Somatic variants as drivers of genetic errors of immunity

Washington University, Saint Louis MO

Investigators

Abstract

Project Summary – Project 2 The diagnosis of the precise genetic cause and mechanism of inborn errors of immunity (IEI) has led to enhanced care and treatment of patients through improved diagnosis, guidance for clinical monitoring based on genotype, and targeted therapies. However, at least 60-70% of patients with suspected IEI lack a molecular diagnosis. The goal of this project is to address the gap in diagnosis through detection and validation of mosaic genetic variants in patients with suspected IEI. The current standard for clinical and research-based testing for IEI is exome and genome sequencing to identify germline changes in genes encoding proteins relevant to the immune response. However, it is now becoming well recognized that IEI can also arise from somatic mosaicism, which, although not inborn, lead to genetic errors of immunity (GEI). Such somatic mutations in GEI lead to a dominant effect, whereby a minor population of immune cells alters the immune response leading to clinical disease. Consistent with this dominant phenotype, immune dysregulation disorders account for most known cases of disease- causing somatic mosaicism in GEI. Somatic mutations can also alter disease phenotype, accounting for a high degree of variable penetrance within families. These somatic mutations can be missed by current genomic sequencing approaches due to insufficient depth of coverage with exome and genome sequencing, as well as the informatic challenges in detecting true mosaicism versus sequencing artifact. Thus, current challenges when working to identify disease-causing somatic mosaicism in GEI include the need for high read-depth sequencing and algorithms to discern low-frequency mosaicism from sequencing artifact, which is particularly important for GEI in which there are no ‘tumor’ and ‘control’ samples within an individual. We present preliminary studies using high-depth targeted sequencing of genes associated with or predicted to be associated with GEI with an immune dysregulation phenotype. Our studies demonstrate the presence of somatic mutations in the targeted genes in at least 12% of undiagnosed patients. In this project, we will utilize an expanded custom sequencing platform to investigate the rate and presence of somatic mosaicism in ~2000 patients with suspected GEI, and a cohort of currently healthy individuals. We will use this data to identify potentially disease-causing variants that will be investigated at the single-cell level to determine their impact on the immune system and expressivity of the identified variants. This project will be supported by Cores A and B of this Program and will benefit from collaboration and sharing with the other projects of this P01. The ability to recognize and accurately diagnose somatic mosaicism in GEI has high potential to alter the care of these patients.