Identification of a novel intergenic EPCAM-MSH2 deletion causing EPCAM-associated Lynch syndrome by long-read nanopore sequencing

Epithelial cell adhesion molecule ( EPCAM )-associated Lynch syndrome arises from deletions at the 3′-end of EPCAM 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 EPCAM-MSH2 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 EPCAM-MSH2 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 MSH2 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 EPCAM deletions, whereby aberrant EPCAM transcription interferes with MSH2 promoter regulation in a tissue-specific manner. These findings support reclassification of this variant to likely pathogenic and establish a diagnosis of EPCAM -associated Lynch syndrome. This report provides the first evidence that intergenic EPCAM-MSH2 deletions are associated with MSH2 epimutations and highlights the diagnostic utility of long-read sequencing for noncoding structural variants.