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

2015

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.