Genetic diagnosis using whole exomesequencing in common variable immunodeficiency

Frontiers in Immunology

Volumn 7, Issue JUN, 2016, Pages

  Maffucci, Patrick ^a   Filion, Charles A ^a   Boisson, Bertrand ^b,c,d   Itan, Yuval ^b   Shang, Lei ^b   Casanova, Jean Laurent ^b,c,d,e   Cunningham Rundles, Charlotte ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b ROCKEFELLER UNIVERSITY   (United States)

^c HÔPITAL NECKER ENFANTS MALADES   (France)

^d IMAGINE INSTITUTE   (France)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Common variable immunodeficiency; Genetic diagnosis; Next generation sequencing; Primary immunodeficiencies; Whole exome sequencing

Indexed keywords

CYTOTOXIC T LYMPHOCYTE ANTIGEN 4; GENOMIC DNA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; STAT3 PROTEIN; SYNTAXIN;

ADULT; ARTICLE; AUTOIMMUNE DISEASE; B LYMPHOCYTE; CLINICAL ARTICLE; FEMALE; GENE MUTATION; GENE SEQUENCE; GENE TARGETING; GENETIC DISORDER; GENETIC VARIABILITY; HEMOPHAGOCYTIC SYNDROME; HUMAN; IMMUNE DEFICIENCY; IMMUNOGLOBULIN DEFICIENCY; LYMPHOCYTE COUNT; MALE; PHENOTYPE; SEGREGATION ANALYSIS;

EID: 84977547054     PISSN: None     EISSN: 16643224     Source Type: Journal    
DOI: 10.3389/fimmu.2016.00220     Document Type: Article

References (33)

1. Picard C, Al-Herz W, Bousfiha A, Casanova J-L, Chatila T, Conley ME, et al. Primary immunodeficiency diseases: an update on the classification from the international union of immunological societies expert committee for primary immunodeficiency 2015. J Clin Immunol (2015) 35:696-726. doi: 10.1007/s10875-015-0201-1
2. Resnick ES, Moshier EL, Godbold JH, Cunningham-Rundles C. Morbidity and mortality in common variable immune deficiency over 4 decades. Blood (2012) 119:1650-7. doi:10.1182/blood-2011-09-377945
3. Fliegauf M, Bryant VL, Frede N, Slade C, Woon S-T, Lehnert K, et al. Haploinsufficiency of the NF-κB1 subunit p50 in common variable immunodeficiency. Am J Hum Genet (2015) 97:389-403. doi:10.1016/j.ajhg.2015.07.008
4. Kuehn HS, Boisson B, Cunningham-Rundles C, Reichenbach J, Stray-Pedersen A, Gelfand EW, et al. Loss of B cells in patients with heterozygous mutations in IKAROS. N Engl J Med (2016) 374:1032-43. doi:10.1056/NEJMoa1512234
5. Salzer U, Warnatz K, Peter H-H. Common variable immunodeficiency: an update. Arthritis Res Ther (2012) 14:223. doi:10.1186/ar4032
6. Conley ME, Casanova J-L. Discovery of single-gene inborn errors of immunity by next generation sequencing. Curr Opin Immunol (2014) 30:17-23. doi:10.1016/j.coi.2014.05.004
7. Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, et al. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA (2014) 312:1870-9. doi:10.1001/jama.2014.14601
8. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 25:1754-60. doi:10.1093/bioinformatics/btp324
9. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res (2010) 20:1297-303. doi:10.1101/gr.107524.110
10. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics (2009) 25:2078-9. doi:10.1093/bioinformatics/btp352
11. Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet (2014) 46:310-5. doi:10.1038/ng.2892
12. Itan Y, Shang L, Boisson B, Ciancanelli MJ, Markle JG, Martinez-Barricarte R, et al. The mutation significance cutoff: gene-level thresholds for variant predictions. Nat Methods (2016) 13:109-10. doi:10.1038/nmeth.3739
13. Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NST, et al. Human gene mutation database (HGMD): 2003 update. Hum Mutat (2003) 21:577-81. doi:10.1002/humu.10212
14. Pan-Hammarström Q, Salzer U, Du L, Bjorkander J, Cunningham-Rundles C, Nelson DL, et al. Reexamining the role of TACI coding variants in common variable immunodeficiency and selective IgA deficiency. Nat Genet (2007) 39:429-30. doi:10.1038/ng0407-429
15. Perkins ND. Integrating cell-signalling pathways with NF-kappaB and IKK function. Nat Rev Mol Cell Biol (2007) 8:49-62. doi:10.1038/nrm2083
16. Angulo I, Vadas O, Garçon F, Banham-Hall E, Plagnol V, Leahy TR, et al. Phosphoinositide 3-kinase d gene mutation predisposes to respiratory infection and airway damage. Science (2013) 342:866-71. doi:10.1126/science.1243292
17. Yoshida T, Georgopoulos K. Ikaros fingers on lymphocyte differentiation. Int J Hematol (2014) 100:220-9. doi:10.1007/s12185-014-1644-5
18. Wang J-W, Gamsby JJ, Highfill SL, Mora LB, Bloom GC, Yeatman TJ, et al. Deregulated expression of LRBA facilitates cancer cell growth. Oncogene (2004) 23:4089-97. doi:10.1038/sj.onc.1207567
19. Alangari A, Alsultan A, Adly N, Massaad MJ, Kiani IS, Aljebreen A, et al. LPS-responsive beige-like anchor (LRBA) gene mutation in a family with inflammatory bowel disease and combined immunodeficiency. J Allergy Clin Immunol (2012) 130:481-8.e2. doi:10.1016/j.jaci.2012.05.043
20. Lo B, Zhang K, Lu W, Zheng L, Zhang Q, Kanellopoulou C, et al. Autoimmune disease. Patients with LRBA deficiency show CTLA4 loss and immune dysregulation responsive to abatacept therapy. Science (2015) 349:436-40. doi:10.1126/science.aaa1663
21. Charbonnier L-M, Janssen E, Chou J, Ohsumi TK, Keles S, Hsu JT, et al. Regulatory T-cell deficiency and immune dysregulation, polyendocrinopathy, enteropathy, X-linked-like disorder caused by loss-of-function mutations in LRBA. J Allergy Clin Immunol (2015) 135:217-27. doi:10.1016/j.jaci.2014.10.019
22. Pagel J, Beutel K, Lehmberg K, Koch F, Maul-Pavicic A, Rohlfs A-K, et al. Distinct mutations in STXBP2 are associated with variable clinical presentations in patients with familial hemophagocytic lymphohistiocytosis type 5 (FHL5). Blood (2012) 119:6016-24. doi:10.1182/blood-2011-12-398958
23. Zhang Q, Davis JC, Lamborn IT, Freeman AF, Jing H, Favreau AJ, et al. Combined immunodeficiency associated with DOCK8 mutations. N Engl J Med (2009) 361:2046-55. doi:10.1056/NEJMoa0905506
24. Flanagan SE, Haapaniemi E, Russell MA, Caswell R, Lango Allen H, De Franco E, et al. Activating germline mutations in STAT3 cause early-onset multi-organ autoimmune disease. Nat Genet (2014) 46:812-4. doi:10.1038/ng.3040
25. Schubert D, Bode C, Kenefeck R, Hou TZ, Wing JB, Kennedy A, et al. Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations. Nat Med (2014) 20:1410-6. doi:10.1038/nm.3746
26. Milner JD, Vogel TP, Forbes L, Ma CA, Stray-Pedersen A, Niemela JE, et al. Early-onset lymphoproliferation and autoimmunity caused by germline STAT3 gain-of-function mutations. Blood (2015) 125:591-9. doi:10.1182/blood-2014-09-602763
27. Saltzman RW, Monaco-Shawver L, Zhang K, Sullivan KE, Filipovich AH, Orange JS. Novel mutation in STXBP2 prevents IL-2-induced natural killer cell cytotoxicity. J Allergy Clin Immunol (2012) 129:1666-8. doi:10.1016/j.jaci.2011.12.1003
28. Dziembowska M, Fondaneche M-C, Vedrenne J, Barbieri G, Wiszniewski W, Picard C, et al. Three novel mutations of the CIITA gene in MHC class II-deficient patients with a severe immunodeficiency. Immunogenetics (2002) 53:821-9. doi:10.1007/s00251-001-0395-7
29. van Schouwenburg PA, Davenport EE, Kienzler A-K, Marwah I, Wright B, Lucas M, et al. Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders. Clin Immunol (2015) 160:301-14. doi:10.1016/j.clim.2015.05.020
30. Grimbacher B, HutloffA, Schlesier M, Glocker E, Warnatz K, Dräger R, et al. Homozygous loss of ICOS is associated with adult-onset common variable immunodeficiency. Nat Immunol (2003) 4:261-8. doi:10.1038/ni902
31. Elgizouli M, Lowe DM, Speckmann C, Schubert D, Hülsdünker J, Eskandarian Z, et al. Activating PI3Kd mutations in a cohort of 669 patients with primary immunodeficiency. Clin Exp Immunol (2016) 183:221-9. doi:10.1111/cei.12706
32. Lee S, Moon JS, Lee C-R, Kim H-E, Baek S-M, Hwang S, et al. Abatacept alleviates severe autoimmune symptoms in a patient carrying a de novo variant in CTLA-4. J Allergy Clin Immunol (2016) 137:327-30. doi:10.1016/j.jaci.2015.08.036
33. Lucas CL, Kuehn HS, Zhao F, Niemela JE, Deenick EK, Palendira U, et al. Dominant-activating germline mutations in the gene encoding the PI(3)K catalytic subunit p110d result in T cell senescence and human immunodeficiency. Nat Immunol (2014) 15:88-97. doi:10.1038/ni.2771