Next Generation Sequencing for Detecting Somatic FAS Mutations in Patients With Autoimmune Lymphoproliferative Syndrome

Abstract

Autoimmune lymphoproliferative syndrome (ALPS) is a primary immune regulatory disorder clinically defined by chronic and benign lymphoproliferation, autoimmunity and an increased risk of lymphoma due to a genetic defect in the FAS-FASL apoptotic pathway. Genetic defects associated with ALPS are germinal and somatic mutations in FAS gene, in addition to germinal mutations in FASLG, FADD, CASP8 and CASP10 genes. The accumulation of CD3+TCRαβ+CD4-CD8- double negative T-cells (DNT) is a hallmark of the disease and 20-25% of ALPS patients show heterozygous somatic mutations restricted to DNT in the FAS gene (ALPS-sFAS patients). Nowadays, somatic mutations in the FAS gene are detected through Sanger sequencing in isolated DNT. In this study, we report an ALPS-sFAS patient fulfilling clinical and laboratory ALPS criteria, who was diagnosed through NGS with a targeted gene panel using DNA from whole blood. Data analysis was carried out with Torrent Suite Software and variant detection was performed by both germinal and somatic variant caller plugin. The somatic variant caller correctly detected other six ALPS-sFAS patients previously diagnosed in the authors’ laboratories. In summary, this approach allows the detection of both germline and somatic mutations related to ALPS by NGS, avoiding the isolation of DNT as the first step. The reads of the somatic variants could be detected even in patients with DNT in the cut off limit. Thus, custom-designed NGS panel testing may be a faster and more reliable method for the diagnosis of new ALPS patients, including those with somatic FAS mutations (ALPS-sFAS).

DCAF12 and HSPA1A May Serve as Potential Diagnostic Biomarkers for Myasthenia Gravis

“…Recently, microarray technology and next-generation sequencing technology have been widely used in medical research, including autoimmune disease research [ 10 , 11 ]. The innovation of this study is that by combining ssGSEA and WGCNA bioinformatic analysis methods to explore the differences in immune cell types between MG and healthy control from the microarray dataset, we then determine the expression and clinical significance of identified immune-related hub genes the DCAF12 and HSPA1A mRNA in MG.…”

Somatic genetic variation in healthy tissue and non-cancer diseases

“…On the other hand, the FAS gene, underlying autoimmune lymphoproliferative syndrome (ALPS), is an interesting example of various genetic mechanisms converging in similar phenotypes. FAS causes ALPS in patients who harbour pathogenic germline variants, somatic variants, and a combination of them [ 51 ]. Up to 20 % of the cases are caused exclusively by somatic variation, which is restricted to a specific cell population and can be detected by NGS [ 51 ].…”

“…FAS causes ALPS in patients who harbour pathogenic germline variants, somatic variants, and a combination of them [ 51 ]. Up to 20 % of the cases are caused exclusively by somatic variation, which is restricted to a specific cell population and can be detected by NGS [ 51 ]. Other outstanding cases are somatic variants in NOD2 causing Blau syndrome [ 52 ]; NLRC4 causing NOMID (neonatal-onset multisystem inflammatory disease) [ 53 ]; and UBA1 associated with the late-onset VEXAS (vacuole, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome, a severe X-linked disorder affecting males and restricted to cells of the myeloid line [ 54 ].…”