Distribution and effects of nonsense polymorphisms in human genes

PLoS ONE

Volumn 3, Issue 10, 2008, Pages

  Yamaguchi Kabata, Yumi ^a,f   Shimada, Makoto K ^a,b,g   Hayakawa, Yosuke ^a,b   Minoshima, Shinsei ^c   Chakraborty, Ranajit ^d   Gojobori, Takashi ^a,e   Imanishi, Tadashi ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b Japan Biological Information Research Center   (Japan)

^c HAMAMATSU UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^d UNIVERSITY OF CINCINNATI   (United States)

^e NATIONAL INSTITUTE OF GENETICS   (Japan)

^f RIKEN   (Japan)

^g FUJITA HEALTH UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; EXON; GENE DELETION; GENE INSERTION; GENETIC CODE; GENETIC DATABASE; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; HUMAN; INTERNET; LONG QT SYNDROME; MYOPATHY; NONSENSE MUTATION; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PARKINSON DISEASE; PHENOTYPIC VARIATION; PREDICTION; RETINOBLASTOMA; SEPSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STOP CODON; TRANSLATION REGULATION; BIOLOGY; GENETIC POLYMORPHISM; GENETICS; HUMAN GENOME; NUCLEIC ACID DATABASE; RNA STABILITY; STATISTICAL DISTRIBUTION;

MESSENGER RNA;

CODON, NONSENSE; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENOME, HUMAN; HUMANS; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA STABILITY; RNA, MESSENGER; STATISTICAL DISTRIBUTIONS;

EID: 54449094545     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0003393     Document Type: Article

References (46)

1. Sherry ST, Ward M, Sirotkin K (1999) dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res 9: 677-679.
2. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. (2001) The sequence of the human genome. Science 291: 1304-1351.
3. Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, et al. (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308: 385-389.
4. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
5. Ozaki K, Ohnishi Y, Iida A, Sekine A, Yamada R, et al. (2002) Functional SNPs in the lymphotoxin-alpha gene that are associated with susceptibility to myocardial infarction. Nat Genet 32: 650-654.
6. The Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
7. Reumers J, Schymkowitz J, Ferkinghoff-Borg J, Stricher F, Serrano L, et al. (2005) SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. Nucleic Acids Res 33: D527-532.
8. Ng PC, Henikoff S (2002) Accounting for human polymorphisms predicted to affect protein function. Genome Res 12: 436-446.
9. Bao L, Zhou M, Cui Y (2005) nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms. Nucleic Acids Res 33: W480-482.
10. Sunyaev S, Ramensky V, Koch I, Lathe W 3rd, Kondrashov AS, et al. (2001) Prediction of deleterious human alleles. Hum Mol Genet 10: 591-597.
11. Ferrer-Costa C, Gelpi JL, Zamakola L, Parraga I, de la Cruz X, et al. (2005) PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinformatics 21: 3176-3178.
12. Yue P, Melamud E, Moult J (2006) SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics 7: 166.
13. Stitziel NO, Binkowski TA, Tseng YY, Kasif S, Liang J (2004) topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Res 32: D520-522.
14. 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.
15. Burton PR, Clayton DG, Cardon LR, Craddock N, Deloukas P, et al. (2007) Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants. Nat Genet 39: 1329-1337.
16. Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, et al. (2007) A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet 39: 207-211.
17. Minoshima S, Mitsuyama S, Ohtsubo M, Kawamura T, Ito S, et al. (2001) The KMDB/MutationView: a mutation database for human disease genes. Nucleic Acids Res 29: 327-328.
18. Hamosh A, Scott AF, Amberger J, Bocchini C, Valle D, et al. (2002) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 30: 52-55.
19. Morton NE, Crow JF, Muller HJ (1956) An Estimate of the Mutational Damage in Man from Data on Consanguineous Marriages. Proc Natl Acad Sci U S A 42: 855-863.
20. Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet 22: 231-238.
21. Fay JC, Wyckoff GJ, Wu CI (2001) Positive and negative selection on the human genome. Genetics 158: 1227-1234.
22. Halushka MK, Fan JB, Bentley K, Hsie L, Shen N, et al. (1999) Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet 22: 239-247.
23. Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, et al. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol 2: e162.
24. Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, et al. (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res 36: D793-799.
25. Chang JC, Kan YW (1979) beta 0 thalassemia, a nonsense mutation in man. Proc Natl Acad Sci U S A 76: 2886-2889.
26. Rosenfeld PJ, Cowley GS, McGee TL, Sandberg MA, Berson EL, et al. (1992) A null mutation in the rhodopsin gene causes rod photoreceptor dysfunction and autosomal recessive retinitis pigmentosa. Nat Genet 1: 209-213.
27. Inoue K, Khajavi M, Ohyama T, Hirabayashi S, Wilson J, et al. (2004) Molecular mechanism for distinct neurological phenotypes conveyed by allelic truncating mutations. Nat Genet 36: 361-369.
28. Mimori A, Hidaka Y, Wu VC, Tarle SA, Kamatani N, et al. (1991) A mutant allele common to the type I adenine phosphoribosyltransferase deficiency in Japanese subjects. Am J Hum Genet 48: 103-107.
29. Holbrook JA, Neu-Yilik G, Hentze MW, Kulozik AE (2004) Nonsense-mediated decay approaches the clinic. Nat Genet 36: 801-808.
30. Thermann R, Neu-Yilik G, Deters A, Frede U, Wehr K, et al. (1998) Binary specification of nonsense codons by splicing and cytoplasmic translation. Embo J 17: 3484-3494.
31. Zhang J, Sun X, Qian Y, LaDuca JP, Maquat LE (1998) At least one intron is required for the nonsense-mediated decay of triosephosphate isomerase mRNA: a possible link between nuclear splicing and cytoplasmic translation. Mol Cell Biol 18: 5272-5283.
32. Frischmeyer PA, van Hoof A, O'Donnell K, Guerrerio AL, Parker R, et al. (2002) An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science 295: 2258-2261.
33. van Hoof A, Frischmeyer PA, Dietz HC, Parker R (2002) Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 295: 2262-2264.
34. Hughes AL, Packer B, Welch R, Bergen AW, Chanock SJ, et al. (2003) Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc Natl Acad Sci U S A 100: 15754-15757.
35. Ehrlich M, Wang RY (1981) 5-Methylcytosine in eukaryotic DNA. Science 212: 1350-1357.
36. Kimura M (1968) Evolutionary rate at the molecular level. Nature 217: 624-626.
37. Han A, Kim WY, Park SM (2007) SNP2NMD: a database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay. Bioinformatics 23: 397-399.
38. Thein SL, Hesketh C, Taylor P, Temperley IJ, Hutchinson RM, et al. (1990) Molecular basis for dominantly inherited inclusion body beta-thalassemia. Proc Natl Acad Sci U S A 87: 3924-3928.
39. Wang X, Grus WE, Zhang J (2006) Gene losses during human origins. PLoS Biol 4: e52.
40. Senee V, Chelala C, Duchatelet S, Feng D, Blanc H, et al. (2006) Mutations in GLIS3 are responsible for a rare syndrome with neonatal diabetes mellitus and congenital hypothyroidism. Nat Genet 38: 682-687.
41. Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW, et al. (2003) Role of duplicate genes in genetic robustness against null mutations. Nature 421: 63-66.
42. Takeda J, Suzuki Y, Nakao M, Barrero RA, Koyanagi KO, et al. (2006) Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Res 34: 3917-3928.
43. Xue Y, Daly A, Yngvadottir B, Liu M, Coop G, et al. (2006) Spread of an inactive form of caspase-12 in humans is due to recent positive selection. Am J Hum Genet 78: 659-670.
44. Olson MV (1999) When less is more: gene loss as an engine of evolutionary change. Am J Hum Genet 64: 18-23.
45. Yamasaki C, Koyanagi KO, Fujii Y, Itoh T, Barrero R, et al. (2005) Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB). Gene 364: 99-107.
46. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418-426.