Mapping common regulatory variants to human haplotypes

Human Molecular Genetics

Volumn 14, Issue 24, 2005, Pages 3963-3971

  Pastinen, Tomi ^a   Ge, Bing ^a   Gurd, Scott ^a   Gaudin, Tiffany ^a   Dore, Carole ^a   Lemire, Mathieu ^a   Lepage, Pierre ^a   Harmsen, Eef ^a   Hudson, Thomas J ^a  

^a MCGILL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMOKINE RECEPTOR CCR7; CIS ACTING ELEMENT; CYCLIN DEPENDENT KINASE 2; HERMES ANTIGEN; INTERFERON REGULATORY FACTOR 4; MINICHROMOSOME MAINTENANCE PROTEIN 2; RAB7 PROTEIN; SOMATOMEDIN C; T CELL FACTOR PROTEIN; TRANSCRIPTION FACTOR PAX8;

ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCUS; GENE MAPPING; GENETIC VARIABILITY; HAPLOTYPE; HETEROZYGOTE; HUMAN; HUMAN CELL; IN VIVO STUDY; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; HAPLOTYPES; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; REGULATORY SEQUENCES, NUCLEIC ACID; VARIATION (GENETICS);

EID: 29644446630     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddi420     Document Type: Article

References (21)

1. Brem, R.B., Yvert, G., Clinton, R. and Kruglyak, L. (2002) Genetic dissection of transcriptional regulation in budding yeast. Science, 296, 752-755.
2. Schadt, E.E., Monks, S.A., Drake, T.A., Lusis, A.J., Che, N., Colinayo, V., Ruff, T.G., Milligan, S.B., Lamb, J.R., Cavet, G. et al. (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature, 422, 297-302.
3. Morley, M., Molony, C.M., Weber, T.M., Devlin, J.L., Ewens, K.G., Spielman, R.S. and Cheung, V.G. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature, 430, 743-747.
4. Pastinen, T. and Hudson, T.J. (2004) Cis-acting regulatory variation in the human genome. Science, 306, 647-650.
5. Bray, N.J., Buckland, P.R., Owen, M.J. and O'Donovan, M.C. (2003) Cis-acting variation in the expression of a high proportion of genes in human brain. Hum. Genet., 113, 149-153.
6. Lo, H.S., Wang, Z., Hu, Y., Yang, H.H., Gere, S., Buetow, K.H. and Lee, M.P. (2003) Allelic variation in gene expression is common in the human genome. Genome Res., 13, 1855-1862.
7. Pastinen, T., Sladek, R., Gurd, S., Sammak, A., Ge, B., Lepage, P., Lavergne, K., Villeneuve, A., Gaudin, T., Brandstrom, H. et al. (2004) A survey of genetic and epigenetic variation affecting human gene expression. Physiol. Genomics, 16, 184-193.
8. Yan, H., Yuan, W., Velculescu, V.E., Vogelstein, B. and Kinzler, K.W. (2002) Allelic variation in human gene expression. Science, 297, 1143.
9. Bray, N.J., Buckland, P.R., Williams, N.M., Williams, H.J., Norton, N., Owen, M.J. and O'Donovan, M.C. (2003) A haplotype implicated in schizophrenia susceptibility is associated with reduced COMT expression in human brain. Am. J. Hum. Genet., 73, 152-161.
10. Knight, J.C., Keating, B.J., Rockett, K.A. and Kwiatkowski, D.P. (2003) In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading. Nat. Genet., 33, 469-475.
11. Altshuler, D., Brooks, L.D., Chakravarti, A., Collins, F.S., Daly, M.J., Donnelly, P.; International HapMap Consortium (2005) A haplotype map of the human genome. Nature, 437, 1299-1320.
12. Ge, B., Gurd, S., Gaudin, T., Dore, C., Lepage, P., Harmsen, E., Hudson, T.J. and Pastinen, T. (2005) Genome Res., 15, 1584-1591.
13. Bonnevie-Nielsen, V., Leigh, F.L., Lu, S., Zheng, D.J., Li, M., Martensen, P.M., Nielsen, T.B., Beck-Nielsen, H., Lau, Y.L. and Pociot, F. (2005) Variation in antiviral 2′,5′-oligoadenylate synthetase (2′5′AS) enzyme activity is controlled by a single-nucleotide polymorphism at a splice-acceptor site in the OAS1 gene. Am. J. Hum. Genet., 76, 623-633.
14. Abecasis, G.R., Cherny, S.S., Cookson, W.O. and Cardon, L.R. (2002) Merlin - rapid analysis of dense genetic maps using sparse gene flow trees. Nat. Genet., 30, 97-101.
15. Hinds, D.A., Stuve, L.L., Nilsen, G.B., Halperin, E., Eskin, E., Ballinger, D.G., Frazer, K.A. and Cox, D.R. (2005) Whole-genome patterns of common DNA variation in three human populations. Science, 307, 1072-1079.
16. Arking, D.E., Becker, D.M., Yanek, L.R., Fallin, D., Judge, D.P., Moy, T.F., Becker, L.C. and Dietz, H.C. (2003) KLOTHO allele status and the risk of early-onset occult coronary artery disease. Am. J. Hum. Genet., 72, 1154-1161.
17. Fornage, M., Lee, C.R., Doris, P.A., Bray, M.S., Heiss, G., Zeldin, D.C. and Boerwinkle, E. (2005) The soluble epoxide hydrolase gene harbors sequence variation associated with susceptibility to and protection from incident ischemic stroke. Hum. Mol. Genet., 14, 2829-2837.
18. Poon, A.H., Laprise, C., Lemire, M., Montpetit, A., Sinnett, D., Schurr, E. and Hudson, T.J. (2004) Association of vitamin D receptor genetic variants with susceptibility to asthma and atopy. Am. J. Respir. Crit Care Med., 170, 967-973.
19. Zhou, X.F., Cui, J., DeStefano, A.L., Chazaro, I., Farrer, L.A., Manolis, A.J., Gavras, H. and Baldwin, C.T. (2005) Polymorphisms in the promoter region of catalase gene and essential hypertension. Dis. Markers, 21, 3-7.
20. Knight, J.C., Keating, B.J. and Kwiatkowski, D.P. (2004) Allele-specific repression of lymphotoxin-alpha by activated B cell factor-1. J. Nat. Genet., 36, 394-399.
21. Barrett, J.C., Fry, B., Maller, J. and Daly, M.J. (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263-265.