Journal article
Rapid molecular diagnostics of severe primary immunodeficiency determined by using targeted next-generation sequencing
Journal of allergy and clinical immunology, Vol.138(4), pp.1142-1151.e2
10/2016
DOI: 10.1016/j.jaci.2016.05.035
PMID: 27484032
Abstract
Primary immunodeficiency diseases (PIDDs) are inherited disorders of the immune system. The most severe form, severe combined immunodeficiency (SCID), presents with profound deficiencies of T cells, B cells, or both at birth. If not treated promptly, affected patients usually do not live beyond infancy because of infections. Genetic heterogeneity of SCID frequently delays the diagnosis; a specific diagnosis is crucial for life-saving treatment and optimal management.
We developed a next-generation sequencing (NGS)–based multigene-targeted panel for SCID and other severe PIDDs requiring rapid therapeutic actions in a clinical laboratory setting.
The target gene capture/NGS assay provides an average read depth of approximately 1000×. The deep coverage facilitates simultaneous detection of single nucleotide variants and exonic copy number variants in one comprehensive assessment. Exons with insufficient coverage (<20× read depth) or high sequence homology (pseudogenes) are complemented by amplicon-based sequencing with specific primers to ensure 100% coverage of all targeted regions.
Analysis of 20 patient samples with low T-cell receptor excision circle numbers on newborn screening or a positive family history or clinical suspicion of SCID or other severe PIDD identified deleterious mutations in 14 of them. Identified pathogenic variants included both single nucleotide variants and exonic copy number variants, such as hemizygous nonsense, frameshift, and missense changes in IL2RG; compound heterozygous changes in ATM, RAG1, and CIITA; homozygous changes in DCLRE1C and IL7R; and a heterozygous nonsense mutation in CHD7.
High-throughput deep sequencing analysis with complete clinical validation greatly increases the diagnostic yield of severe primary immunodeficiency. Establishing a molecular diagnosis enables early immune reconstitution through prompt therapeutic intervention and guides management for improved long-term quality of life.
Details
- Title: Subtitle
- Rapid molecular diagnostics of severe primary immunodeficiency determined by using targeted next-generation sequencing
- Creators
- Diana K Bayer - Department of Pediatrics, Division of Pediatric Allergy/Immunology and Pulmonology, University of Iowa Carver College of Medicine, Iowa City, IowaHui Yu - Baylor Genetics, Houston, TexVictor Wei Zhang - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TexJing Wang - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TexAsbjørg Stray-Pedersen - Department of Pediatrics, Section of Immunology, Allergy, and Rheumatology, Baylor College of Medicine and Texas Children's Hospital, Houston, TexImelda Celine Hanson - Department of Pediatrics, Section of Immunology, Allergy, and Rheumatology, Baylor College of Medicine and Texas Children's Hospital, Houston, TexLisa R Forbes - Department of Pediatrics, Section of Immunology, Allergy, and Rheumatology, Baylor College of Medicine and Texas Children's Hospital, Houston, TexM. Teresa de la Morena - Division of Allergy and Immunology, University of Texas Southwestern Medical Center, Children's Medical Center, Dallas, TexIvan K Chinn - Department of Pediatrics, Section of Immunology, Allergy, and Rheumatology, Baylor College of Medicine and Texas Children's Hospital, Houston, TexElizabeth Gorman - Baylor Genetics, Houston, TexNancy J Mendelsohn - Children's Hospital and Clinics of Minnesota, Minneapolis, MinnTamara Pozos - Pediatric Infectious Diseases and Immunology, Children's Hospitals and Clinics of Minnesota, St Paul, MinnWojciech Wiszniewski - Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TexSarah K Nicholas - Department of Pediatrics, Section of Immunology, Allergy, and Rheumatology, Baylor College of Medicine and Texas Children's Hospital, Houston, TexAnne B Yates - University of Mississippi Medical Center, Jackson, MissLindsey E Moore - University of Mississippi Medical Center, Jackson, MissKnut Erik Berge - Department of Medical Genetics, Oslo University Hospital, Oslo, NorwayHanne Sorte - Department of Medical Genetics, Oslo University Hospital, Oslo, NorwayDaifulah ALZahrani - Department of Pediatrics, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi ArabiaRaif S Geha - Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MassYanming Feng - Baylor Genetics, Houston, TexGuoli Wang - Baylor Genetics, Houston, TexJordan S Orange - Department of Pediatrics, Section of Immunology, Allergy, and Rheumatology, Baylor College of Medicine and Texas Children's Hospital, Houston, TexJames R Lupski - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TexLee-Jun Wong - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
- Resource Type
- Journal article
- Publication Details
- Journal of allergy and clinical immunology, Vol.138(4), pp.1142-1151.e2
- Publisher
- Elsevier Inc
- DOI
- 10.1016/j.jaci.2016.05.035
- PMID
- 27484032
- ISSN
- 0091-6749
- eISSN
- 1097-6825
- Language
- English
- Date published
- 10/2016
- Academic Unit
- Stead Family Department of Pediatrics; Rheumatology, Allergy, and Immunology; Internal Medicine
- Record Identifier
- 9984093328302771
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