Abstract
Primary immunodeficiencies (PIDs) refer to a clinically, immunologically, and genetically heterogeneous group of over 350 disorders affecting development or function of the immune system. The increasing use of next-generation sequencing (NGS) technology has greatly facilitated identification of genetic defects in PID patients in daily clinical practice. Several NGS approaches are available, from the unbiased whole exome sequencing (WES) to specific gene panels. Here, we report on a 3-year experience with clinical exome sequencing (CES) for genetic diagnosis of PIDs. We used the TruSight One sequencing panel, which includes 4,813 disease-associated genes, in 61 unrelated patients (pediatric and adults). The analysis was done in 2 steps: first, we focused on a virtual PID panel and then, we expanded the analysis to the remaining genes. A molecular diagnosis was achieved in 19 (31%) patients: 12 (20%) with mutations in genes included in the virtual PID panel and 7 (11%) with mutations in other genes. These latter cases provided interesting and somewhat unexpected findings that expand the clinical and genetic spectra of PID-related disorders, and are useful to consider in the differential diagnosis. We also discuss 5 patients (8%) with incomplete genotypes or variants of uncertain significance. Finally, we address the limitations of CES exemplified by 7 patients (11%) with negative results on CES who were later diagnosed by other approaches (more specific PID panels, WES, and comparative genomic hybridization array). In summary, the genetic diagnosis rate using CES was 31% (including a description of 12 novel mutations), which rose to 42% after including diagnoses achieved by later use of other techniques. The description of patients with mutations in genes not included in the PID classification illustrates the heterogeneity and complexity of PID-related disorders.
Highlights
Primary immunodeficiencies (PIDs) are a phenotypically and genetically heterogeneous group of inborn errors of immunity leading to a predisposition to infections, autoimmune, or autoinflammatory diseases, lymphoproliferation, and malignancies
Biological data analysis involved 2 steps: First, we analyzed the variants in a virtual PID panel of 260 genes that contained the TruSight One (TSO) genes included in the current IUIS classification (Supplementary Table 3) [3], and we extended the analysis to the full TSO gene panel in patients with negative results in the virtual PID panel
5 patients showed variants of uncertain significance (VUS) or incomplete genotypes in genes related to their clinical phenotype
Summary
Primary immunodeficiencies (PIDs) are a phenotypically and genetically heterogeneous group of inborn errors of immunity leading to a predisposition to infections, autoimmune, or autoinflammatory diseases, lymphoproliferation, and malignancies. The diagnostic workup for PIDs has advanced from clinical evaluation with a detailed personal and family history to a more recent series of complex laboratory assays, including extensive flow cytometry studies, cell culture, or western blotting. As most described PIDs have a monogenic cause, molecular genetic testing is usually the key to providing a definite diagnosis [2]. A positive genetic diagnosis can direct the patient toward suitable prevention, monitoring, and treatment options. In the case of inherited mutations, testing of relatives is important to expand medical care, and genetic counseling to all affected family members and carriers. Achieving a definite genetic diagnosis in a suspected case of PID can be a complex and laborious process that sometimes fails to yield positive results
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