SNV/indel hypermutator phenotype in biallelic RAD51C variant: Fanconi anemia

Abstract

We previously reported a fetus with Fanconi anemia (FA), complementation group O due to compound heterozygous variants involving RAD51C. Interestingly, the trio exome sequencing analysis also detected eight apparent de novo mosaic variants with variant allele fraction (VAF) ranging between 11.5 and 37%. Here, using whole genome sequencing and a 'home-brew' variant filtering pipeline and DeepMosaic module, we investigated the number and signature of de novo heterozygous and mosaic variants and the hypothesis of a rare phenomenon of hypermutation. Eight-hundred-thirty apparent de novo SNVs and 21 de novo indels had VAFs below 37.41% and were considered postzygotic somatic mosaic variants. The VAFs showed a bimodal distribution, with one component having an average VAF of 25% (range: 18.7-37.41%) (n = 446), representing potential postzygotic first mitotic events, and the other component with an average VAF of 12.5% (range 9.55-18.69%) (n = 384), describing potential second mitotic events. No increased rate of CNV formation was observed. The mutational pattern analysis for somatic single base substitution showed SBS40, SBS5, and SBS3 as the top recognized signatures. SBS3 is a known signature associated with homologous recombination-based DNA damage repair error. Our data demonstrate that biallelic RAD51C variants show evidence for defective genomic DNA damage repair and thereby result in a hypermutator phenotype with the accumulation of postzygotic de novo mutations, at least in the prenatal period. This 'genome hypermutator phenomenon' might contribute to the observed hematological manifestations and the predisposition to tumors in patients with FA. We propose that other FA groups should be investigated for genome-wide de novo variants.

Fig. 1.. De novo variant allele frequency distribution

VAF density plots in the FA proband (red histogram) with two components of the bimodal distribution (red curve line) compared with the control subject (blue histogram and line) generated using the home-brew pipelines: (i) with manual IGV curation step (A), and (ii) with increased sensitivity (ploidy = 50 in GATK HC) and automated filtration using DeepMosaic (B). The lines denote the potential postzygotic mutational events (VAF <37.4%) and the potential germline cell events (VAF 37.41–62.6%).

Fig. 2.. Genome-wide distribution of de novo substitution and examples of de novo substitution pattern in the FA patient

a. Rainfall plot of de novo substitutions. b-e. Integrative Genomics Viewer (IGV) visualization of the proband (top) and parents (bottom) short read sequencing data at four loci, illustrating four different substitution patterns: b) Single-base substitution (SBS), c) double-base substitution (DBS), d) clustered-base substitution (CBS), e) biallelic-base substitution (BBS)

Fig. 3.. Mutational pattern of de novo single base substitution.

a) 96 tri-nucleotide profile b) Pan-nucleotide river plot with the extended context (2 bp)

Figure 4.. Mutational single base substitution signature.

a) The top 20 known single base substitution (SBS) signatures ranked by the cosine similarity (from top to bottom). b) The absolute contribution of the fitted SBS signatures.