial screening in both primary and metastasis tumor tissue blocks, using the reference panel of 5 microsatellite markers standardized by the National Cancer Institute (NCI) for the screening of HNPCC (BAT-25, BAT-26, D2S123, D5S346 and D17S250). Subsequent mutation analysis of the hMLH1 and hMSH2 genes was performed.ResultsThree of five microsatellite markers (BAT-25, BAT-26 and D5S346) presented different alleles in the proband's tumor as compared to those inherited from his parents. The tumor was classified as high frequency microsatellite instability (MSI-H). We identified in the HNPCC family a novel germline missense (c.1864C>A) mutation in exon 12 of hMSH2 gene, leading to a proline 622 to threonine (p.Pro622Thr) amino acid substitution.ConclusionThis approach allowed us to establish the tumor MSI status using the NCI recommended panel in the absence of proband's non-tumor tissue and before sequencing the obligate carrier. According to the Human Gene Mutation Database (HGMD) and the International Society for Gastrointestinal Hereditary Tumors (InSiGHT) Database this is the first report of this mutation.

Lynch Syndrome Genes

Since the discovery of the major human genes with DNA mismatch repair (MMR) function in 1993-1995, mutations in four, MSH2, MLH1, MSH6, and PMS2, have been convincingly linked to susceptibility of hereditary nonpolyposis colorectal cancer (HNPCC)/Lynch syndrome. Among these, PMS2 mutations are associated with diverse clinical features, including those of the Turcot syndrome. Two additional MMR genes, MLH3 and PMS1, have also been proposed to play a role in Lynch syndrome predisposition, but the clinical significance of mutations in these genes is less clear. According to the database maintained by the International Collaborative Group on Hereditary Nonpolyposis Colorectal Cancer (ICG-HNPCC), current InSiGHT (International Society for Gastrointestinal Hereditary Tumors), approximately 500 different HNPCC-associated MMR gene mutations are known that primarily involve MLH1 (approximately 50%), MSH2 (approximately 40%), and MSH6 (approximately 10%). Examination of HNPCC/Lynch syndrome-associated MMR genes and their mutations has revealed several other important functions for their protein products beyond postreplicative mismatch repair as well as many alternative mechanisms of pathogenicity. Despite these advances, much is yet to be learned about the molecular basis of correlations between genetic changes and clinical features of the disease.

Mutations Associated with HNPCC Predisposition — Update of ICG-HNPCC/INSiGHT Mutation Database

In 1994, the International Collaborative Group on Hereditary Nonpolyposis Colorectal Cancer (ICG-HNPCC) established an international database of mutations identified in families with Lynch (HNPCC) syndrome. The data are publicly available at http://www.nfdht.nl. The information stored in the database was systematically analyzed in 1997, and at that time, 126 different predisposing mutations were reported affecting the DNA mismatch repair genes MSH2 and MLH1 and occurring in 202 families. In 2003, the ICG-HNPCC and the Leeds Castle Polyposis Group (LCPG) merged into a new group, INSiGHT (International Society for Gastrointestinal Hereditary Tumors). The present update of the database of DNA mismatch repair gene mutations of INSiGHT includes 448 mutations that primarily involve MLH1 (50%), MSH2 (39%), and MSH6 (7%) and occur in 748 families from different parts of the world.