Assessing the spectrum of germline variation in Fanconi anemia genes among patients with head and neck carcinoma before age 50

Abstract

Background: Patients with Fanconi anemia (FA) have an increased risk for head and neck squamous cell carcinoma (HNSCC). The authors sought to determine the prevalence of undiagnosed FA and FA carriers among patients with HNSCC as well as an age cutoff for FA genetic screening.

Methods: Germline DNA samples from 417 patients with HNSCC aged <50 years were screened for sequence variants by targeted next-generation sequencing of the entire length of 16 FA genes.

Results: The sequence revealed 194 FA gene variants in 185 patients (44%). The variant spectrum was comprised of 183 nonsynonymous point mutations, 9 indels, 1 large deletion, and 1 synonymous variant that was predicted to effect splicing. One hundred eight patients (26%) had at least 1 rare variant that was predicted to be damaging, and 57 (14%) had at least 1 rare variant that was predicted to be damaging and had been previously reported. Fifteen patients carried 2 rare variants or an X-linked variant in an FA gene. Overall, an age cutoff for FA screening was not identified among young patients with HNSCC, because there were no significant differences in mutation rates when patients were stratified by age, tumor site, ethnicity, smoking status, or human papillomavirus status. However, an increased burden, or mutation load, of FA gene variants was observed in carriers of the genes FA complementation group D2 (FANCD2), FANCE, and FANCL in the HNSCC patient cohort relative to the 1000 Genomes population.

Conclusions: FA germline functional variants offer a novel area of study in HNSCC tumorigenesis. FANCE and FANCL, which are components of the core complex, are known to be responsible for the recruitment and ubiquitination, respectively, of FANCD2, a critical step in the FA DNA repair pathway. In the current cohort, the increased mutation load of FANCD2, FANCE, and FANCL variants among younger patients with HNSCC indicates the importance of the FA pathway in HNSCC. Cancer 2017;123:3943-54. © 2017 American Cancer Society.

Keywords: Fanconi anemia; germline variations; head and neck cancers; recessive inherited disorders; squamous cell carcinoma.

Figure 1. Schematics of FA gene variant analysis in HNSCC patients

Data from SNP array were analyzed for copy number variations. SNV discovery was performed from targeted sequencing of 16 FA genes. Synonymous variants were analyzed for splicing effects. Indels, nonsynonymous, and splicing variants were screened for quality and filtered using population-specific frequencies, where applicable. The resulting rare variants were screened for presence in the FA mutation database (FAmutDB) and ClinVar, and analyzed by functional prediction algorithms to determine potential pathogenicity. ^ Unreported variants were present at a frequency below .5% in the public databases but not reported to the FA mutation database, ClinVar, or BIC. * Novel variants were not present at any frequency in the public databases used for filtering.

Figure 2. The 194 rare variants, by mutation type, observed in the 16 FA genes from 185/417 HNSCC patients

The plot shows the number and type of rare variants observed in each FA gene along with the number of rare variants that were predicted to be damaging. ^includes one stoploss; *includes one synonymous variant