Diagnostics of Primary Immunodeficiency Diseases: A Sequencing Capture Approach

Abstract

Primary Immunodeficiencies (PID) are genetically inherited disorders characterized by defects of the immune system, leading to increased susceptibility to infection. Due to the variety of clinical symptoms and the complexity of current diagnostic procedures, accurate diagnosis of PID is often difficult in daily clinical practice. Thanks to the advent of “next generation” sequencing technologies and target enrichment methods, the development of multiplex diagnostic assays is now possible. In this study, we applied a selector-based target enrichment assay to detect disease-causing mutations in 179 known PID genes. The usefulness of this assay for molecular diagnosis of PID was investigated by sequencing DNA from 33 patients, 18 of which had at least one known causal mutation at the onset of the experiment. We were able to identify the disease causing mutations in 60% of the investigated patients, indicating that the majority of PID cases could be resolved using a targeted sequencing approach. Causal mutations identified in the unknown patient samples were located in STAT3, IGLL1, RNF168 and PGM3. Based on our results, we propose a stepwise approach for PID diagnostics, involving targeted resequencing, followed by whole transcriptome and/or whole genome sequencing if causative variants are not found in the targeted exons.

Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders

“…A stepwise approach for PIDD diagnostics with targeted next generation sequencing (NGS), 20 followed as needed by WES and/or whole-genome sequencing (WGS) has been previously proposed. 19 Our findings support such an approach, although use of WES and/or WGS may ultimately become preferred to targeted multi-gene panel testing as technologies advance to provide results in a comparable timeframe. The need for rapid analysis is emphasized by the fact that acquisition of the proper diagnosis directly altered management of 25% of probands in our cohort.…”

“…45 Additional PIDD affected individuals with PGM3 mutations were reported simultaneously, 68, 69 and more than 10 families have been published since. 19, 45, 68-70 New and potentially novel PIDD genes were found in 21 families in our cohort (19%), and biological investigations to confirm these associations according to published standards 42 have been performed or are in progress.…”

Comprehensive genetic testing for primary immunodeficiency disorders in a tertiary hospital: 10-year experience in Auckland, New Zealand

“…Targeted NGS or gene panels are less complicated and laborious than WES or WGS. The diagnostic rate for unsolved cases using gene panels have been reported in the range of 15–25% [22, 25–27]. Most of these cases were atypical clinical presentations of known PIDs.…”

Diagnostics of Primary Immunodeficiencies through Next-Generation Sequencing

“…This can be the first-line alternative as it involves a smaller dataset than WES or whole genome sequencing (WGS) and is easier for the management of the datasets (16–18). However, as the spectrum of distinct clinical entities and the presenting phenotypes are expanding because of the discovery of novel genes and of the identification of wider clinical phenotypes, the differential diagnosis and subsequent diagnostic targets must improve in parallel.…”