DNA Sequence-Based Phenotypic Association Analysis

Advances in Genetics

Volumn 60, Issue , 2008, Pages 195-217

  Schork, Nicholas J ^a,b,c   Wessel, Jennifer ^a,c   Malo, Nathalie ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b San Diego   (United States)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BIOLOGICAL MODEL; BIOLOGY; DNA SEQUENCE; HUMAN; METHODOLOGY; PHENOTYPE; REVIEW; STATISTICS;

ANIMALS; COMPUTATIONAL BIOLOGY; HUMANS; MODELS, GENETIC; PHENOTYPE; SEQUENCE ANALYSIS, DNA;

EID: 40749154333     PISSN: 00652660     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-2660(07)00409-9     Document Type: Review

References (50)

1. Agresti A. "Categorical Data Analysis." (2002), John Wiley and Sons, New York
2. Altshuler D., and Clark A.G. Genetics. Harvesting medical information from the human family tree. Science 307 5712 (2005) 1052-1053
3. Boffelli D., McAuliffe J., Ovcharenko D., Lewis K.D., Ovcharenko I., Pachter L., and Rubin E.M. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299 (2003) 1391-1394
4. Cameron A.C., and Trivedi P.K. "Regression Analysis of Count Data." (1998), Cambridge University Press, New York
5. Cohen J.C., Pertsemlidis A., Fahmi S., Esmail S., Vega G.L., Grundy S.M., and Hobbs H.H. Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levels. Proc. Natl. Acad. Sci. USA 103 (2006) 1810-1815
6. Conti D.V., and Witte J.S. Hierarchical modeling of linkage disequilibrium: Genetic structure and spatial relations. Am. J. Hum. Genet. 72 2 (2003) 351-363
7. Draper N.R., and Smith H. "Applied Regression Analysis." (1981), John Wiley and Sons, New York
8. Drysdale C.M., McGraw D.W., Stack C.B., Stephens J.C., Judson R.S., Nandabalan K., Arnold K., Ruano G., and Liggett S.B. Complex promoter and coding region beta 2-adrenergic receptor haplotypes alter receptor expression and predict in vivo responsiveness. Proc. Natl. Acad. Sci. USA 97 19 (2000) 10483-10488
9. Durbin R., Eddy S.R., Krogh A., and Mitchison G. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids." (1999), Cambridge University Press, Boston
10. Edgington E.S. "Randomization Tests,". 3rd Edition (1995), Marcel Dekker, New York
11. Felsenstein J. Phylogenies from molecular sequences: Inference and reliability. Annu. Rev. Genet. 22 (1988) 521-565
12. Fitzgerald S.M., Goyal R.K., Osborne W.R., Roy J.D., Wilson J.W., and Ferrell R.E. Identification of functional single nucleotide polymorphism haplotypes in the cytidine deaminase promoter. Hum. Genet. 119 (2006) 276-283
13. Good P.I. "Permutation Tests." (2000), Springer, New York
14. Gower J.C. Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53 (1966) 325-338
15. Greenwood T.A., and Kelsoe J.R. Promoter and intronic variants affect the transcriptional regulation of the human dopamine transporter gene. Genomics 82 5 (2003) 511-520
16. Gu C.C., Yu K., and Rao D.C. Characterization of LD structures and the utility of HapMap in genetic association studies. In: Rao D.C., and Gu C.C. (Eds). "Genetic Dissection of Complex Traits". 2nd Edition, pp. 407-429 (2008), Academic Press, San Diego
17. Hirschhorn J.N., Lohmueller K., Byrne E., and Hirschhorn K. A comprehensive review of genetic association studies. Genet. Med. 4 (2002) 45-61
18. Horan M., Millar D.S., Hedderich J., Lewis G., Newsway V., Mo N., Fryklund L., Procter A.M., Krawczak M., and Cooper D.N. Human growth hormone 1 (GH1) gene expression: Complex haplotype-dependent influence of polymorphic variation in the proximal promoter and locus control region. Hum. Mutat. 21 (2003) 408-423
19. Jorgenson E., and Witte J.S. A gene-centric approach to genome-wide association studies. Nat. Rev. Genet. 7 (2006) 885-891
20. Kelada S.N., Costa-Mallen P., Checkoway H., Carlson C.S., Weller T.S., Swanson P.D., Franklin G.M., Longstreth W.T., Afsharinejad Z., and Costa L.G. Dopamine transporter (SLC6A3) 5′ region haplotypes significantly affect transcriptional activity in vitro but are not associated with Parkinson's disease. Pharmacogenet. Genomics 15 (2005) 659-668
21. Kooperberg C., and Ruczinski I. Identifying interacting SNPs using Monte Carlo logic regression. Genet. Epidemiol. 28 (2005) 157-170
22. Kotowski I.K., Pertsemlidis A., Luke A., Cooper R.S., Vega G.L., Cohen J.C., and Hobbs H.H. A spectrum of PCSK9 alleles contributes to plasma levels of low-density lipoprotein cholesterol. Am. J. Hum. Genet. 78 (2006) 410-422
23. Lander E., Linton L., Birren B., Nusbaum C., Zody M., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R., Gage D., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
24. Law A.J., Lipska B.K., Weickert C.S., Hyde T.M., Straub R.E., Hashimoto R., Harrison P.J., Kleinman J.E., and Weinberger D.R. Neuregulin 1 transcripts are differentially expressed in schizophrenia and regulated by 5′ SNPs associated with the disease. Proc. Natl. Acad. Sci. USA 103 17 (2006) 6747-6752
25. Liu N., and Wang T. A weighted measure for the similarity analysis of DNA sequences. J. Mol. Biol. 12 (2006) 897-903
26. McArdle B.H., and Anderson M.J. Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology 82 (2001) 290-297
27. Myers R.L., Airey D.C., Manier D.H., Shelton R.C., and Sanders-Bush E. Polymorphisms in the regulatory region of the human serotonin 5-HT(2A) receptor gene (HTR2A) influence gene expression. Biol. Psychiatry 61 (2006) 167-173 2007, [Epub ahead of print]
28. Myers S.N., Goyal R.K., Roy J.D., Fairfull L.D., Wilson J.W., and Ferrell R.E. Functional single nucleotide polymorphism haplotypes in the human equilibrative nucleoside transporter 1. Pharmacogenet. Genomics 16 (2006) 315-320
29. Nakajima M., Hattori E., Yamada K., Iwayama Y., Toyota T., Iwata Y., Tsuchiya K.J., Sugihara G., Hashimoto K., Watanabe H., Iyo M., Hoshika A., et al. Association and synergistic interaction between promoter variants of the DRD4 gene in Japanese schizophrenics. J. Hum. Genet. 52 (2007) 86-91 2007, [Epub ahead of print]
30. Nievergelt C.M., Libiger O., and Schork N.J. Generalized molecular analysis of variance. PLOS Genet. 3 (2007) e51 (Epub. 2007 Feb. 22)
31. Pardi F., Lewis C.M., and Whittaker J.C. SNP selection for association studies: Maximizing power across SNP choice and study size. Ann. Hum. Genet. 69 (2005) 733-746
32. Phillips A.J. Homology assessment and molecular sequence alignment. J. Biomed. Inform. 39 1 (2006) 18-33
33. Pritchard J.K., and Cox N.J. The allelic architecture of human disease genes: Common disease-common variant ... or not?. Hum. Mol. Genet. 11 (2002) 2417-2423
34. Redon R., Ishikawa S., Fitch K.R., Feuk L., Perry G.H., Andrews T.D., Fiegler H., Shapero M.H., Carson A.R., Chen W., Cho E.K., Dallaire S., et al. Global variation in copy number in the human genome. Nature 444 (2006) 444-454
35. Reich D.E., and Lander E.S. On the allelic spectrum of human disease. Trends Genet. 17 (2001) 502-510
36. Risch N., and Merikangas K. The future of genetic studies of complex human diseases. Science 273 (1996) 1516-1517
37. Salamon H., Tarhio J., Ronningen K., and Thomson G. On distinguishing unique combinations in biological sequences. J. Comput. Biol. 3 3 (1996) 407-423
38. Salem R.M., Wessel J., and Schork N.J. A comprehensive literature review of haplotyping software and methods for use with unrelated individuals. Hum. Genomics 2 1 (2005) 39-66
39. Stengard J.H., Clark A.G., Weiss K.M., Kardia S., Nickerson D.A., Salomaa V., Ehnholm C., Boerwinkle E., and Sing C.F. Contributions of 18 additional DNA sequence variations in the gene encoding apolipoprotein E to explaining variation in quantitative measures of lipid metabolism. Am. J. Hum. Genet. 71 (2002) 501-517
40. Tao H., Cox D.R., and Frazer K.A. Allele-specific KRT1 expression is a complex trait. PLOS Genet. 2 (2006) 848-858
41. Templeton A.R., Maxwell T., Posada D., Stengard J.H., Boerwinkle E., and Sing C.F. Tree scanning: A method for using haplotype trees in phenotype/genotype association studies. Genetics 169 (2005) 441-453
42. Valdes A.M., and Thomson G. Detecting disease-predisposing variants: The haplotype method. Am. J. Hum. Genet. 60 3 (1997) 703-716
43. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., Gocayne J.D., Amanatides P., et al. The sequence of the human genome. Science 291 (2001) 1304-1351 Erratum in
44. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., Gocayne J.D., Amanatides P., et al. The sequence of the human genome. Science 292 5523 (2001 Jun 5) 1838
45. Wen G., Mahata S.K., Cadman P., Mahata M., Ghosh S., Mahapatra N.R., Rao F., Stridsberg M., Smith D.W., Mahboubi P., Schork N.J., O'Connor D.T., et al. Both rare and common polymorphisms contribute functional variation at CHGA, a regulator of catecholamine physiology. Am. J. Hum. Genet. 74 (2004) 197-207
46. Wessel J., and Schork N.J. Generalized genomic distance-based regression methodology for multilocus association analysis. Am. J. Hum. Genet. 79 5 (2006) 792-806
47. Wessel J., Libiger O., and Schork N.J. Whole genome association studies using window-based Multivariate Distance Matrix Regression analysis. Genet. Epidemiol. (2006) (in review)
48. Wu T.J., Huang Y.H., and Li L.A. Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences. Bioinformatics 21 (2005) 4125-4132
49. Zapala M., and Schork N.J. Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables. Proc. Natl. Acad. Sci. 103 (2006) 19430-19435
50. Zapala M., and Schork N.J. Statistical properties of multivariate distance matrix regression for high-dimensional data analysis (2006) (in preparation)