Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders

Abstract

Background: Primary immunodeficiency diseases (PIDDs) are clinically and genetically heterogeneous disorders thus far associated with mutations in more than 300 genes. The clinical phenotypes derived from distinct genotypes can overlap. Genetic etiology can be a prognostic indicator of disease severity and can influence treatment decisions.

Objective: We sought to investigate the ability of whole-exome screening methods to detect disease-causing variants in patients with PIDDs.

Methods: Patients with PIDDs from 278 families from 22 countries were investigated by using whole-exome sequencing. Computational copy number variant (CNV) prediction pipelines and an exome-tiling chromosomal microarray were also applied to identify intragenic CNVs. Analytic approaches initially focused on 475 known or candidate PIDD genes but were nonexclusive and further tailored based on clinical data, family history, and immunophenotyping.

Results: A likely molecular diagnosis was achieved in 110 (40%) unrelated probands. Clinical diagnosis was revised in about half (60/110) and management was directly altered in nearly a quarter (26/110) of families based on molecular findings. Twelve PIDD-causing CNVs were detected, including 7 smaller than 30 Kb that would not have been detected with conventional diagnostic CNV arrays.

Conclusion: This high-throughput genomic approach enabled detection of disease-related variants in unexpected genes; permitted detection of low-grade constitutional, somatic, and revertant mosaicism; and provided evidence of a mutational burden in mixed PIDD immunophenotypes.

Keywords: Primary immunodeficiency disease; copy number variants; whole-exome sequencing.

Figure 1

Status of molecular diagnosis after WES of 278 PIDD families. Findings are grouped in categories based on whether the detected disease causing variant(s) a) affects known disease genes, b) are located in more than one gene contributing to the assumed mixed phenotype (PIDD or non-PIDD) in the individual, c) affects a confirmed novel disease gene d) affects a potentially novel PIDD gene, e) leads to immunophenotypic expansion: a modified immune phenotype observed in the affected individual, modified from that which is historically characteristic of the particular gene, f) affects a phenotypic relevant gene, that were not presumably the major disease etiology, or only one deleterious variant in a disease relevant AR gene (in total 57 cases), or g) no identifiable molecular explanation was identified using the technologies applied here (111 cases).

Figure 2

Diagnostic yield in the PIDD cohort (n=278 families) by subgroup distribution based on the proband's diagnosis prior to WES+CNV testing.

Figure 3

Distribution of main likely disease genes in 111 families with established molecular diagnosis after WES+CNV testing by PIDD subgroup prior to testing.

Figure 4

Disease-associated variants and inheritance patterns observed among the 110 families in the PIDD cohort where a likely molecular diagnosis was established. (A) Spectrum of disease-associated variants detected in the PIDD cohort. In total 148 different variants were identified among the 110 families where a likely molecular diagnosis was established. The SNVs are classified based on assumed effect on protein. The indel led to a frameshift and stop codon and the in-frame deletion is previously reported to be disease causing by altered protein function. With exception of the DKC1 duplication, all 12 CNVs are deletions. All CNVs are assumed to result in loss of function. (B) Inheritance patterns observed among the 110 families in the PIDD cohort where a likely molecular diagnosis was established. The mosaic variant in KRAS is only compatible with life in somatic mosaic state, thus a Mendelian inheritance pattern is not applicable.

Figure 5

Alteration of specific diagnosis and change in management due to molecular findings by WES+CNV testing. The distribution is shown by PIDD subgroup which was based on clinical presentation at time of inclusion.