Candidate single nucleotide polymorphism selection using publicly available tools: A guide for epidemiologists

American Journal of Epidemiology

Volumn 164, Issue 8, 2006, Pages 794-804

  Bhatti, Parveen ^a   Church, Deanna M ^b   Rutter, Joni L ^c   Struewing, Jeffery P ^a   Sigurdson, Alice J ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c NATIONAL INSTITUTE ON DRUG ABUSE   (United States)

Author keywords

Amino acid sequence; Base sequence; Epidemiologic methods; Genetic predisposition to disease; Polymorphism; Single nucleotide

Indexed keywords

DNA DEPENDENT PROTEIN KINASE; DOUBLE STRANDED DNA;

DNA; GENETIC VARIATION; POLYMORPHISM;

ARTICLE; BIOINFORMATICS; DNA STRAND BREAKAGE; ENZYME ACTIVE SITE; EVALUATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; HUMAN GENOME; QUANTITATIVE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TECHNOLOGY; VALIDATION PROCESS;

ALGORITHMS; AMINO ACID SEQUENCE; BASE SEQUENCE; EPIDEMIOLOGIC METHODS; GENETIC PREDISPOSITION TO DISEASE; HUMANS; INTERNET; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 33749484971     PISSN: 00029262     EISSN: 14766256     Source Type: Journal    
DOI: 10.1093/aje/kwj269     Document Type: Article

References (58)

1. Collins FS, Guyer MS, Charkravarti A. Variations on a theme: cataloging human DNA sequence variation. Science 1997;278:1580-1.
2. Lander ES. The new genomics: global views of biology. Science 1996;274:536-9.
3. Mohrenweiser HW. Genetic variation and exposure related risk estimation: will toxicology enter a new era? DNA repair and cancer as a paradigm. Toxicol Pathol 2004;32(suppl 1):136-45.
4. Cargill M, Altshuler D, Ireland J, et al. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet 1999;22:231-8.
5. Pharoah PD, Dunning AM, Ponder BA, et al. Association studies for finding cancer-susceptibility genetic variants. Nat Rev Cancer 2004;4:850-60.
6. Rebbeck TR, Ambrosone CB, Bell DA, et al. SNPs, haplotypes, and cancer: applications in molecular epidemiology. Cancer Epidemiol Biomarkers Prev 2004;13:681-7.
7. Johnson GC, Esposito L, Barratt BJ, et al. Haplotype tagging for the identification of common disease genes. Nat Genet 2001;29:233-7.
8. Ferrer-Costa C, Orozco M, de la Cruz X. Use of bioinformatics tools for the annotation of disease-associated mutations in animal models. Proteins 2005;61:878-87.
9. Siepel A, Bejerano G, Pedersen JS, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005;15:1034-50.
10. Chamary JV, Hurst LD. Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else? Trends Genet 2005;21:256-9.
11. Duan J, Wainwright MS, Comeron JM, et al. Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum Mol Genet 2003;12:205-16.
12. Costa LG, Vitalone A, Cole TB, et al. Modulation of paraoxonase (PON1) activity. Biochem Pharmacol 2005;69:541-50.
13. Rantala M, Silaste ML, Tuominen A, et al. Dietary modifications and gene polymorphisms alter serum paraoxonase activity in healthy women. J Nutr 2002;132:3012-17.
14. Kim VN, Nam JW. Genomics of microRNA. Trends Genet 2006;22:165-73.
15. Rebbeck TR, Martinez ME, Sellers TA, et al. Genetic variation and cancer: improving the environment for publication of association studies. Cancer Epidemiol Biomarkers Prev 2004;13:1985-6.
16. Savas S, Kim D, Ahmad M, et al. Identifying functional genetic variants in DNA repair pathway using protein conservation analysis. Cancer Epidemiol Biomarkers Prev 2004;13:801-7.
17. Xi T, Jones IM, Mohrenweiser HW. Many amino acid substitution variants identified in DNA repair genes during human population screenings are predicted to impact protein function. Genomics 2004;83:970-9.
18. Zhu Y, Spitz MR, Amos CI, et al. An evolutionary perspective on single-nucleotide polymorphism screening in molecular cancer epidemiology. Cancer Res 2004;64:2251-7.
19. Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome Res 2001;11:863-74.
20. Ramensky VBP, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 2002;30:3894-900.
21. Wacholder S, Chanock S, Garcia-Closas M, et al. Assessing the probability that a positive report is false: an approach for molecular epidemiology studies. J Natl Cancer Inst 2004;96:434-42.
22. Thomas DC. The need for a systematic approach to complex pathways in molecular epidemiology. Cancer Epidemiol Biomarkers Prev 2005;14:557-9.
23. Witte JS. Genetic analysis with hierarchical models. Genet Epidemiol 1997;14:1137-42.
24. Stram DO. Tag SNP selection for association studies. Genet Epidemiol 2004;27:365-74.
25. Dudas A, Chovanec M. DNA double-strand break repair by homologous recombination. Mutat Res 2004;566:131-67.
26. Jackson SP. Sensing and repairing DNA double-strand breaks. Carcinogenesis 2002;23:687-96.
27. Lees-Miller SP, Meek K. Repair of DNA double strand breaks by non-homologous end joining. Biochimie 2003;85:1161-73.
28. Staats B, Qi L, Beerman M, et al. Genewindow: an interactive tool for visualization of genomic variation. Nat Genet 2005;37:109-10.
29. Strachan T, Read AP. Human molecular genetics 2. 2nd ed. Oxford, United Kingdom: BIOS Scientific Publishers, 1999.
30. Blencowe BJ. Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends Biochem Sci 2000;25:106-10.
31. Cartegni L, Wang J, Zhu Z, et al. ESEfinder: a Web resource to identify exonic splicing enhancers. Nucleic Acids Res 2003;31:3568-71.
32. Fairbrother WG, Yeo GW, Yeh R, et al. RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res 2004;32(Web server issue):W187-90.
33. Mattick JS. Introns: evolution and function. Curr Opin Genet Dev 1994;4:823-31.
34. Sonenberg N. mRNA translation: influence of the 5′ and 3′ untranslated regions. Curr Opin Genet Dev 1994;4:310-15.
35. Frazer KA, Elnitski L, Church DM, et al. Cross-species sequence comparisons: a review of methods and available resources. Genome Res 2003;13:1-12.
36. Mayor C, Brudno M, Schwartz JR, et al. VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 2000;16:1046-7.
37. Ovcharenko I, Nobrega MA, Loots GG, et al. ECR browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res 2004;32 (Web server issue):W280-6.
38. Schwartz S, Zhang Z, Frazer KA, et al. PipMaker-a Web server for aligning two genomic DNA sequences. Genome Res 2000;10:577-86.
39. Kel AE, Gossling E, Reuter I, et al. MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 2003;31:3576-9.
40. Pesole G, Liuni S. Internet resources for the functional analysis of 5′ and 3′ untranslated regions of eukaryotic mRNAs. Trends Genet 1999;15:378.
41. Mignone F, Grillo G, Licciulli F, et al. UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 2005;33(database issue):D141-6.
42. Freimuth RR, Stormo GD, McLeod HL. PolyMAPr: programs for polymorphism database mining, annotation, and functional analysis. Hum Mutat 2005;25:110-17.
43. Conde L, Vaquerizas JM, Ferrer-Costa C, et al. PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. Nucleic Acids Res 2005;33(Web server issue):W501-5.
44. Sandelin A, Alkema W, Engstrom P, et al. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 2004;32(database issue):D91-4.
45. Thanaraj TA, Stamm S, Clark F, et al. ASD: the alternative splicing database. Nucleic Acids Res 2004;32(database issue):D64-9.
46. Hemminger BM, Saelim B, Sullivan PF. TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits. Bioinformatics 2006;22:626-7.
47. Xu H, Gregory SG, Hauser ER, et al. SNPselector: a Web tool for selecting SNPs for genetic association studies. Bioinformatics 2005;21:4181-6.
48. Aka P, Mateuca R, Buchet JP, et al. Are genetic polymorphisms in OGG1, XRCC1 and XRCC3 genes predictive for the DNA strand break repair phenotype and genotoxicity in workers exposed to low dose ionising radiations? Mutat Res 2004;556:169-81.
49. Au WW, Salama SA, Sierra-Torres CH. Functional characterization of polymorphisms in DNA repair genes using cytogenetic challenge assays. Environ Health Perspect 2003;111:1843-50.
50. Figueiredo JC, Knight JA, Briollais L, et al. Polymorphisms XRCC1-R399Q and XRCC3-T241M and the risk of breast cancer at the Ontario site of the Breast Cancer Family Registry. Cancer Epidemiol Biomarkers Prev 2004;13:583-91.
51. Han J, Colditz GA, Samson LD, et al. Polymorphisms in DNA double-strand break repair genes and skin cancer risk. Cancer Res 2004;64:3009-13.
52. Jacobsen NR, Nexo BA, Olsen A, et al. No association between the DNA repair gene XRCC3 T241M polymorphism and risk of skin cancer and breast cancer. Cancer Epidemiol Biomarkers Prev 2003;12:584-5.
53. Kuschel B, Auranen A, McBride S, et al. Variants in DNA double-strand break repair genes and breast cancer susceptibility. Hum Mol Genet 2002;11:1399-407.
54. Smith TR, Levine EA, Perrier ND, et al. DNA-repair genetic polymorphisms and breast cancer risk. Cancer Epidemiol Biomarkers Prev 2003;12:1200-4.
55. Smith TR, Miller MS, Lohman K, et al. Polymorphisms of XRCC1 and XRCC3 genes and susceptibility to breast cancer. Cancer Lett 2003;190:183-90.
56. Webb PM, Hopper JL, Newman B, et al. Double-strand break repair gene polymorphisms and risk of breast or ovarian cancer. Cancer Epidemiol Biomarkers Prev 2005;14:319-23.
57. Carlson CS, Eberle MA, Rieder MJ, et al. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 2004;74:106-20.
58. Hinds DA, Stuve LL, Nilsen GB, et al. Whole-genome patterns of common DNA variation in three human populations. Science 2005;307:1072-9.