Abstract 4289: Whole-exome sequencing study of nevoid basal cell carcinoma syndrome (NBCCS) families to identify disease-causing exonic mutations
Authors: Gianferante Matthew , Goldstein Alisa , Wang Mingyi , Zhu Bin , Hicks Belynda ,   NCI DCEG Cancer Genomics Research Laboratory, Mirabello Lisa 
Published: July 2017

NBCCS is an autosomal dominant disorder with nearly complete penetrance and variable expression. Clinical findings include multiple basal cell carcinomas, keratocysts of the jaw, pits of the palms and/or soles, and more rarely medulloblastoma. The PTCH1 gene is the major NBCCS susceptibility gene; it regulates the sonic hedgehog (SHH) pathway. Here, we are evaluating mutations in unknown NBCCS families to identify potential disease-causing mutations.

Our study included specimens and clinical data from 21 NBCCS families. PTCH1 targeted sequencing and CGH array were previously performed. We subsequently whole-exome sequenced (WES) affected family members with no mutation detected from prior targeted analyses (N=9). We focused our analyses on rare variants of PTCH1, genes that directly interact with PTCH1, SHH pathway genes, and cancer predisposing genes. Variants were considered rare if minor allele frequency (MAF) was less than 1% in publicly available databases (ESP, ExAC, and 1000 genome), 1000 in-house population cancer-free controls, and an in-house database of approximately 2,000 familial samples that underwent WES in parallel with our NBCCS families. We used in-silico prediction models, variant impact on the protein (i.e., nonsynonymous, nonsense, frameshift, splice site), and public mutation databases to assess pathogenicity. Rare variants in PTCH1 were considered pathogenic if they were (a) previously reported as disease-causing in NBCCS, or (b) predicted high impact (ie, frameshift, nonsense mutation), or (c) predicted damaging by at least five of seven in-silico prediction programs (CADD, PolyPhen 2, SIFT, Assessor, Mutation Taster, LRT, FATHMM).

Ten families (N= 17 individuals) without a PTCH1 mutation were assessed with WES. WES identified PTCH1 mutations in six families. Overall, only one PTCH1 variant was previously reported (p.S732fs) in HGMD or ClinVar databases. Six novel variants were identified: three frameshifts, p.Y92fs, p.S732fs and p.T212fs; one nonsense, p.W862*; one nonsynonymous variant, p.E835K; and, one splice site variant, c.2716-2A&gt;C. The nonsynonymous variant was a heterozygous C to T transversion (chromosome 9, position 98 229 452) and predicted damaging.

In the four families without a PTCH1 mutation, two separate families had a rare nonsynonymous variant in the same gene that directly interacts with PTCH1. Both variants had a MAF of less than 0.1%, but only one was predicted damaging. Another family had a rare nonsynonymous variant in a known cancer predisposing gene that was deleterious in five of seven in-silico prediction tools and found in both the proband and affected mother.

Overall, in our 21 NBCCS families, 81% had PTCH1 gene mutations detected with targeted sequencing, aCGH, or WES. Additionally, WES detected two potentially new disease-associated genes that we are currently evaluating further.

Citation Format: Matthew Gianferante, Alisa Goldstein, Mingyi Wang, Bin Zhu, Belynda Hicks, NCI DCEG Cancer Genomics Research Laboratory, Lisa Mirabello. Whole-exome sequencing study of nevoid basal cell carcinoma syndrome (NBCCS) families to identify disease-causing exonic mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4289. doi:10.1158/1538-7445.AM2017-4289