Targeted next-generation sequencing identified novel mismatch repair risk-variants involved in hereditary colorectal cancer

Abstract

Colorectal cancer (CRC) is the third most common malignancy worldwide, with over 1 million new cases annually. Around 30% of cases are believed to be familial with causal genetic alterations. However, fewer than 10% of cases are so far genetically explained. Lynch syndrome (LS) is the most common hereditary CRC syndrome, explaining around 5% of all cases. LS is caused by pathogenic germline mutations in one of four DNA mismatch repair (MMR) genes: MLH1, MSH2, MSH6, and PMS2. Extensive research is currently attempting to decipher the complete underlying genetic patterns of CRC, with the hope of improving cancer diagnosis and treatment. In this project, a gene-panel consisting of 124 genes across 95 CRC patients was sequenced using NGS. The patients included in this study have a family history of CRC, but previous genetic testing has not identified causal mutations. The aim of the present Master of Science project was to search for potentially disease-causing pathogenic germline mutations within 22 MMR system-associated genes. Using in silico prediction tools, the deleterious potential of the detected variants was assessed. 20 candidate predisposition mutations were identified across 12 MMR-associated genes in 22 patients. Based on available information about the gene, mutation position, patient phenotype, findings in previous studies, and prediction tools, the identified variants are suggested to be involved in the development of cancer. To confirm these indications, further studies of the variants are needed. Segregation analysis will reveal familial inheritance and penetrance status of the mutations, and functional studies are required to elucidate the consequences on protein function. This project has demonstrated the successful sequencing of a multipatient gene panel. The NGS approach is rapidly making an entrance in diagnostics, and this study has shown an efficient and reliable method of sequencing numerous genes and samples in parallel. To facilitate unambiguous data interpretation and standardized analysis further advances are needed before widespread routine application will be advantageous in the clinic.