Driving mosaicism: somatic variants in reference population databases and effect on variant interpretation in rare genetic disease

Abstract

Background Genetic variation databases provide invaluable information on the presence and frequency of genetic variants in the ‘untargeted’ human population, aggregated with the primary goal to facilitate the interpretation of clinically important variants. The presence of somatic variants in such databases can affect variant assessment in undiagnosed rare disease (RD) patients. Previously, the impact of somatic mosaicism was only considered in relation to two Mendelian disease-associated genes. Here, we expand the analyses to identify additional mosaicism-prone genes in blood-derived reference population databases. Results To identify additional mosaicism-prone genes relevant to RDs, we focused on known/previously established ClinVar pathogenic and likely pathogenic single-nucleotide variants, residing in genes associated with early onset, severe autosomal dominant diseases. We asked whether any of these variants are present in a higher-than-expected frequency in the reference population databases and whether there is evidence of somatic origin (i.e., allelic imbalance) rather than germline heterozygosity (~ half of the reads supporting alternative allele). The mosaicism-prone genes identified were further categorized according to the processes they are involved in. Beyond the previously reported ASXL1 and DNMT3A, we identified 7 additional autosomal dominant RD-associated genes with known pathogenic single-nucleotide variants present in the reference population databases and good evidence of allelic imbalance: BRAF, CBL, FGFR3, IDH2, KRAS, PTPN11 and SETBP1. From this group of 9 genes, the majority (n = 7) was important for hematopoiesis. In addition, 4 of these genes were involved in cell proliferation. Further assessment of the known 156 hematopoietic genes led to identification of 48 genes (21 not yet associated with RDs) with at least some evidence of mosaicism detectable in reference population databases. Conclusions These results stress the importance of considering genes involved in hematopoiesis and cell proliferation when interpreting the presence and frequency of genetic variants in blood-derived reference population databases, both public and private. This is especially important when considering new variants of uncertain significance in known hematopoietic/cell proliferation RD genes and future novel gene–disease associations involving this class of genes.

Multiple congenital malformations arise from somatic mosaicism for constitutively active Pik3ca signaling

“…Nearly half of sporadic venous malformations (VMs) bear activating TEK mutations, while most others express activating PIK3CA H1047R, or E452K or C420R mutations, in a mutually exclusive manner (Castel et al, 2016). These, particularly H1047R, are also the most frequent hotspot mutations for malignancies in nearly 50 sites and in over 21,000 samples curated by COSMIC (v95) to date (Tate et al, 2019;Avramović et al, 2021). The work we present here is the first to demonstrate that activation of a complex signaling pathway by the identical mutation in abluminal pericytes, fibroblasts and vascular smooth muscle, rather than endothelial cells, also can induce congenital vascular malformations and tumorigenesis.…”

“…Nearly half of sporadic venous malformations (VMs) bear activating TEK mutations, while most others express activating PIK3CA H1047R, or E452K or C420R mutations, in a mutually exclusive manner ( Castel et al, 2016 ). These, particularly H1047R, are also the most frequent hotspot mutations for malignancies in nearly 50 sites and in over 21,000 samples curated by COSMIC (v95) to date ( Tate et al, 2019 ; Avramović et al, 2021 ).…”

Single Cell Biology: Exploring Somatic Cell Behaviors, Competition and Selection in Chronic Disease

“…For example, a recent study showed that the expansion of mutant HSCs is driven by their resistance to inflammatory signals, driven by their mature cell progeny ( Avagyan et al, 2021 ). Besides the hematopoietic lineages, DNA isolated from peripheral blood may also contain nucleic acids from other sources including endothelial cell “progenitors,” neoplastic cells from multiple tissues, chimaeric fetal cells, subcellular exosomes and cell-free nucleic acids ( Szilagyi et al, 2020 ; Avramovic et al, 2021 ). The complexity of these DNA sources also impacts our interpretation of the mechanisms of cell competition in chronic disease ( Avramovic et al, 2021 ).…”

“…Unassayed somatic variation and underlying clonal competition must be considered as potential contributors in all genotype-phenotype associations ( Avramovic et al, 2021 ). It will require serial genotyping and/or single cell analysis of genotypes to deconvolute fully the contributions of clonal competition to the large number of established genetic associations, and at present genotyping depth is the rate-limiting step in the detection of clonal imbalance.…”

Identification of germline population variants misclassified as cancer-associated somatic variants

“…While some variant callers have advanced filtering of germline variants from tumor-only data using multiple population databases, they require a baseline knowledge of bioinformatics and typically remove germline variants without characterizing more information about the potential germline variants ( 16 ). Other efforts have interrogated somatic variants that have been included in population databases ( 17 ).…”