title: Diagnostics of primary immunodeficiency diseases: a sequencing capture approach.
abstract: Primary Immunodeficiencies (PID) are genetically inherited disorders characterized by defects of the immune system, leading to increased susceptibility to infection. Due to the variety of clinical symptoms and the complexity of current diagnostic procedures, accurate diagnosis of PID is often difficult in daily clinical practice. Thanks to the advent of "next generation" sequencing technologies and target enrichment methods, the development of multiplex diagnostic assays is now possible. In this study, we applied a selector-based target enrichment assay to detect disease-causing mutations in 179 known PID genes. The usefulness of this assay for molecular diagnosis of PID was investigated by sequencing DNA from 33 patients, 18 of which had at least one known causal mutation at the onset of the experiment. We were able to identify the disease causing mutations in 60% of the investigated patients, indicating that the majority of PID cases could be resolved using a targeted sequencing approach. Causal mutations identified in the unknown patient samples were located in STAT3, IGLL1, RNF168 and PGM3. Based on our results, we propose a stepwise approach for PID diagnostics, involving targeted resequencing, followed by whole transcriptome and/or whole genome sequencing if causative variants are not found in the targeted exons.
authors.affiliation: Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
authors.forename: Lotte N
authors.initials: LN
authors.lastname: Moens
authors.affiliation: Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
authors.forename: Elin
authors.initials: E
authors.lastname: Falk-Sörqvist
authors.affiliation: Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden.
authors.forename: A Charlotta
authors.initials: AC
authors.lastname: Asplund
authors.affiliation: Department of Clinical Immunology, Children's Memorial Health Institute, Warsaw, Poland.
authors.forename: Ewa
authors.initials: E
authors.lastname: Bernatowska
authors.affiliation: Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden.
authors.forename: C I Edvard
authors.initials: CI
authors.lastname: Smith
authors.affiliation: Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
authors.forename: Mats
authors.initials: M
authors.lastname: Nilsson
mesh_terms: D015894:Genome, Human; D060148:HapMap Project; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007153:Immunologic Deficiency Syndromes / Q000175:diagnosis / Q000235:genetics* / Q000473:pathology; D009154:Mutation / Q000235:genetics*; D010733:Phosphoglucomutase / Q000235:genetics; D050796:STAT3 Transcription Factor / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*; D044767:Ubiquitin-Protein Ligases / Q000235:genetics
chemical_list: D050796:STAT3 Transcription Factor; C494086:STAT3 protein, human; C535210:RNF168 protein, human; D044767:Ubiquitin-Protein Ligases; C549916:PGM3 protein, human; D010733:Phosphoglucomutase