Computational refinement of functional single nucleotide polymorphisms associated with ATM gene

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Doss, C George Priya ^a   Rajith, B ^a  

^a VIT UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

AMINO ACID SEQUENCE; ARTICLE; ATM GENE; CANCER SUSCEPTIBILITY; GENE; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC REGULATION; GENETIC VARIABILITY; HUMAN; MATHEMATICAL ANALYSIS; NUCLEOTIDE SEQUENCE; PROTEIN PROCESSING; SCORING SYSTEM; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM;

AMINO ACID SEQUENCE; CELL CYCLE PROTEINS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DATABASES, GENETIC; DNA-BINDING PROTEINS; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN-SERINE-THREONINE KINASES; REGULATORY SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT; TUMOR SUPPRESSOR PROTEINS;

EID: 84859720188     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0034573     Document Type: Article

References (69)

1. Botstein D, Risch N, (2003) Discovering genotypes underlying human phenotypes: past successes for Mendelian disease, future approaches for complex disease. Nat Genet 33: 228-237.
2. Lee JE, Choi JH, Lee MG, (2005) Gene SNPs and mutations in clinical genetic testing: haplotype-based testing and analysis. Mutat Res 573: 195-20.
3. Bandele OJ, Wang X, Campbell MR, Pittman GS, Bell DA, (2010) Human single-nucleotide polymorphisms alter p53 sequence-specific binding at gene regulatory elements. Nucleic Acids Res 39: 178-89.
4. Nadeau JH, (2002) Single nucleotide polymorphisms: Tackling complexity. Nature 420: 517-518.
5. Sandoval N, Platzer M, Rosenthal A, Dörk T, Bendix R, et al. (1999) Characterization of ATM gene mutations in 66 ataxia telangiectasia families. Hum Mol Genet 8: 69-79.
6. Ho AY, Fan G, Atencio DP, Green S, Formenti SC, et al. (2007) Possession of ATM sequence variants as predictor for late normal tissue responses in breast cancer patients treated with radiotherapy. Int J Radiat Oncol Biol Phys.69: 677-84.
7. Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, et al. (2007) Patterns of somatic mutation in human cancer genomes. Nature 446: 153-158.
8. Izatt L, Greenman J, Hodgson SV, Ellis D, Watts S, et al. (1999) Identification of Germline missense mutations and rare allelic variants in the ATM gene in early-onset breast cancer. Genes Chromosomes Canc 26: 286-294.
9. Sasaki T, Tian H, Kukita Y, Inazuka M, Tahira T, et al. (1998) ATM mutations in patients with ataxia telangiectasia screened by a hierarchical strategy. Hum Mutat 12: 186-195.
10. Stankovic T, Kidd AMJ, Sutcliffe A, McGuire GM, Robinson P, et al. (1998) ATM mutations and phenotypes in ataxia-telangiectasia families in the British Isles: expression of mutant ATM and the risk of leukemia, lymphoma, and breast cancer. Am J Hum Genet 62: 334-345.
11. Li A, Swift M, (2000) Mutations at the ataxia-telangiectasia locus and clinical phenotypes of A-T patients. Am J Med Genet 92: 170-7.
12. Bullrich F, Rasio D, Kitada S, Starostik P, Kipps T, et al. (1999) ATM mutations in B-cell chronic lymphocytic leukemia. Cancer Res 59: 24-27.
13. Stankovic T, Weber P, Stewart G, Bedenham T, Murray J, et al. (1999) Inactivation of ataxia telangiectasia mutated gene in B-cell chronic lymphocytic leukaemia. Lancet 353: 26-29.
14. Vorechovsky I, Rasio D, Luo L, Monaco C, Hammarstroem L, et al. (1996) The ATM gene and susceptibility to breast cancer: analysis of 38 breast tumors reveals no evidence for mutation. Cancer Res 56: 2726-2732.
15. Vorechovsky I, Luo L, Dyer MJS, Catovsky D, Amlot PL, et al. (1997) Clustering of missense mutations in the ataxia-telangiectasia gene in a sporadic T-cell leukaemia. Nat Genet 17: 96-99.
16. Broeks A, de Klein A, Floore AN, Muijtjens M, Kleijer WJ, et al. (1998) ATM germline mutations in classical ataxia-telangiectasia patients in the Dutch population. Hum Mutat 12: 330-337.
17. Castellvi-Bel S, Sheikhavandi S, Telatar M, Tai LQ, Hwang MJ, et al. (1999) New mutations, polymorphisms, and rare variants in the ATM gene detected by a novel SSCP strategy. Hum Mutat pp. 14156-162.
18. Schaffner C, Idler I, Stilgenbauer S, Doehner H, Lichter P, (2000) Mantle cell lymphoma is characterized by inactivation of the ATM gene. Proc Natl Acad Sci 97: 2773-2778.
19. Yuille MAR, Coignet LJA, Abraham SM, Yaqub F, Luo L, et al. (1998) ATM is usually rearranged in T-cell prolymphocytic leukaemia. Oncogene 16: 789-796.
20. Becker-Catania SG, Chen G, Hwang MJ, Wang Z, Sun X, et al. (2000) Ataxia-telangiectasia: phenotype/genotype studies of ATM protein expression, mutations, and radiosensitivity. Mol Genet Metab 70: 122-133.
21. Schaffner C, Stilgenbauer S, Rappold GA, Doehner H, Lichter P, (1999) Somatic ATM mutations indicate a pathogenic role of ATM in B-cell chronic lymphocytic leukemia Blood 94: 748-753.
22. Stoppa-Lyonnet D, Soulier J, Lauge A, Dastot H, Garand R, et al. (1998) Inactivation of the ATM gene in T-cell prolymphocytic leukemias. Blood 91: 3920-3926.
23. Fukao T, Song XQ, Yoshida T, Tashita H, Kaneko H, (1998) Ataxia-telangiectasia in the Japanese population: identification of R1917X, W2491R, R2909G, IVS33+2T->A, and 7883del5, the latter two being relatively common mutations. Hum Mutat 12: 338-343.
24. Toyoshima M, Hara T, Zhang H, Yamamoto T, Akaboshi S, et al. (1998) Ataxia-telangiectasia without immunodeficiency: novel point mutations within and adjacent to the phosphatidylinositol 3-kinase-like domain. Am J Med Genet 75: 141-144.
25. Stilgenbauer S, Schaffner C, Litterst A, Liebisch P, Gilad S, et al. (1997) Biallelic mutations in the ATM gene in T-prolymphocytic leukemia. Nat Med 3: 1155-1159.
26. Gilad S, Khosravi R, Shkedy D, Uziel T, Ziv Y, et al. (1996) Predominance of null mutations in ataxia-telangiectasia. Hum Mol Genet 5: 433-439.
27. Watters D, Khanna KK, Beamish H, Birrell G, Spring K, et al. (1997) Cellular localisation of the ataxia-telangiectasia (ATM) gene product and discrimination between mutated and normal forms. Oncogene 14: 1911-1921.
28. Kumar P, Henikoff S, Ng PC, (2009) SIFT: Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4: 1073-81.
29. Ramensky V, Bork P, Sunyaev S, (2002) Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30: 3894-3900.
30. Capriotti E, Fariselli P, Rossi I, Casadio R, (2008) A three-state prediction of single point mutations on protein stability changes. BMC Bioinformatics 9 (Suppl 2): S6.
31. Yuan HY, Chiou JJ, Tseng WH, Liu CH, Liu CK, et al. (2006) FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Res 34: 635-41.
32. Grillo G, Turi A, Licciulli F, Mignone F, Liuni S, et al. (2010) UTRdb and UTRsite (RELEASE 2010) a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 38: D75-80.
33. Conde L, Vaquerizas JM, Dopazo H, Arbiza L, Reumers J, et al. (2006) PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res 34: 621-25.
34. Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N, (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res 38: 529-33.
35. Walsh CT, (2006) Posttranslational modification of proteins: expanding nature's inventory Englewood, CO Roberts and Company Publishers.
36. Grasbon-Frodl E, Lorenz H, Mann U, Nitsch RM, Windl O, et al. (2004) Loss of glycosylation associated with the T183A mutation in human prion disease. Acta Neuropathol 108: 476-84.
37. Ansong C, Tolić N, Purvine SO, Porwollik S, Jones M, et al. (2011) Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium. BMC Genomics 25: 12-433.
38. Xue Y, Liu Z, Cao J, Ma Q, Gao X, et al. (2010) GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection. Protein Eng Des Sel 24: 255-60.
39. Julenius K, Mølgaard A, Gupta R, Brunak S, (2005) Prediction, conservation, analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology 15: 153-164.
40. Chen H, Xue Y, Huang N, Yao X, Sun Z, (2006) MeMo: a web tool for prediction of protein methylation modifications. Nucleic Acids Res 1: 249-53.
41. Li A, Xue Y, Jin C, Wang M, Yao X, (2006) Prediction of Nepsilon-acetylation on internal lysines implemented in Bayesian Discriminant Method. Biochem Biophys Res Commun 350: 818-24.
42. Ren J, Gao X, Jin C, Zhu M, Wang X, et al. (2009) Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0. Proteomics 9: 3409-3412.
43. Basu A, Rose KL, Zhang J, Beavis RC, Ueberheide B, et al. (2009) Proteome wide prediction of acetylation substrates. PNAS 106: 13785-13790.
44. Reinders J, Sickmann A, (2007) Modificomics: Posttranslational modifications beyond protein phosphorylation and glycosylation. Biomol Eng 24: 169-177.
45. Morandell S, Stasyk T, Grosstessner-Hain K, Roitinger E, Mechtler K, et al. (2006) Phosphoproteomics strategies for the functional analysis of signal transduction. Proteomics 6: 4047-4056.
46. Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, et al. (2005) LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics 21: 2814-2820.
47. Flanagan SE, Patch AM, Ellard S, (2010) Using SIFT and PolyPhen to predict loss-of-function and gain-of-function mutations. Genet Test Mol Biomarkers 14: 533-7.
48. Khan S, Vihinen M, (2010) Performance of protein stability predictors. Hum Mutat 31: 675-8.
49. Doniger SW, Kim HS, Swain D, Corcuera D, Williams M, (2008) catalog of neutral and deleterious polymorphism in yeast. PLoS Genet 29; 4: e1000183.
50. Aly TA, Eller E, Ide A, Gowan K, Babu SR, et al. (2006) Multi-SNP analysis of MHC region: remarkable conservation of HLA-A1-B8-DR3 haplotype. Diabetes 55: 1265-9.
51. Taylor KH, Taylor JF, White SN, Womack JE, (2006) Identification of genetic variation and putative regulatory regions in bovine CARD15. Mamm Genome 17: 892-901.
52. Zhou FF, Xue Y, Yao X, Xu Y, (2006) A general user interface for prediction servers of proteins' post-translational modification sites. Nature Protocol 1: 1318-1321.
53. Kozlov SV, Graham ME, Jakob B, Tobias F, Kijas AW, et al. (2011) Autophosphorylation and ATM activation: additional sites add to the complexity. J Biol Chem 286: 9107-19.
54. Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER, Hurov KE, Luo J, et al. (2007) ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 316: 1160-1166.
55. Sun Y, Xu Y, Roy K, Price BD, (2007) DNA damage-induced acetylation of lysine 3016 of ATM activates ATM kinase activity. Mol Cell Biol 27: 8502-9.
56. Mitui M, Campbell C, Coutinho G, Sun X, Lai CH, et al. (2003) Independent mutational events are rare in the ATM gene: haplotype prescreening enhances mutation detection rate. Hum Mutat 22: 43-50.
57. C GPD, Sethumadhavan R, (2009) Investigation on the role of nsSNPs in HNPCC genes-a bioinformatics approach. J Biomed Sci 24: 16-42.
58. C GPD, Sethumadhavan R, (2009) Computational and structural analysis of deleterious functional SNPs in ARNT Oncogene. Interdiscip Sci 3: 220-8.
59. C GPD, Sudandiradoss C, Rajasekaran R, Choudhury P, Sinha P, et al. (2008) Applications of computational algorithm tools to identify functional SNPs. Funct Integr Genomics 8: 309-316.
60. C GPD, Rajasekaran R, Arjun P, Sethumadhavan R, (2010) Prioritization of candidate SNPs in colon cancer using bioinformatics tools: An alternative approach for a cancer biologist. Interdiscip Sci 4: 320-46.
61. B R, C GPD, (2011) Path to Facilitate the Prediction of Functional Amino Acid Substitutions in Red Blood Cell Disorders - A Computational Approach. PLoS ONE 6 (9): e24607.
62. Ng PC, Henikoff S, (2006) Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 7: 61-80.
63. Schneider TD, Stormo GD, Gold L, Ehrenfeucht A, (1986) Information content of binding sites on nucleotide sequences. J Mol Biol 188: 415-431.
64. Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, et al. (1999) Characterization of single nucleotide polymorphisms in coding regions of human genes. NatGenet 22: 231-238.
65. Palmer JS, Duffy DL, Box NF, Aitken JF, O'Gorman LE, (2000) Melanocortin-1 receptor polymorphisms and risk of melanoma: Is the association explained solely by pigmentation phenotype? Am J Hum Genet 66: 176-186.
66. Sonenberg N, (1994) mRNA translation: Influence of the 5′ and 3′ untranslated Regions. Curr Opin Genet 4: 310-315.
67. Bedford MT, Richard S, (2005) Arginine methylation an emerging regulator of protein function. Mol Cell 18: 263-272.
68. Xu W, Zhao S, (2011) Metabolism is regulated by protein acetylation. Front Biol 3: 213-218.
69. Plackett RL, (1983) Karl Pearson and the Chi-Squared Test. Int Stat Rev 51: 59-72.