Genetic Testing in Patients With Autoimmune Lymphoproliferative Syndrome: Experience of 802 Patients at Cincinnati Children’s Hospital Medical Center

The aim of this study was to investigate the efficacy and diagnostic yield of a targeted next-generation sequencing (NGS) panel in identifying patients with autoimmune lymphoproliferative syndrome (ALPS).This study included 802 patients with suspected ALPS who were referred to Cincinnati Children’s Hospital between May 2014 and January 2023.In this single-center retrospective study, NGS panel testing was performed on genomic DNA extracted from peripheral blood samples from patients with suspected ALPS who were referred from various institutions. NGS was conducted on 9 genes for samples obtained through October 2019 (68% of patients) and on 15 genes for patients tested between November 2019 and January 2023 (32% of patients). Flow cytometry ALPS immune panel and Fas-mediated lymphocyte apoptosis testing were also conducted.The diagnostic yield of ALPS NGS panel testing among 802 patients with suspected ALPS was 7.7% (62/802). Among all patients, the median age at testing was 12 years (range: 1 month to 76 years) with a male predominance (63%). Of the 62 patients with ALPS, 84% (52/62) had pathogenic or likely pathogenic FAS variants, whereas the remaining 16% (10/62) had pathogenic or likely pathogenic variants in CLTA4, MAGT1, KRAS, ADA2, and NRAS. No patients with ALPS had pathogenic variants in FASLG or CASP10 or somatic FAS variants with allele fraction greater than 5%. A total of 6.5% patients tested (52/802) had heterozygous pathogenic or likely pathogenic FAS variant. Clinical phenotype among FAS positive cases included splenomegaly, lymphadenopathy, and elevated double-negative T cells.ALPS NGS testing is a cost-effective and expeditious method of identifying FAS and other gene mutations diagnostic for ALPS, but some patients may need more extensive immunologic, clinical, and genetic assessments.This study evaluates the largest cohort of NGS genetic testing for patients with suspected ALPS in North America. ALPS is a rare primary immunodeficiency disorder with defective lymphocyte apoptosis that may present clinically with chronic lymphadenopathy, splenomegaly, autoimmune cytopenias, and increased lymphoma risk.1,2 There is clinical overlap in presentation of ALPS and other lymphoproliferative disorders. This study highlights a quick and effective method for differentiating ALPS from non-ALPS/ALPID (autoimmune lymphoproliferative immunodeficiency) via ALPS NGS panel testing with a diagnostic yield of 7.7%. Further immunologic, clinical phenotype, and genetic assessments may be required to reach a diagnosis. This study was performed at a single center, which limits its generalizability. Additional clinical details (including phenotype and medications) were limited as many patients were referred from outside institutions. General pediatricians and pediatric subspecialists need to recognize the utility of NGS or whole-genome/exome genetic testing in rendering a timely and precise diagnosis for patients with ALPS.