Genetic Analyses to Identify Causative Germline Variants and Molecular Subtypes in Colorectal Polyposis Syndromes

Abstract

Colorectal polyposis syndromes are rare and genetically heterogeneous precancerous conditions with an increased risk to develop colorectal cancer. In a substantial fraction of patients, no genetic cause can be identified during routine diagnostics. As part of the European Solve-RD project, a multi-layered genomic approach was applied to a multi-center cohort of 219 patients with unexplained polyposis to identify novel causal germline variants and characterize early steps of polyp formation. The systematic reanalysis of existing leukocyte exome sequencing data using updated bioinformatic pipelines and variant interpretation guidelines was able to resolve 3% of the cohort with a definitive genetic diagnosis. Furthermore, candidate variants were identified in another 4%. Building on these findings, a comprehensive molecular profiling was conducted. Exome sequencing was performed for 299 colorectal tumors (273 polyps, 26 carcinomas) from the same cohort. Key differences were identified between adenomas and serrated polyps in somatic driver gene events. Furthermore, the etiology in 19% of cases could be resolved through detection of APC mutational mosaicism. In 9% of serrated polyps, a CIMP-high methylation status was detected. Mutational signature analysis indicated that serrated polyps are molecularly more similar to normal colon tissue than adenomas. In addition, leukocyte genome sequencing was performed in a separate cohort of 98 patients with unexplained ultra-rare tumor syndromes. Thereby, 7% of cases could be clarified and several non-coding candidate variants were identified that may contribute to disease. The study demonstrates the value of a systematic combined analysis of both leukocyte and tumor exome data to solve unexplained polyposis cases. Molecular tumor profiling of the largest collection of both adenomatous and serrated polyps from patients with unexplained polyposis provided clues on the tumorigenic processes involved. Follow-up projects should extend these analyses beyond predefined gene lists and apply innovative technologies to discover novel candidates and gain further insights in tumorigenesis