Identifying causal mutations for Primary Immunodeficiencies in Southeast Asian region using whole exome sequencing

Abstract

PIDs are rare inborn errors of the immune system and vast majority of PIDs are monogenic diseases. Study of potential genetic defects of PID offers enormous opportunities to the understanding of host-pathogen interactions at the molecular and functional level. Like many other rare Mendelian disorders, disease genes of PIDs were mostly identified by linkage studies or candidate gene screening. Next generation sequencing, especially whole exome sequencing, provides an opportunity for identifying the causal mutations when linkage or candidate gene approach fail to identify the genetic cause. “Asian Primary Immunodeficiency Network (APID) ” is a collaborative network with an on-line PID patient registry that contains a wealth of clinical and genetic data for researchers and clinicians. With this collection, we have reported the largest Chinese cohorts of common PIDs including chronic granulomatous disease, Wiskott-Aldrich syndrome and X-linked agammaglobulinemia, as well as rare genetic mutations which have not been described in the Chinese population. However, among the 259 patients tested, only 164 patients were confirmed to have molecular defects based on a candidate gene approach. We have selected about a dozen patients whose clinical and immunological phenotypes are definitive but no mutation in the currently known PID genes has been found through candidate gene screening for whole exome sequencing. These include agammaglobulinemia with absence of B cells and with BTK mutations excluded; severe combined immunodeficiency disorders; mendelian susceptibility to mycobacterial diseases; and autoimmune lymphoproliferative disorder. On average, we have around 70X coverage of the targeted exome, with about 94% of the regions covered 5X or above. Since for each patient, thousands of novel variants are identified, and pinpointing the causal mutations is a daunting challenge. The following approaches are adopted to help with the data analysis. Since recessive mutations and X-linked mutations in male patients are a strong possibility for some patients, homozygous mutations or compound heterozygous mutations, and mutations on the X-chromosome are preferentially considered. Several patients are from consanguineous marriage families, so homozygous mutations in long homozygous stretches in the genome (likely autozygous regions) are considered for causal mutation identification. Mutations with support from other affected members are also preferentially considered.