Assessment of the gene mosaicism burden in blood and its implications for immune disorders

Abstract

There are increasing evidences showing the contribution of somatic genetic variants to non-cancer diseases. However, their detection using massive parallel sequencing methods still has important limitations. In addition, the relative importance and dynamics of somatic variation in healthy tissues are not fully understood. We performed high-depth whole-exome sequencing in 16 samples from patients with a previously determined pathogenic somatic variant for a primary immunodeficiency and tested different variant callers detection ability. Subsequently, we explored the load of somatic variants in the whole blood of these individuals and validated it by amplicon-based deep sequencing. Variant callers allowing low frequency read thresholds were able to detect most of the variants, even at very low frequencies in the tissue. The genetic load of somatic coding variants detectable in whole blood is low, ranging from 1 to 2 variants in our dataset, except for one case with 17 variants compatible with clonal haematopoiesis under genetic drift. Because of the ability we demonstrated to detect this type of genetic variation, and its relevant role in disorders such as primary immunodeficiencies, we suggest considering this model of gene mosaicism in future genetic studies and considering revisiting previous massive parallel sequencing data in patients with negative results.

Figure 1

Previously reported causal somatic mutations detected by each variant caller (in green), assessed as the presence of the variant in the raw VCF files. The germline variant in S4a was detected in Strelka germline mode but not in the somatic one. All VAF were extracted from a previous publication.

Figure 2

Filtering process followed to obtain somatic candidate variants. We got around 40 variants per blood sample that we then experimentally validated by ADS.

Figure 3

VAF of validated somatic variants in S5 patient per tissue and cell type. Green is used for the group of variants with higher VAF (around 24%), red for those with intermediate VAF (around 4%) and blue for those with low VAF (around 1.5%, the only group present in B cells). Of note, there is one variant in the X chromosome whose frequency has been divided by 2 in order to visualize it grouped with the others.