Mutation analysis in primary immunodeficiency diseases: Case studies

Current Opinion in Allergy and Clinical Immunology

Volumn 9, Issue 6, 2009, Pages 517-524

  Hsu, Amy P ^a   Fleisher, Thomas A ^b   Niemela, Julie E ^b  

^a NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Bioinformatics tools; DNA sequencing; Immune function; Mutation analysis; Primary immunodeficiency

Indexed keywords

DNA POLYMERASE; GENOMIC DNA; IMMUNOGLOBULIN A; IMMUNOGLOBULIN E; IMMUNOGLOBULIN G; IMMUNOGLOBULIN M; INTERLEUKIN 1 RECEPTOR ASSOCIATED KINASE 4; MYELOID DIFFERENTIATION FACTOR 88; TOLL LIKE RECEPTOR;

BACTERIAL INFECTION; BACTERIAL PNEUMONIA; BIOINFORMATICS; CHRONIC DIARRHEA; CLINICAL EVALUATION; COMBINED IMMUNODEFICIENCY; DIFFERENTIAL DIAGNOSIS; DNA SEQUENCE; DNA SPLICING; EPSTEIN BARR VIRUS; FAILURE TO THRIVE; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; FLOW CYTOMETRY; FLUORESCENCE IN SITU HYBRIDIZATION; FOLLOW UP; GENE INSERTION; GENE MUTATION; HUMAN; HYPOHIDROTIC ECTODERMAL DYSPLASIA; IDIOPATHIC THROMBOCYTOPENIC PURPURA; IMMUNE DEFICIENCY; LYMPHOCYTOPENIA; LYMPHOPROLIFERATIVE DISEASE; MISSENSE MUTATION; MUTATIONAL ANALYSIS; NATURAL KILLER CELL; OUTCOME ASSESSMENT; PNEUMOCYSTIS JIROVECI; PNEUMOCYSTIS PNEUMONIA; PRIORITY JOURNAL; PYOGENIC BACTERIUM; RECURRENT INFECTION; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

AUTOIMMUNE LYMPHOPROLIFERATIVE SYNDROME; BACTERIAL INFECTIONS; CD40 LIGAND; CHILD; DIAGNOSTIC ERRORS; DNA MUTATIONAL ANALYSIS; ECTODERMAL DYSPLASIA 1, ANHIDROTIC; FEMALE; HUMANS; HYPER-IGM IMMUNODEFICIENCY SYNDROME, TYPE 1; I-KAPPA B KINASE; INFANT; INTERLEUKIN RECEPTOR COMMON GAMMA SUBUNIT; INTERLEUKIN-1 RECEPTOR-ASSOCIATED KINASES; LYMPHATIC DISEASES; MALE; MUTATION; PURPURA, THROMBOCYTOPENIC, IDIOPATHIC; SEVERE COMBINED IMMUNODEFICIENCY;

EID: 70350783953     PISSN: 15284050     EISSN: 14736322     Source Type: Journal    
DOI: 10.1097/ACI.0b013e3283328f59     Document Type: Review

References (37)

1. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977; 74:5463-5467.
2. Smith LM, Sanders JZ, Kaiser RJ, et al. Fluorescence detection in automated DNA sequence analysis. Nature 1986; 321:674-679.
3. Ronaghi M, Uhlén M, Nyrén P. A sequencing method based on real-time pyrophosphate. Science 1998; 281:363-365.
4. Drmanac S, Chui G, Diaz R, et al. Sequencing by hybridization (SBH): advantages, achievements, and opportunities. Adv Biochem Eng Biotechnol 2002; 77:75-101.
5. Bajorath J, Seyama K, Nonoyama S, et al. Classification of mutations in the human CD40 ligand, gp39, that are associated with X-linked hyper IgM syndrome. Protein Sci 1996; 5:531-534.
6. Thusberg J, Vihinen M. The structural basis of hyper IgM deficiency: CD40L mutations. Protein Eng Des Sel 2007; 20:133-141.
7. Karpusas M, Hsu YM, Wang J, et al. 2 a° crystal structure of an extracellular fragment of human CD40 ligand. Structure 1995; 3:1031-1039.
8. Picard C, Puel A, Bonnet M, et al. Pyogenic bacterial infections in humans with IRAK-4 deficiency. Science 2003; 299:2076-2079.
9. Frischmeyer PA, Dietz HC. Nonsense-mediated mRNA decay in health and disease. Hum Mol Genet 1999; 8:1893-1900.
10. Lohi H, Turnbull J, Zhao XC, et al. Genetic diagnosis in Lafora disease: genotype-phenotype correlations and diagnostic pitfalls. Neurology 2007; 68:996-1001.
11. Bekri S, May A, Cotter PD, et al. A promoter mutation in the erythroid-specific 5-aminolevulinate synthase (ASAS2) gene causes X-linked sideroblastic anemia. Blood 2003; 102:698-704.
12. Buckley RH. Molecular defects in human severe combined immunodeficiency and approaches to immune reconstitution. Annu Rev Immunol 2004; 22: 625-655.
13. Guo DC, Gupta P, Tran-Fadulu V, et al. An FBN1 pseudoexon mutation in a patient with Marfan syndrome: confirmation of cryptic mutations leading to disease. J Hum Gene 2008; 53:1007-1011.
14. Davis RL, Homer VM, George PM, Brennan SO. A deep intronic mutation in FGB creates a consensus exonic splicing enhancer motif that results in afibrinogenemia caused by aberrant mRNA splicing, which can be corrected in vitro with antisense oligonucleotide treatment. Hum Mutat 2009; 30:221-227.
15. Jacquette A, Le Roux G, Lacombe C, et al. Compound heterozygosity for two new mutations in the beta-globin gene [codon 9 (pTA) and polyadenylation site (AATAAA->AAAAAA)] leads to thalassemia intermedia in a Tunisian patient. Hemoglobin 2004; 28:243-248.
16. Bennett CL, Brunkow ME, Ramsdell F, et al. A rare polyadenylation signal mutation of the FOXP3 gene (AAUAAAAAUGAA) leads to the IPEX syndrome. Immunogenetics 2001; 53:435-439.
17. Defendi F, Decleva E, Martel C, et al. A novel point mutation in the CYBB gene promoter leading to a rare X minus chronic granulomatous disease variant: impact on the microbicidal activity of neutrophils. Biochim Biophys Acta 2009; 1792:201-210.
18. Hanson EP, Monaco-Shawver L, Solt LA, et al. Hypomorphic nuclear factorkappaB essential modulator mutation database and reconstitution system identifies phenotypic and immunologic diversity. J Allergy Clin Immunol 2008; 122:1169-1177.
19. Berezin C, Glaser F, Rosenberg J, et al. ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics 2004; 20:1322-1324.
20. Ramensky V, Bork P, Sunyaev S. Human nonsynonymous SNPs: server and survey. Nucleic Acids Res 2002; 30:3894-3900.
21. Ng PC, Henikoff S. Predicting the effects of coding nonsynonymous variants on protein function using the SIFT algorithm. Genome Res 2001; 11:863-874.
22. Aradhya S, Bardaro T, Galgóczy P, et al. Multiple pathogenic and benign genomic rearrangements occur at a 35 kb duplication involving the NEMO and LAGE2 genes. Hum Mol Genet 2001; 10:2557-2567.
23. Bardaro T, Falco G, Sparago A, et al. Two cases of misinterpreation of molecular results in contintinentia peigmenti, and a PCR-based method to discriminate NEMO/IKKgamma gene deletion. Hum Mutat 2003; 21:8-11.
24. Fleisher TA. The autoimmune lymphoproliferative syndrome: an experiment of nature involving lymphocyte apoptosis. Immunol Res 2008; 40:87-92.
25. Helzelova E, Vonarbourg C, Stolzenberg MC, et al. Autoimmune lymphoproliferative syndrome with somatic Fas mutations. N Engl J Med 2004; 351: 1409-1418.
26. Cartegni L, Chew SL, Krainer AR. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 2002; 3:285-298.
27. Pfarr N, Prawitt D, Kirschfink M, et al. Linking C5 deficiency to an exonic splicing enhancer mutation. J Immunol 2005; 174:4172-4177.
28. Fackenthal JD, Cartegni L, Krainer AR, Olopade OI. BRCA2 T2722R is a deleterious allele that causes exon skipping. Am J Hum Genet 2002; 71: 625-631.
29. Cogan JD, Ramel B, Lehto M, et al. A recurring dominant negative mutation causes autosomal dominant growth hormone deficiency: a clinical research center study. J Clin Endocrinol Metab 1995; 80:3591-3595.
30. Cogan JD, Prince MA, Lekhakula S, et al. A novel mechanism of aberrant premRNA splicing in humans. Hum Mol Genet 1997; 6:909-912.
31. Moseley CT, Mullis PE, Prince MA, Phillips JA III. An exon splice enhancer mutation causes autosomal dominant GH deficiency. J Clin Endocr Metab 2002; 87:847-852.
32. Aznarez I, Chan EM, Zielenski J, et al. Characterization of disease-associated mutations affecting an exonic splicing enhancer and two cryptic splice sites in exon 13 of the cystic fibrosis transmembrane conductance regulator gene. Hum Mol Genet 2003; 12:2031-2040.
33. Mendell JT, Dietz HC. When the message goes awry: disease producing mutations that influence mRNA content and performance. Cell 2001; 107:411-414.
34. Fairbrother WG, Yeh RF, Sharp PA, Burge CB. Predictive identification of exonic splicing enhancers in human genes. Science 2002; 297:1007-1013.
35. Cartegni L, Wang J, Zhu Z, et al. ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acid Res 2003; 31:3568-3571.
36. Hartmann L, Theiss S, Niederacher D, Schaal H. Diagnostics of pathogenic splicing mutations: does bioinformatics cover all bases? Front Biosci 2008; 13:3252-3272.
37. Kimchi-Sarfaty C, Oh JM, Kim IW, et al. A 'silent' polymorphism in the MDR1 gene changes substrate specificity. Science 2007; 315:525-528.