Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

Abstract

Background: Diagnosis of primary immunodeficiencies (PIDs) is complex and cumbersome yet important for the clinical management of the disease. Exome sequencing may provide a genetic diagnosis in a significant number of patients in a single genetic test.

Methods: In May 2013, we implemented exome sequencing in routine diagnostics for patients suffering from PIDs. This study reports the clinical utility and diagnostic yield for a heterogeneous group of 254 consecutively referred PID patients from 249 families. For the majority of patients, the clinical diagnosis was based on clinical criteria including rare and/or unusual severe bacterial, viral, or fungal infections, sometimes accompanied by autoimmune manifestations. Functional immune defects were interpreted in the context of aberrant immune cell populations, aberrant antibody levels, or combinations of these factors.

Results: For 62 patients (24%), exome sequencing identified pathogenic variants in well-established PID genes. An exome-wide analysis diagnosed 10 additional patients (4%), providing diagnoses for 72 patients (28%) from 68 families altogether. The genetic diagnosis directly indicated novel treatment options for 25 patients that received a diagnosis (34%).

Conclusion: Exome sequencing as a first-tier test for PIDs granted a diagnosis for 28% of patients. Importantly, molecularly defined diagnoses indicated altered therapeutic options in 34% of cases. In addition, exome sequencing harbors advantages over gene panels as a truly generic test for all genetic diseases, including in silico extension of existing gene lists and re-analysis of existing data.

Keywords: Exome sequencing; Genetic diagnosis; Primary immunodeficiencies; Routine diagnostics.

Fig. 1

Clinical and immunophenotypic overview of the 254 patients included in the diagnostic PID cohort, including percentages of patients with genetic diagnoses per subgroup. a For 219 patients, pathogens and/or autoimmunity was identified. b Immunophenotypic defects were characterized in 194 patients. Quantification of blood cell numbers, antibody levels, and cytokine production aided to determine the genetic diagnosis for these patients. c The diagnostic yield per cohort based on the country from which the patients were referred. Compared to European patients, a higher percentage of patients from Saudi Arabia received a genetic diagnosis

Fig. 2

Schematic flowchart overview of the diagnostic exome procedure. Two hundred fifty-four patients from 249 families were referred for exome sequencing. Gene panel analysis resulted in a genetic diagnosis for 24% of patients. Eighty-one percent of diagnosis-negative patients provided consent for exome-wide analysis of their data. This analysis resulted in a genetic diagnosis for 10 additional patients (6% of exome-wide analyzed patients, 4% of the entire cohort). Data of the remaining 146 patients are re-analyzed for analysis of novel and recently published genes

Fig. 3

For one Saudi Arabian SCID patient (146.1), exome-based homozygosity mapping identified a large homozygous region on chromosome 19. Further analysis of JAK3 revealed a homozygous deletion of exon 10

Fig. 4

Differences in percentage diagnostic yield based on age and homozygous regions. a The age distribution of the entire cohort, the European cohort, the Saudi Arabian cohort, and the cases with a genetic diagnosis. b The number of large (> 5 Mb) homozygous regions per cohort. The increased number of homozygous regions in the Saudi Arabian cohort influenced diagnostic yield of the overall cohort