Validation of a Clinical NGS Panel for Detecting Somatic Variants in 69 Inborn Errors of Immunity Genes

Nearly 500 genes underlie primary immunodeficiencies (PID). Yet, many patients have no pathogenic variants reported after testing by germline sequencing. Some of these cases will be caused by somatic variants in the inborn errors of immunity genes, increasingly recognized as an important cause of immunodeficiency. However, detecting these somatic variants is challenging. Typically, whole exome and whole genome do not sequence deeply enough to detect variants with low allele fractions. Furthermore, the relevant immunity genes mostly do not overlap with existing targeted cancer genetic panels. Thus, in collaboration with members from the NICER Consortium, we designed a somatic NGS genetic panel to fill this gap in clinical testing by targeting a large number of inborn errors of immunity genes at a sufficiently high read depth with a speedy turnaround time to meet the testing needs of some of the sickest patients in the hospital. Here we describe our clinical validation of this NGS genetic panel. The test targets 69 genes, requires 60 ng of DNA, aims for ∼5,000x average read depth and sensitivity down to 2% variant allele fraction, with a turnaround time of 5 days.