Unbiased targeted next-generation sequencing molecular approach for primary immunodeficiency diseases

Journal of Allergy and Clinical Immunology

Volumn 137, Issue 6, 2016, Pages 1780-1787

  Al Mousa, Hamoud ^a,b   Abouelhoda, Mohamed ^a,c   Monies, Dorota M ^a,c   Al Tassan, Nada ^a,c   Al Ghonaium, Abdulaziz ^a   Al Saud, Bandar ^a,b   Al Dhekri, Hasan ^a   Arnaout, Rand ^a   Al Muhsen, Saleh ^a,d   Ades, Nazema ^a   Elshorbagi, Sahar ^a   Al Gazlan, Sulaiman ^a   Sheikh, Farrukh ^a   Dasouki, Majed ^a   El Baik, Lina ^a   Elamin, Tanzeil ^a   Jaber, Amal ^a   Kheir, Omnia ^a   El Kalioby, Mohamed ^a   Subhani, Shazia ^a,c   Al Idrissi, Eman ^e   Al Zahrani, Mofareh ^e   Alhelale, Maryam ^f   Alnader, Noukha ^a   Al Otaibi, Afaf ^a   Kattan, Rana ^c   Al Abdelrahman, Khalid ^c   Al Breacan, Muna M ^a   Bin Humaid, Faisal S ^a   Wakil, Salma Majid ^a   Alzayer, Fadi ^a   Al Dusery, Haya ^a   Faquih, Tariq ^a   Al Hissi, Safa ^a   Meyer, Brian F ^a,c   Hawwari, Abbas ^a   more..

^a KING FAISAL SPECIALIST HOSPITAL AND RESEARCH CENTER   (Saudi Arabia)

^b ALFAISAL UNIVERSITY   (Saudi Arabia)

^c KING ABDULAZIZ CITY FOR SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^d KING SAUD UNIVERSITY   (Saudi Arabia)

^e KING FAHAD MEDICAL CITY   (Saudi Arabia)

^f Prince Sultan Military Medical City   (Saudi Arabia)

Author keywords

diagnosis; genetic; Immunodeficiency; mutation; next generation sequencing; primary immunodeficiency; Saudi; targeted; variants

Indexed keywords

ARTICLE; AUTOIMMUNE DISEASE; BARE LYMPHOCYTE SYNDROME; CHEDIAK HIGASHI SYNDROME; CHRONIC GRANULOMATOUS DISEASE; COMBINED IMMUNODEFICIENCY; CONTROLLED CLINICAL TRIAL; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DIAGNOSTIC VALUE; ENTEROPATHY; GENE; GENE MUTATION; GENETIC ANALYZER; GENETIC SCREENING; GENOTYPE; GENOTYPE PHENOTYPE CORRELATION; HUMAN; HYPER IGM SYNDROME; IMMUNE DEFICIENCY; INDEL MUTATION; MAJOR CLINICAL STUDY; MOLECULAR DIAGNOSIS; MOLECULAR GENETICS; NEXT GENERATION SEQUENCING; OMENN SYNDROME; PHENOTYPE; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; COPY NUMBER VARIATION; DNA MUTATIONAL ANALYSIS; GENETIC MARKER; GENETIC PREDISPOSITION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HIGH THROUGHPUT SEQUENCING; IMMUNOLOGIC DEFICIENCY SYNDROMES; IMMUNOLOGY; MUTATION; WORKFLOW;

GENETIC MARKER;

COMPUTATIONAL BIOLOGY; DNA COPY NUMBER VARIATIONS; DNA MUTATIONAL ANALYSIS; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; IMMUNOLOGIC DEFICIENCY SYNDROMES; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; WORKFLOW;

EID: 84966312215     PISSN: 00916749     EISSN: 10976825     Source Type: Journal    
DOI: 10.1016/j.jaci.2015.12.1310     Document Type: Article

References (24)

1. W. Al-Herz, A. Bousfiha, J.L. Casanova, T. Chatila, M.E. Conley, C. Cunningham-Rundles, and et al. Primary immunodeficiency diseases: an update on the classification from the international union of immunological societies expert committee for primary immunodeficiency Front Immunol 5 2014 162
2. L.D. Notarangelo, and R. Sorensen Is it necessary to identify molecular defects in primary immunodeficiency disease? J Allergy Clin Immunol 122 2008 1069 1073
3. A. Villa, L.D. Notarangelo, and C.M. Roifman Omenn syndrome: inflammation in leaky severe combined immunodeficiency J Allergy Clin Immunol 122 2008 1082 1086
4. S. Santagata, A. Villa, C. Sobacchi, P. Cortes, and P. Vezzoni The genetic and biochemical basis of Omenn syndrome Immunol Rev 178 2000 64 74
5. A. Villa, C. Sobacchi, L.D. Notarangelo, F. Bozzi, M. Abinun, T.G. Abrahamsen, and et al. V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations Blood 97 2001 81 88
6. A. Villa, C. Sobacchi, and P. Vezzoni Recombination activating gene and its defects Curr Opin Allergy Clin Immunol 1 2001 491 495
7. C. Sobacchi, V. Marrella, F. Rucci, P. Vezzoni, and A. Villa RAG-dependent primary immunodeficiencies Hum Mutat 27 2006 1174 1184
8. J.P. de Villartay, A. Lim, H. Al-Mousa, S. Dupont, J. Dechanet-Merville, E. Coumau-Gatbois, and et al. A novel immunodeficiency associated with hypomorphic RAG1 mutations and CMV infection J Clin Invest 115 2005 3291 3299
9. N. Navin, and J. Hicks Future medical applications of single-cell sequencing in cancer Genome Med 3 2011 31
10. S. Fokstuen, P. Makrythanasis, S. Nikolaev, F. Santoni, D. Robyr, A. Munoz, and et al. Multiplex targeted high-throughput sequencing for Mendelian cardiac disorders Clin Genet 85 2014 365 370
11. A. Guilmatre, G. Highnam, C. Borel, D. Mittelman, and A.J. Sharp Rapid multiplexed genotyping of simple tandem repeats using capture and high-throughput sequencing Hum Mutat 34 2013 1304 1311
12. J. Chou, T.K. Ohsumi, and R.S. Geha Use of whole exome and genome sequencing in the identification of genetic causes of primary immunodeficiencies Curr Opin Allergy Clin Immunol 12 2012 623 628
13. I.J. Nijman, J.M. van Montfrans, M. Hoogstraat, M.L. Boes, L. van de Corput, E.D. Renner, and et al. Targeted next-generation sequencing: a novel diagnostic tool for primary immunodeficiencies J Allergy Clin Immunol 133 2014 529 534
14. S. Ghosh, F. Krux, V. Binder, M. Gombert, T. Niehues, O. Feyen, and et al. Array-based sequence capture and next-generation sequencing for the identification of primary immunodeficiencies Scand J Immunol 75 2012 350 354
15. J.L. Stoddard, J.E. Niemela, T.A. Fleisher, and S.D. Rosenzweig Targeted NGS: a cost-effective approach to molecular diagnosis of PIDs Front Immunol 5 2014 531
16. L.N. Moens, E. Falk-Sorqvist, A.C. Asplund, E. Bernatowska, C.I. Smith, and M. Nilsson Diagnostics of primary immunodeficiency diseases: a sequencing capture approach PLoS One 9 2014 e114901
17. F.H. Routier, E.F. Hounsell, P.M. Rudd, N. Takahashi, A. Bond, F.C. Hay, and et al. Quantitation of the oligosaccharides of human serum IgG from patients with rheumatoid arthritis: a critical evaluation of different methods J Immunol Methods 213 1998 113 130
18. Z. Alsum, A. Hawwari, O. Alsmadi, S. Al-Hissi, E. Borrero, A. Abu-Staiteh, and et al. Clinical, immunological and molecular characterization of DOCK8 and DOCK8-like deficient patients: single center experience of twenty-five patients J Clin Immunol 33 2013 55 67
19. K. Wang, M. Li, and H. Hakonarson ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data Nucleic Acids Res 38 2010 e164
20. Y. Yang, D.M. Muzny, J.G. Reid, M.N. Bainbridge, A. Willis, P.A. Ward, and et al. Clinical whole-exome sequencing for the diagnosis of mendelian disorders N Engl J Med 369 2013 1502 1511
21. B.J. Evans Minimizing liability risks under the ACMG recommendations for reporting incidental findings in clinical exome and genome sequencing Genet Med 15 2013 915 920
22. M.M. Weiss, B. Van der Zwaag, J.D. Jongbloed, M.J. Vogel, H.T. Bruggenwirth, R.H. Lekanne Deprez, and et al. Best practice guidelines for the use of next-generation sequencing applications in genome diagnostics: a national collaborative study of Dutch genome diagnostic laboratories Hum Mutat 34 2013 1313 1321
23. P. Kumar, S. Henikoff, and P.C. Ng Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm Nat Protoc 4 2009 1073 1081
24. I.A. Adzhubei, S. Schmidt, L. Peshkin, V.E. Ramensky, A. Gerasimova, P. Bork, and et al. A method and server for predicting damaging missense mutations Nat Methods 7 2010 248 249