Identification of a novel intergenic <i>EPCAM-MSH2</i> deletion causing EPCAM-associated Lynch syndrome by long-read nanopore sequencing.

Abstract

Epithelial cell adhesion molecule (<i>EPCAM</i>)-associated Lynch syndrome arises from deletions at the 3'-end of <i>EPCAM</i> that disrupt transcriptional termination, generate read-through transcripts and cause epigenetic silencing of MSH2 in EPCAM-expressing tissues. However, the clinical significance of deletions confined to the <i>EPCAM-MSH2</i> intergenic region remains uncertain without in-depth investigation.We investigated a family with a strong history of Lynch syndrome-related cancers in whom diagnostic testing by short-read sequencing identified a heterozygous deletion spanning the <i>EPCAM-MSH2</i> intergenic region that was initially classified as a variant of uncertain significance. The variant was further characterised using long-read Oxford Nanopore sequencing with adaptive sampling and methylation profiling.Long-read sequencing defined precise breakpoints, and tumour analysis demonstrated <i>MSH2</i> promoter hypermethylation with complete loss of MSH2 protein expression in the absence of germline promoter methylation. The molecular phenotype closely mirrored the recognised mechanism for 3'-end <i>EPCAM</i> deletions, whereby aberrant <i>EPCAM</i> transcription interferes with <i>MSH2</i> promoter regulation in a tissue-specific manner.These findings support reclassification of this variant to likely pathogenic and establish a diagnosis of <i>EPCAM</i>-associated Lynch syndrome. This report provides the first evidence that intergenic <i>EPCAM-MSH2</i> deletions are associated with <i>MSH2</i> epimutations and highlights the diagnostic utility of long-read sequencing for noncoding structural variants.