title: Investigation of Genetic Defects in Severe Combined Immunodeficiency Patients from Turkey by Targeted Sequencing.
abstract: Primary immunodeficiencies (PIDs) represent a large group of disorders with an increased susceptibility to infections. Severe combined immunodeficiency (SCID) is the most severe form of primary immunodeficiencies (PIDs) with marked T-cell lymphopenia. Investigation of the genetic aetiology using classical Sanger sequencing is associated with considerable diagnostic delay. We here established a custom-designed, next-generation sequencing (NGS)-based panel to efficiently identify disease-causing genetic defects in PID patients and applied this method in SCID patients of Turkish origin with previously undefined genetic aetiology. We used HaloPlex enrichment technology, a targeted, NGS-based method which was designed to diagnose patients with SCID and other PIDs. Our HaloPlex panel included a total of 356 PID-related genes, and we searched disease-causing mutations in 19 Turkish SCID patients without a genetic diagnosis. The coverage of targeted regions ranged from 97.47% to 99.62% with an average of 98.31% for all patients. All known SCID genes were covered with a percentage of at least 97.3%. We made a genetic diagnosis in six of 19 (33%) patients, including four novel disease-causing mutations identified in RAG1, JAK3 and IL2RG, respectively. We showed that this NGS-based method can provide rapid genetic diagnosis for patients suffering from SCID, potentially facilitating clinical treatment decisions.
authors.affiliation: Department of Immunology, Ihsan Dogramaci Children's Hospital, Hacettepe University, Ankara, Turkey.|CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
authors.forename: B
authors.initials: B
authors.lastname: Erman
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
authors.forename: I
authors.initials: I
authors.lastname: Bilic
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
authors.forename: T
authors.initials: T
authors.lastname: Hirschmugl
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
authors.forename: E
authors.initials: E
authors.lastname: Salzer
authors.affiliation: Department of Paediatrics, St. Anna Kinderspital, Medical University of Vienna, Vienna, Austria.
authors.forename: H
authors.initials: H
authors.lastname: Boztug
authors.affiliation: Department of Immunology, Ihsan Dogramaci Children's Hospital, Hacettepe University, Ankara, Turkey.
authors.forename: Ö
authors.initials: Ö
authors.lastname: Sanal
authors.affiliation: Department of Immunology, Ihsan Dogramaci Children's Hospital, Hacettepe University, Ankara, Turkey.
authors.forename: D
authors.initials: D
authors.lastname: Çağdaş Ayvaz
authors.affiliation: Department of Immunology, Ihsan Dogramaci Children's Hospital, Hacettepe University, Ankara, Turkey.
authors.forename: I
authors.initials: I
authors.lastname: Tezcan
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.|Department of Paediatrics, St. Anna Kinderspital, Medical University of Vienna, Vienna, Austria.|Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.|Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.
authors.forename: K
authors.initials: K
authors.lastname: Boztug
mesh_terms: D001483:Base Sequence; D003564:Cytidine Deaminase / Q000235:genetics; D005260:Female; D020022:Genetic Predisposition to Disease; D059014:High-Throughput Nucleotide Sequencing; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D007223:Infant; D053631:Interleukin Receptor Common gamma Subunit / Q000235:genetics; D053709:Interleukin-10 Receptor alpha Subunit / Q000235:genetics; D053710:Interleukin-10 Receptor beta Subunit / Q000235:genetics; D053616:Janus Kinase 3 / Q000235:genetics; D008297:Male; D017422:Sequence Analysis, DNA; D016511:Severe Combined Immunodeficiency / Q000235:genetics*; D019098:Telomerase / Q000235:genetics; D014421:Turkey; D000098830:AICDA (Activation-Induced Cytidine Deaminase)
chemical_list: D018398:Homeodomain Proteins; C081846:IL10RB protein, human; C507941:IL2RG protein, human; D053631:Interleukin Receptor Common gamma Subunit; D053709:Interleukin-10 Receptor alpha Subunit; D053710:Interleukin-10 Receptor beta Subunit; C064658:RAG-1 protein; C507933:JAK3 protein, human; D053616:Janus Kinase 3; C509186:TERT protein, human; D019098:Telomerase; D000098830:AICDA (Activation-Induced Cytidine Deaminase); D003564:Cytidine Deaminase