Exome and genome sequencing for inborn errors of immunity

J Allergy Clin Immunol. 2016 Oct;138(4):957-969. doi: 10.1016/j.jaci.2016.08.003.

Abstract

The advent of next-generation sequencing (NGS) in 2010 has transformed medicine, particularly the growing field of inborn errors of immunity. NGS has facilitated the discovery of novel disease-causing genes and the genetic diagnosis of patients with monogenic inborn errors of immunity. Whole-exome sequencing (WES) is presently the most cost-effective approach for research and diagnostics, although whole-genome sequencing offers several advantages. The scientific or diagnostic challenge consists in selecting 1 or 2 candidate variants among thousands of NGS calls. Variant- and gene-level computational methods, as well as immunologic hypotheses, can help narrow down this genome-wide search. The key to success is a well-informed genetic hypothesis on 3 key aspects: mode of inheritance, clinical penetrance, and genetic heterogeneity of the condition. This determines the search strategy and selection criteria for candidate alleles. Subsequent functional validation of the disease-causing effect of the candidate variant is critical. Even the most up-to-date dry lab cannot clinch this validation without a seasoned wet lab. The multifariousness of variations entails an experimental rigor even greater than traditional Sanger sequencing-based approaches in order not to assign a condition to an irrelevant variant. Finding the needle in the haystack takes patience, prudence, and discernment.

Keywords: Next-generation sequencing; primary immunodeficiency; targeted sequencing; whole-exome sequencing; whole-genome sequencing.

Publication types

  • Review
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Exome / genetics*
  • Genetic Diseases, Inborn*
  • Genetic Variation
  • Genome, Human / genetics*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Immunologic Deficiency Syndromes / genetics*