Gert Matthijs

EPCAM germline and somatic rearrangements in Lynch syndrome: identification of a novel 3'EPCAM deletion.

3′EPCAM (Epithelial Cell Adhesion Molecule) genomic rearrangements can be a cause of mismatch repair deficiency in rare Lynch syndrome families. 3′EPCAM deletions include the polyadenylation signal and might result in promoter hypermethylation of the centromeric MSH2 gene in cis. A somatic rearrangement in trans affecting MSH2 is responsible for the final mismatch repair deficiency in the corresponding tumors but the mechanisms are not well documented. In this report two germline 3′EPCAM deletions are described together with the corresponding somatic mutations in the patients colorectal tumors. Mutation and breakpoint analysis resulted in the identification of one novel (c.556‐531_*872del) and one known EPCAM deletion (c.859‐689_*14697del). Both deletions resulted from Alu mediated homologous recombination causing aberrant EPCAM‐MSH2 fusion transcripts. The colorectal tumors of the deletion carriers were MSI‐high. Strong hypermethylation of the MSH2 promoter was measured. Analysis of somatic genomic rearrangements showed a 4 Mb deletion including the EPCAM, MSH2 and MSH6 genes in one tumor and copy neutral loss of heterozygosity in the EPCAM‐MSH2 region in the other tumor. This indicates that hemi‐ and homozygous hypermethylation of the MSH2 promoter and hence complete silencing of MSH2 expression was responsible for the mismatch repair deficiency in both colorectal tumors.

Critical points for an accurate human genome analysis

Next‐generation sequencing is radically changing how DNA diagnostic laboratories operate. What started as a single‐gene profession is now developing into gene panel sequencing and whole‐exome and whole‐genome sequencing (WES/WGS) analyses. With further advances in sequencing technology and concomitant price reductions, WGS will soon become the standard and be routinely offered. Here, we focus on the critical steps involved in performing WGS, with a particular emphasis on points where WGS differs from WES, the important variables that should be taken into account, and the quality control measures that can be taken to monitor the process. The points discussed here, combined with recent publications on guidelines for reporting variants, will facilitate the routine implementation of WGS into a diagnostic setting.