A large-scale sequencing study identifies a novel non-coding structural variant as a high-penetrance susceptibility variant for melanoma

Approximately 10% of cutaneous malignant melanoma cases are familial. Variants in CDKN2A account for ~40% of melanoma-prone families, with 10% more explained by other established genes. Strikingly, many unexplained families nonetheless show genetic linkage to chromosomal band 9p21, which harbors CDKN2A , suggesting that high-penetrance non-coding variants in the region may contribute to familial risk.As a part of a large-scale study of high-risk melanoma families from the Mediterranean region, we conducted germline whole-genome sequencing (WGS) on a melanoma case from a four-case family from Genoa, Italy, that is negative for variation in known susceptibility genes. We identified a novel 100kb deletion mapping to 9p21 205kb from CDKN2A and verified cosegregation in the two other available cases. The deletion is not protein-coding but contains annotated melanocyte enhancer elements and open chromatin that we find to interact with the promoters of the p16 and p14 transcripts of CDKN2A in melanocytes using H3K27Ac Hi-ChIP.To identify additional deletion carriers in whole-exome sequencing (WES) data, we searched for nearby exonic variants that cosegregate in the discovery family to serve as a proxy of the deletion, identifying a rare cosegregating missense variant in MTAP (rs755147810; chr9: 21,802,755:T:G; p.Ser3Ala; gnomADv4.1 Non-Finish European MAF: 3.4x10 -6 ). We assessed this variant in WES data from 3,574 high-risk Mediterranean melanoma patients and 2,673 controls, identifying 17 additional Italian melanoma cases (mostly from Genoa) and a single control, and subsequently confirmed all carriers of rs755147810 harbored the deletion. We verified cosegregation of the deletion in all available cases from four additional families (3/3, 2/2, 2/2 and 2/2 cases). The association of the MTAP variant with melanoma risk was highly significant when considering unrelated individuals from Italy, Spain, and Greece (3,219 cases and 2,266 controls; P = 4.34 x 10 -4 ; OR = 13.88) as well as Italian samples alone (2,170 cases, 1,888 controls; P = 4.14 x 10 -4 ; OR = 14.01). Analysis of a shared haplotype among carriers suggests a founder haplotype with the most recent common ancestor (MRCA) dating approximately 26 generations, i.e. the 17 th century, when Italy was repeatedly struck by devastating outbreaks of plague that profoundly affected major urban and commercial centers. The coincidence of the estimated MRCA timeframe with this major population collapse suggests that the demographic effects of the plague epidemic may have contributed to the persistence of this genetic variant in modern populations.In conclusion, our study provides evidence of a distant high-penetrance non-coding variant conferring melanoma susceptibility, with potential translational impact on facilitating screening and early-detection efforts in high-risk individuals.