SNPs in Multi-Species Conserved Sequences (MCS) as useful markers in association studies: A practical approach

BMC Genomics

Volumn 8, Issue , 2007, Pages

  McCauley, Jacob L ^a   Kenealy, Shannon J ^a   Margulies, Elliott H ^b   Schnetz Boutaud, Nathalie ^a   Gregory, Simon G ^c   Hauser, Stephen L ^d   Oksenberg, Jorge R ^d   Pericak Vance, Margaret A ^e   Haines, Jonathan L ^a   Mortlock, Douglas P ^a  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c DUKE UNIVERSITY MEDICAL CENTER   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME 1Q; CONTROLLED STUDY; FAMILY; GENE FUNCTION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC LINKAGE; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MULTIPLE SCLEROSIS; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; CHROMOSOME 1; GENE LINKAGE DISEQUILIBRIUM; GENETIC MARKER; GENETIC PREDISPOSITION; GENETICS; GENOME;

ANIMALS; CHROMOSOMES, HUMAN, PAIR 1; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOTYPE; HUMANS; LINKAGE (GENETICS); LINKAGE DISEQUILIBRIUM; MULTIPLE SCLEROSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 34548312486     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-266     Document Type: Article

References (25)

1. Hauser MA Li YJ Takeuchi S Walters R Noureddine M Maready M Darden T Hulette C Martin E Hauser E Genomic convergence: Identifying candidate genes for Parkinson's disease by combining serial analysis of gene expression and genetic linkage Hum Mol Genet 2003 12 671-7 10.1093/hmg/ 12.6.671 12620972
2. Li YJ Oliveira SA Xu P Martin ER Stenger JE Scherzer CR Hauser MA Scott WK Small GW Nance MA Glutathione S-transferase omega-1 modifies age-at-onset of Alzheimer disease and Parkinson disease Hum Mol Genet 2003 12 3259-67 10.1093/hmg/ddg357 14570706
3. Hardison RC Conserved noncoding sequences are reliable guides to regulatory elements Trends Genet 2000 16 369-72 10.1016/ S0168-9525(00)02081-3 10973062
4. Wjst M Target SNP selection in complex disease association studies BMC Bioinformatics 2004 5 92 487897 15248903 10.1186/1471-2105-5-92
5. Emison ES McCallion AS Kashuk CS Bush RT Grice E Lin S Portnoy ME Cutler DJ Green ED Chakravarti A A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk Nature 2005 434 857-63 10.1038/nature03467 15829955
6. Loots GG Locksley RM Blankespoor CM Wang ZE Miller W Rubin EM Frazer KA Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons Science 2000 288 136-40 10.1126/ science.288.5463.136 10753117
7. Mortlock DP Guenther C Kingsley DM A general approach for identifying distant regulatory elements applied to the Gdf6 gene Genome Res 2003 13 2069-81 403689 12915490 10.1101/gr.1306003
8. Nobrega MA Ovcharenko I Afzal V Rubin EM Scanning human gene deserts for long-range enhancers Science 2003 302 413 10.1126/science.1088328 14563999
9. Grant SF Reid DM Blake G Herd R Fogelman I Ralston SH Reduced bone density and osteoporosis associated with a polymorphic Sp1 binding site in the collagen type I alpha 1 gene Nat Genet 1996 14 203-5 10.1038/ ng1096-203 8841196
10. Mayor C Brudno M Schwartz JR Poliakov A Rubin EM Frazer KA Pachter LS Dubchak I VISTA: Visualizing global DNA sequence alignments of arbitrary length Bioinformatics 2000 16 1046-7 10.1093/bioinformatics/16.11.1046 11159318
11. Schwartz S Zhang Z Frazer KA Smit A Riemer C Bouck J Gibbs R Hardison R Miller W PipMaker-a web server for aligning two genomic DNA sequences Genome Res 2000 10 577-86 310868 10779500 10.1101/gr.10.4.577
12. Waterston RH Lindblad-Toh K Birney E Rogers J Abril JF Agarwal P Agarwala R Ainscough R Alexandersson M An P Initial sequencing and comparative analysis of the mouse genome Nature 2002 420 520-62 10.1038/ nature01262 12466850
13. Dubchak I Brudno M Loots GG Pachter L Mayor C Rubin EM Frazer KA Active conservation of noncoding sequences revealed by three-way species comparisons Genome Res 2000 10 1304-6 310906 10984448 10.1101/gr.142200
14. Margulies EH Blanchette M Haussler D Green ED Identification and characterization of multi-species conserved sequences Genome Res 2003 13 2507-18 403793 14656959 10.1101/gr.1602203
15. Kenealy SJ Babron MC Bradford Y Schnetz-Boutaud N Haines JL Rimmler JB Schmidt S Pericak-Vance MA Barcellos LF Lincoln RR A second-generation genomic screen for multiple sclerosis Am J Hum Genet 2004 75 1070-8 1182142 15494893 10.1086/426459
16. Kenealy SJ Herrel LA Bradford Y Schnetz-Boutaud N Oksenberg JR Hauser SL Barcellos LF Schmidt S Gregory SG Pericak-Vance MA Examination of seven candidate regions for multiple sclerosis: Strong evidence of linkage to chromosome 1q44 Genes Immun 2006 7 73-6 10.1038/sj.gene.6364275 16341055
17. The International HapMap Consortium A haplotype map of the human genome Nature 2005 437 1299-320 1880871 16255080 10.1038/nature04226
18. Drake JA Bird C Nemesh J Thomas DJ Newton-Cheh C Reymond A Excoffier L Attar H Antonarakis SE Dermitzakis ET Conserved noncoding sequences are selectively constrained and not mutation cold spots Nat Genet 2006 38 223-7 10.1038/ng1710 16380714
19. UCSC Genome Browser http://genome.cse.ucsc.edu/
20. International HapMap Project http://www.hapmap.org/cgi-perl/gbrowse/ gbrowse/hapmap/
21. MCS Calculator http://zoo.nhgri.nih.gov/binCons/index.cgi
22. de Bakker PI Yelensky R Pe'er I Gabriel SB Daly MJ Altshuler D Efficiency and power in genetic association studies Nat Genet 2005 37 1217-23 10.1038/ng1669 16244653
23. Venter JC Adams MD Myers EW Li PW Mural RJ Sutton GG Smith HO Yandell M Evans CA Holt RA The sequence of the human genome Science 2001 291 1304-51 10.1126/science.1058040 11181995
24. WebMCS http://zoo.nhgri.nih.gov/mcs/
25. Gabriel SB Schaffner SF Nguyen H Moore JM Roy J Blumenstiel B Higgins J DeFelice M Lochner A Faggart M The structure of haplotype blocks in the human genome Science 2002 296 2225-9 10.1126/science.1069424 12029063