Gene hunting in the genomic era: approaches to diagnostic dilemmas in primary immunodeficiencies

Over the past four decades, over 180 molecular defects causing primary immunodeficiencies (PIDs) have been discovered through advances in immunology and genetics. Recent studies have identified ways to solve difficult cases such as diseases with autosomal dominant inheritance, incomplete penetrance, or mutations in non-coding regions. In their review, Platt et al focus on selected causes to illustrate a spectrum of approaches for identifying causative mutations [J Allergy Clin Immunol 2014; 134(2): 262-68].  They broadly classified these approaches into 3 different strategies: 1) educated guesses based on known signaling pathways essential for immune cell development and function, 2) similarity of clinical phenotypes to mouse models, and 3) unbiased genetic approaches. They also address methods of overcoming challenges in identifying molecular causes of PIDS.

Since the majority of PIDs are monogenic, whole exome/genome sequencing has expedited the discovery of pathogenic mutations, particularly when combined with classical methods of identifying genetic defects. Recently, an unbiased approach to sequencing called next generation sequencing (NGS) has revolutionized genetics by making it possible to sequence entire human genomes within days. Although this technology offers comprehensive sequencing data, it is challenging to distinguish pathogenic variants within the 3.2 billion bases present in the human genome. NGS and other methods have greatly expedited the discovery of pathogenic mutations; however, there are still limitations.

Advances in immunology and genetics have facilitated the discovery of novel defects underlying PIDs. However, the authors explain that there is still much progress to be made despite what is already known. Epigenetic modifications regulating gene expression, such as DNA methylation, histone modifications, and non-coding RNAs, modulate the immune system and defects in these mechanisms may contribute to PIDs. Furthermore, the use of NGS can be used to investigate the transcriptome to detect disease-causing splice variants leading to exon skipping, alternative splicing, and alternative start and polyadenylation sites. These advances can benefit patients in that the identification of the defects underlying PID enables genetic counseling and pre-implantation diagnosis. The authors conclude that pinpointing these genetic defects is the foundation for the development of gene therapy as a cure.