Identification of genetic variants for clinical management of familial colorectal tumors

Mev Dominguez-Valentin,Monika Morak,Sigve Nakken,Elke Holinski-Feder,Eivind Hovig,Hélène Tubeuf,Anke M Nissen,Alexandra Martins,Per Olaf Ekstrøm,Daniel Vodak,Pål Møller

doi:10.1186/s12881-018-0533-9

Abstract

BackgroundThe genetic mechanisms for families who meet the clinical criteria for Lynch syndrome (LS) but do not carry pathogenic variants in the mismatch repair (MMR) genes are still undetermined. We aimed to study the potential contribution of genes other than MMR genes to the biological and clinical characteristics of Norwegian families fulfilling Amsterdam (AMS) criteria or revised Bethesda guidelines.MethodsThe Hereditary Cancer Biobank of the Norwegian Radium Hospital was interrogated to identify individuals with a high risk of developing colorectal cancer (CRC) for whom no pathogenic variants in MMR genes had been found in routine diagnostic DNA sequencing. Forty-four cancer susceptibility genes were selected and analyzed by using our in-house designed TruSeq amplicon-based assay for targeted sequencing. RNA splicing- and protein-dedicated in silico analyses were performed for all variants of unknown significance (VUS). Variants predicted as likely to affect splicing were experimentally analyzed by resorting to minigene assays.ResultsWe identified a patient who met the revised Bethesda guidelines and carried a likely pathogenic variant in CHEK2 (c.470 T > C, p.I157T). In addition, 25 unique VUS were identified in 18 individuals, of which 2 exonic variants (MAP3K1 c.764A > G and NOTCH3 c.5854G >A) were analyzed in the minigene splicing assay and found not to have an effect on RNA splicing.ConclusionsAmong high-risk CRC patients that fulfill the AMS criteria or revised Bethesda guidelines, targeted gene sequencing identified likely pathogenic variant and VUS in other genes than the MMR genes (CHEK2, NOTCH3 and MAP3K1). Our study suggests that the analysis of genes currently excluded from routine molecular diagnostic screens may confer cancer susceptibility.

Highlights

The genetic mechanisms for families who meet the clinical criteria for Lynch syndrome (LS) but do not carry pathogenic variants in the mismatch repair (MMR) genes are still undetermined
In an effort to discover inherited genetic variants that influence biological and clinical characteristics of familial colorectal cancer (CRC) developed in unrelated high-risk patients, who previously tested negative for pathogenic variants in MMR genes, we examined 44 cancer associated genes using generation sequencing (NGS), and applied minigene-based assay to analyze the impact of a subset of genetic variants on RNA splicing
Clinical characteristics and family history Upon querying the Hereditary Cancer Biobank of the Norwegian Radium Hospital for cases that fulfill the AMS and/or the revised Bethesda guidelines, we identified 34 unrelated potential high-risk CRC individuals who did not carry pathogenic variants in MMR genes

Summary

Introduction

The genetic mechanisms for families who meet the clinical criteria for Lynch syndrome (LS) but do not carry pathogenic variants in the mismatch repair (MMR) genes are still undetermined. Patients with CRC are referred to germline mismatch repair (MMR) testing based on the identification of high-risk phenotypic features (i.e. early age of onset, family history, clinical criteria), but beyond microsatellite instability (MSI) and MMR. A high proportion of cases who meet the clinical criteria for LS (~ 60%) do not carry pathogenic variants in the MMR genes and have been reported as familial colorectal cancer type X (FCCTX) or Lynch-like syndrome (LLS) according to their MSI status [12,13,14,15,16]. The genetic mechanisms are undetermined in the majority of these families [14]

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