Large distant deletion disrupts CDKN2A enhancer and predisposes to melanoma

Deleterious CDKN2A germline variants account for ~40% of familial melanoma cases, while rare variants in CDK4, BAP1, and telomere-maintenance genes collectively attribute ~10% of familial risk. We sought to identify new high-penetrance susceptibility variants by sequencing 305 melanoma cases from 89 multi-case families negative for known predisposition gene variants. In one family, cutaneous melanoma co-segregated with a rare variant in DMRTA1 (p.Glu383Gln), located less than 480 kb upstream of CDKN2A on chromosome 9. Whole-genome sequencing then revealed an intergenic 234kb deletion that co-segregated with melanoma in 18 out of 21 cases across four generations. Further investigations revealed a further 10 families carrying this deletion, co-segregating with melanoma. The deleted region was predicted to encompass regulatory sequences and to interact with the CDKN2A promoter region. Tiled CRISPR inhibition of the predicted enhancer region confirmed interactions between the distant upstream deletion with CDKN2A resulting in decreased p16 transcript mRNA expression. Deletion carriers exhibited nearcomplete loss of p16 mRNA expression from the affected chromosome. This distant noncoding deletion is one of the most common founder variants predisposing to melanoma and reveals a new mechanism controlling p16 expression. Routine screening for this deletion in individuals with perceived high risk of melanoma is warranted.