Rapid molecular diagnostics of severe primary immunodeficiency determined by using targeted next-generation sequencing

Hui Yu, Victor Wei Zhang, Asbjørg Stray-Pedersen, Imelda Celine Hanson, Lisa R. Forbes, M. Teresa de la Morena, Ivan K. Chinn, Elizabeth Gorman, Nancy J. Mendelsohn, Tamara Pozos, Wojciech Wiszniewski, Sarah K. Nicholas, Anne B. Yates, Lindsey E. Moore, Knut Erik Berge, Hanne Sorte, Diana K. Bayer, Daifulah ALZahrani, Raif S. Geha, Yanming Feng & 5 others Guoli Wang, Jordan S. Orange, James R. Lupski, Jing Wang, Lee Jun Wong

Research output: Contribution to journalArticle

26 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1142-1151.e2
JournalJournal of Allergy and Clinical Immunology
Volume138
Issue number4
DOIs
StatePublished - Oct 1 2016
Externally publishedYes

Fingerprint

Severe Combined Immunodeficiency
Molecular Pathology
Nucleotides
High-Throughput Nucleotide Sequencing
Pseudogenes
Genetic Heterogeneity
Nonsense Codon
Sequence Homology
T-Cell Antigen Receptor
Exons
Immune System
B-Lymphocytes
Therapeutics
Quality of Life
Parturition
Newborn Infant
T-Lymphocytes
Mutation
Infection
Genes

Keywords

  • molecular diagnostics
  • next-generation sequencing
  • Severe combined immunodeficiency
  • severe combined immunodeficiency newborn screening

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology

Cite this

Yu, H., Zhang, V. W., Stray-Pedersen, A., Hanson, I. C., Forbes, L. R., de la Morena, M. T., ... Wong, L. J. (2016). Rapid molecular diagnostics of severe primary immunodeficiency determined by using targeted next-generation sequencing. Journal of Allergy and Clinical Immunology, 138(4), 1142-1151.e2. https://doi.org/10.1016/j.jaci.2016.05.035

Rapid molecular diagnostics of severe primary immunodeficiency determined by using targeted next-generation sequencing. / Yu, Hui; Zhang, Victor Wei; Stray-Pedersen, Asbjørg; Hanson, Imelda Celine; Forbes, Lisa R.; de la Morena, M. Teresa; Chinn, Ivan K.; Gorman, Elizabeth; Mendelsohn, Nancy J.; Pozos, Tamara; Wiszniewski, Wojciech; Nicholas, Sarah K.; Yates, Anne B.; Moore, Lindsey E.; Berge, Knut Erik; Sorte, Hanne; Bayer, Diana K.; ALZahrani, Daifulah; Geha, Raif S.; Feng, Yanming; Wang, Guoli; Orange, Jordan S.; Lupski, James R.; Wang, Jing; Wong, Lee Jun.

In: Journal of Allergy and Clinical Immunology, Vol. 138, No. 4, 01.10.2016, p. 1142-1151.e2.

Research output: Contribution to journalArticle

Yu, H, Zhang, VW, Stray-Pedersen, A, Hanson, IC, Forbes, LR, de la Morena, MT, Chinn, IK, Gorman, E, Mendelsohn, NJ, Pozos, T, Wiszniewski, W, Nicholas, SK, Yates, AB, Moore, LE, Berge, KE, Sorte, H, Bayer, DK, ALZahrani, D, Geha, RS, Feng, Y, Wang, G, Orange, JS, Lupski, JR, Wang, J & Wong, LJ 2016, 'Rapid molecular diagnostics of severe primary immunodeficiency determined by using targeted next-generation sequencing', Journal of Allergy and Clinical Immunology, vol. 138, no. 4, pp. 1142-1151.e2. https://doi.org/10.1016/j.jaci.2016.05.035
Yu, Hui ; Zhang, Victor Wei ; Stray-Pedersen, Asbjørg ; Hanson, Imelda Celine ; Forbes, Lisa R. ; de la Morena, M. Teresa ; Chinn, Ivan K. ; Gorman, Elizabeth ; Mendelsohn, Nancy J. ; Pozos, Tamara ; Wiszniewski, Wojciech ; Nicholas, Sarah K. ; Yates, Anne B. ; Moore, Lindsey E. ; Berge, Knut Erik ; Sorte, Hanne ; Bayer, Diana K. ; ALZahrani, Daifulah ; Geha, Raif S. ; Feng, Yanming ; Wang, Guoli ; Orange, Jordan S. ; Lupski, James R. ; Wang, Jing ; Wong, Lee Jun. / Rapid molecular diagnostics of severe primary immunodeficiency determined by using targeted next-generation sequencing. In: Journal of Allergy and Clinical Immunology. 2016 ; Vol. 138, No. 4. pp. 1142-1151.e2.
@article{3798848418ac465d931e1790891aa123,
title = "Rapid molecular diagnostics of severe primary immunodeficiency determined by using targeted next-generation sequencing",
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.",
keywords = "molecular diagnostics, next-generation sequencing, Severe combined immunodeficiency, severe combined immunodeficiency newborn screening",
author = "Hui Yu and Zhang, {Victor Wei} and Asbj{\o}rg Stray-Pedersen and Hanson, {Imelda Celine} and Forbes, {Lisa R.} and {de la Morena}, {M. Teresa} and Chinn, {Ivan K.} and Elizabeth Gorman and Mendelsohn, {Nancy J.} and Tamara Pozos and Wojciech Wiszniewski and Nicholas, {Sarah K.} and Yates, {Anne B.} and Moore, {Lindsey E.} and Berge, {Knut Erik} and Hanne Sorte and Bayer, {Diana K.} and Daifulah ALZahrani and Geha, {Raif S.} and Yanming Feng and Guoli Wang and Orange, {Jordan S.} and Lupski, {James R.} and Jing Wang and Wong, {Lee Jun}",
year = "2016",
month = "10",
day = "1",
doi = "10.1016/j.jaci.2016.05.035",
language = "English (US)",
volume = "138",
pages = "1142--1151.e2",
journal = "Journal of Allergy and Clinical Immunology",
issn = "0091-6749",
publisher = "Mosby Inc.",
number = "4",

}

TY - JOUR

T1 - Rapid molecular diagnostics of severe primary immunodeficiency determined by using targeted next-generation sequencing

AU - Yu, Hui

AU - Zhang, Victor Wei

AU - Stray-Pedersen, Asbjørg

AU - Hanson, Imelda Celine

AU - Forbes, Lisa R.

AU - de la Morena, M. Teresa

AU - Chinn, Ivan K.

AU - Gorman, Elizabeth

AU - Mendelsohn, Nancy J.

AU - Pozos, Tamara

AU - Wiszniewski, Wojciech

AU - Nicholas, Sarah K.

AU - Yates, Anne B.

AU - Moore, Lindsey E.

AU - Berge, Knut Erik

AU - Sorte, Hanne

AU - Bayer, Diana K.

AU - ALZahrani, Daifulah

AU - Geha, Raif S.

AU - Feng, Yanming

AU - Wang, Guoli

AU - Orange, Jordan S.

AU - Lupski, James R.

AU - Wang, Jing

AU - Wong, Lee Jun

PY - 2016/10/1

Y1 - 2016/10/1

N2 - 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.

AB - 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.

KW - molecular diagnostics

KW - next-generation sequencing

KW - Severe combined immunodeficiency

KW - severe combined immunodeficiency newborn screening

UR - http://www.scopus.com/inward/record.url?scp=84992170316&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84992170316&partnerID=8YFLogxK

U2 - 10.1016/j.jaci.2016.05.035

DO - 10.1016/j.jaci.2016.05.035

M3 - Article

VL - 138

SP - 1142-1151.e2

JO - Journal of Allergy and Clinical Immunology

JF - Journal of Allergy and Clinical Immunology

SN - 0091-6749

IS - 4

ER -