Abstract
Background: Primary Immunodeficiencies (PIDs) are a heterogeneous group of genetic immune disorders. While some PIDs can manifest with more than one phenotype, signs, and symptoms of various PIDs overlap considerably. Recently, novel defects in immune-related genes and additional variants in previously reported genes responsible for PIDs have been successfully identified by Next Generation Sequencing (NGS), allowing the recognition of a broad spectrum of disorders.Objective: To evaluate the strength and weakness of targeted NGS sequencing using custom-made Ion Torrent and Haloplex (Agilent) panels for diagnostics and research purposes.Methods: Five different panels including known and candidate genes were used to screen 105 patients with distinct PID features divided in three main PID categories: T cell defects, Humoral defects and Other PIDs. The Ion Torrent sequencing platform was used in 73 patients. Among these, 18 selected patients without a molecular diagnosis and 32 additional patients were analyzed by Haloplex enrichment technology.Results: The complementary use of the two custom-made targeted sequencing approaches allowed the identification of causative variants in 28.6% (n = 30) of patients. Twenty-two out of 73 (34.6%) patients were diagnosed by Ion Torrent. In this group 20 were included in the SCID/CID category. Eight out of 50 (16%) patients were diagnosed by Haloplex workflow. Ion Torrent method was highly successful for those cases with well-defined phenotypes for immunological and clinical presentation. The Haloplex approach was able to diagnose 4 SCID/CID patients and 4 additional patients with complex and extended phenotypes, embracing all three PID categories in which this approach was more efficient. Both technologies showed good gene coverage.Conclusions: NGS technology represents a powerful approach in the complex field of rare disorders but its different application should be weighted. A relatively small NGS target panel can be successfully applied for a robust diagnostic suspicion, while when the spectrum of clinical phenotypes overlaps more than one PID an in-depth NGS analysis is required, including also whole exome/genome sequencing to identify the causative gene.
Highlights
Primary immunodeficiencies (PIDs) are a phenotypically and genetically heterogeneous group of more than 300 monogenic inherited disorders resulting in immune defects that predispose patients to infections, autoimmune disorders, lymphoproliferative disease, and malignancies [1,2,3]
We report the clinical and molecular characterization of 105 PID patients presenting with either typical or overlapping PID phenotypes
Patients were clustered according to initial clinical presentation in 3 main categories (Figure 1A): T-cell defects; Humoral defects; Other PIDs
Summary
Primary immunodeficiencies (PIDs) are a phenotypically and genetically heterogeneous group of more than 300 monogenic inherited disorders resulting in immune defects that predispose patients to infections, autoimmune disorders, lymphoproliferative disease, and malignancies [1,2,3]. PIDs with a more severe phenotype lead to life-threatening infections and life-limiting complications that require a prompt and accurate diagnosis in order to initiate lifesaving therapy [4, 5]. Phenotypic and genotypic heterogeneity of PIDs make genetic diagnosis often complex and delayed. Primary Immunodeficiencies (PIDs) are a heterogeneous group of genetic immune disorders. Novel defects in immune-related genes and additional variants in previously reported genes responsible for PIDs have been successfully identified by Generation Sequencing (NGS), allowing the recognition of a broad spectrum of disorders
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