Whole Exome Sequencing in Inborn Errors of Immunity

Abstract and Introduction

Abstract

Purpose of review: Next-generation sequencing, especially whole exome sequencing (WES), has revolutionized the molecular diagnosis of inborn errors of immunity. This review summarizes the generation and analysis of next-generation sequencing data.

Recent findings: The focus is on prioritizing strategies for unveiling the potential disease-causing variant. We also highlighted oversights and imperfections of WES and targeted panel sequencing, as well as the need for functional validation.

Summary: The information is crucial for a judicious use of WES by researchers, but even more so by the clinical immunologist.

Introduction

Inborn errors of immunity are a heterogeneous group of genetically determined diseases caused by defects in one or more components of immunity. These defects can manifest as increased susceptibility to infection, autoimmunity, autoinflammation, allergy, and malignancy or a combination of these.^[1] In the last decade, advances in human genetics and bioinformatics have permitted an acceleration in the discovery of new genes associated with known or new monogenic diseases, with the greatest leap determined by the implementation of next-generation sequencing (NGS; reviewed in^[2–4]). This is particularly relevant for inborn errors of immunity, where since 2010 a hundred new genes have been reported, of the over 300 genes so far described.^[1,5,6] Inborn errors of immunity are likely to be monogenic and display genetic pleiotropy (different clinical and immunological phenotypes originate from mutations of the same gene) and genetic heterogeneity (mutations in different genes give rise to the same phenotype).^[6,7] For these reasons, NGS has accelerated the unraveling of these disorders at the genetic level. Incomplete penetrance is also a common feature of inborn errors of immunity. This can originate from oligogenic/polygenic models of disease, which are sometimes difficult to characterize. Epigenetic or environmental factors (e.g., previous encounter with a pathogen) may also play a role.^[8] In this complex context, only in selected cases does Sanger sequencing of single genes lead to a definitive diagnosis. Moreover, many novel genetic etiologies are yet to be unraveled and many new phenotypes are likely to be ascribed to known genotypes.^[9]

The aim of this review is to provide information about the technical aspects of NGS and to illustrate its advantages and drawbacks in the setting of inborn errors of immunity. In particular, we will focus on some shortcomings of whole exome sequencing (WES).