Hui Yu1, Victor Wei Zhang2, Asbjørg Stray-Pedersen3, Imelda Celine Hanson4, Lisa R Forbes4, M Teresa de la Morena5, Ivan K Chinn4, Elizabeth Gorman1, Nancy J Mendelsohn6, Tamara Pozos7, Wojciech Wiszniewski8, Sarah K Nicholas4, Anne B Yates9, Lindsey E Moore9, Knut Erik Berge10, Hanne Sorte10, Diana K Bayer11, Daifulah ALZahrani12, Raif S Geha13, Yanming Feng1, Guoli Wang1, Jordan S Orange4, James R Lupski14, Jing Wang2, Lee-Jun Wong15. 1. Baylor Genetics, Houston, Tex. 2. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex. 3. Department of Pediatrics, Section of Immunology, Allergy, and Rheumatology, Baylor College of Medicine and Texas Children's Hospital, Houston, Tex; Center for Human Immunobiology, Immunology, Allergy and Rheumatology, Texas Children's Hospital, Feigin Center, Houston, Tex; Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Norwegian National Unit for Newborn Screening, Oslo University Hospital, Oslo, Norway. 4. Department of Pediatrics, Section of Immunology, Allergy, and Rheumatology, Baylor College of Medicine and Texas Children's Hospital, Houston, Tex; Center for Human Immunobiology, Immunology, Allergy and Rheumatology, Texas Children's Hospital, Feigin Center, Houston, Tex. 5. Division of Allergy and Immunology, University of Texas Southwestern Medical Center, Children's Medical Center, Dallas, Tex. 6. Children's Hospital and Clinics of Minnesota, Minneapolis, Minn. 7. Pediatric Infectious Diseases and Immunology, Children's Hospitals and Clinics of Minnesota, St Paul, Minn. 8. Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex. 9. University of Mississippi Medical Center, Jackson, Miss. 10. Department of Medical Genetics, Oslo University Hospital, Oslo, Norway. 11. Department of Pediatrics, Division of Pediatric Allergy/Immunology and Pulmonology, University of Iowa Carver College of Medicine, Iowa City, Iowa. 12. Department of Pediatrics, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia. 13. Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass. 14. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Tex. 15. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex. Electronic address: ljwong@bcm.edu.
Abstract
BACKGROUND: 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. OBJECTIVE: 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. METHODS: 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. RESULTS: 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. CONCLUSION: 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.
BACKGROUND: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. OBJECTIVE: 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. METHODS: 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. RESULTS: 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. CONCLUSION: 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.
Authors: Margot A Cousin; Matthew J Smith; Ashley N Sigafoos; Jay J Jin; Marine I Murphree; Nicole J Boczek; Patrick R Blackburn; Gavin R Oliver; Ross A Aleff; Karl J Clark; Eric D Wieben; Avni Y Joshi; Pavel N Pichurin; Roshini S Abraham; Eric W Klee Journal: J Clin Immunol Date: 2018-04-18 Impact factor: 8.317
Authors: Guillem de Valles-Ibáñez; Ana Esteve-Solé; Mònica Piquer; E Azucena González-Navarro; Jessica Hernandez-Rodriguez; Hafid Laayouni; Eva González-Roca; Ana María Plaza-Martin; Ángela Deyà-Martínez; Andrea Martín-Nalda; Mónica Martínez-Gallo; Marina García-Prat; Lucía Del Pino-Molina; Ivón Cuscó; Marta Codina-Solà; Laura Batlle-Masó; Manuel Solís-Moruno; Tomàs Marquès-Bonet; Elena Bosch; Eduardo López-Granados; Juan Ignacio Aróstegui; Pere Soler-Palacín; Roger Colobran; Jordi Yagüe; Laia Alsina; Manel Juan; Ferran Casals Journal: Front Immunol Date: 2018-05-14 Impact factor: 7.561
Authors: Janne Strand; Kiran Aftab Gul; Hans Christian Erichsen; Emma Lundman; Mona C Berge; Anette K Trømborg; Linda K Sørgjerd; Mari Ytre-Arne; Silje Hogner; Ruth Halsne; Hege Junita Gaup; Liv T Osnes; Grete A B Kro; Hanne S Sorte; Lars Mørkrid; Alexander D Rowe; Trine Tangeraas; Jens V Jørgensen; Charlotte Alme; Trude E H Bjørndalen; Arild E Rønnestad; Astri M Lang; Terje Rootwelt; Jochen Buechner; Torstein Øverland; Tore G Abrahamsen; Rolf D Pettersen; Asbjørg Stray-Pedersen Journal: Front Immunol Date: 2020-07-09 Impact factor: 7.561