Next-Generation Sequencing Based Clinical Molecular Diagnosis of Primary Immunodeficiency Diseases

Abstract

Primary immunodeficiency diseases (PIDs) are a group of disorders caused by defects in one or multiple components of the immune system. PID patients usually present with recurrent or severe infections and can be difficult to manage with conventional treatments. The types of infections in patients with PIDs are related to which arm of the immune system is affected, and often provide the first clues to the nature of the immunologic defect. Without appropriate therapy, many patients die in infancy or early childhood. Because of the clinical heterogeneity and broadly overlapping phenotypes among the PIDs, it is often challenging to reach a definitive clinical diagnosis. Compelling evidence has demonstrated that most PIDs are genetic disorders, and there are more than 240 genes that have been identified in association with different PIDs. Accurate gene sequencing in PIDs not only can bring a definite molecular diagnosis at an early stage, but can also improve the clinical prognosis of patients by facilitating initiation of appropriate therapies based on the underlying diagnosis. However, Sanger-based single gene sequencing is time-consuming and costly if multiple genes need to be analyzed sequentially due to genetic and phenotypic heterogeneity. Thus, it is not practical for the prompt definitive diagnosis of PIDs. Next-generation sequencing (NGS) is a recently developed, massively parallel sequencing technology, which can sequence all targeted regions (multiple genes, whole exome, or whole genome) of the human genome simultaneously. In fact, the NGS technology has made it possible to sequence all known disease causing genes in one experiment. As a result, NGS has become a primary approach for both clinical molecular diagnosis and discovery of novel genes in Mendelian human disorders (Gilissen et al. Genome Biol 12:228, 2011; Shendure and Ji Nat Biotechnol 26:1135–1145, 2008). In this chapter, we describe the most recent applications of NGS technology to PIDs with a focus on clinical molecular diagnosis.