A survey of human genetic variation reveals a basis for Sturge-Weber syndrome and non-syndromic port-wine stain

Background The extent of germline human genetic variation (HGV) may be accurately assessed using DNA microarray and sequencing technologies. Somatic HGV depends on cell type and developmental time point, and is may be more difficult to accurately assess than germline HGV. Sturge-Weber syndrome (SWS) is a sporadic congenital neurocutaneous disorder characterized by a port-wine stain (PWS) affecting the ophthalmic branch of the trigeminal nerve and abnormal capillary-venous vessels in the leptomeninges of the brain, hypothesized to be caused by somatic HGV, with the developmental time point of the mutation determining the severity and presentation (syndromic or non-syndromic) of the phenotype.;Methods To assess somatic HGV in a common laboratory genetics system, we genotyped multiple lymphoblastoid cell lines (LCLs) derived from peripheral blood mononuclear cells (PBMCs) of single individuals as well as two comparison groups using single nucleotide polymorphism (SNP) microarrays. We extended our findings using and a large study consisting of DNA derived from blood and LCLs. To determine the extent of somatic HGV in SWS we performed whole genome sequencing of DNA derived from paired visibly affected and normal tissue from three SWS subjects. We then assayed the presence of an identified somatic mosaic mutation in 97 samples from 50 SWS, PWS, or control subjects using amplicon sequencing and SNaPshot assays.;Results We observed high concordances between genotypes and copy number in all sample comparisons between blood and LCLs, with variation confined to either sporadic rare events, or several recurrent events. In SWS, we identified a non-synonymous SNP (c. 548G>A, p.Arg183G1n) in GNAQ, present in 88% (23/26) of affected tissues from subjects with SWS, 92% (12/13) of apparently non-syndromic PWS tissues, none (0/4) of affected tissue from subjects with an unrelated cerebrovascular malformation, and none (0/6) of tissues from normal individuals, with mutant allele frequencies ranging 1 - 18.1%. Mitogen-activated protein kinases ERK1/2 and JNK activities were modestly increased in the presence of trans-expressed GNAQ p.Arg183GIn in HEK293T cells.;Conclusions SWS is caused by a somatic activating mutation in GNAQ, proving a long-standing but unproven hypothesis correct. This causal association extends to non-syndromic PWS and possibly to other syndromes with a PWS phenotype.