Use of admixture and association for detection of quantitative trait loci in the Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Ethnic Samples (T2D-GENES) study

BMC Proceedings

Volumn 8, Issue , 2014, Pages

  Yorgov, Daniel ^a   Edwards, Karen L ^b,c   Santorico, Stephanie A ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME 3; CONFERENCE PAPER; CONTROLLED STUDY; DIASTOLIC BLOOD PRESSURE; GENOTYPE; HISPANIC; HUMAN; LOOP MEDIATED ISOTHERMAL AMPLIFICATION; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTOLIC BLOOD PRESSURE; WHOLE GENOME SEQUENCING;

EID: 85018193442     PISSN: None     EISSN: 17536561     Source Type: Journal    
DOI: 10.1186/1753-6561-8-S1-S6     Document Type: Conference Paper

References (18)

1. Kao WHL, Klag MJ, Meoni LA, Reich D, Berthier-Schaad Y, Li M, Coresh J, Patterson N, Tandon A, Powe NR, et al: MYH9 is associated with nondiabetic end-stage renal disease in African Americans. Nat Genet. 2008, 1185-1192. 10.1038/ng.232. 40
2. Kopp JB, Smith MW, Nelson GW, Johnson RC, Freedman BI, Bowden DW, Oleksyk T, McKenzie LM, Kajiyama H, Ahuja TS, et al: MYH9 is a major-effect risk gene for focal segmental glomerulosclerosis. Nat Genet. 2008, 40: 1175-1184. 10.1038/ng.226.
3. Reich D, Patterson N, Ramesh V, De Jager PL, McDonald GJ, Tandon A, Choy E, Hu D, Tamraz B, Pawlikowska L, et al: Admixture mapping of an allele affecting interleukin 6 soluble receptor and interleukin 6 levels. Am J Hum Genet. 2007, 80: 716-726. 10.1086/513206.
4. Lettre G, Palmer CD, Young T, Ejebe KG, Allayee H, Benjamin EJ, Bennett F, Bowden DW, Chakravarti A, Dreisbach A, et al: Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. PLoS Genet. 2011, 7: e1001300-10.1371/journal.pgen.1001300.
5. Pasaniuc B, Zaitlen N, Lettre G, Chen GK, Tandon A, Kao WHL, Ruczinski I, Fornage M, Siscovick DS, Zhu X, et al: Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a breast cancer consortium. PLoS Genet. 2011, 7: e1001371-10.1371/journal.pgen.1001371.
6. Shriner D, Adeyemo A, Rotimi CN: Joint ancestry and association testing in admixed individuals. PLoS Comput Biol. 2011, 7: e1002325-10.1371/journal.pcbi.1002325.
7. Tang H, Siegmund DO, Johnson NA, Romieu I, London SJ: Joint testing of genotype and ancestry association in admixed families. Genet Epidemiol. 2010, 34: 783-791. 10.1002/gepi.20520.
8. Wang X, Zhu X, Qin H, Cooper RS, Ewens WJ, Li C, Li M: Adjustment for local ancestry in genetic association analysis of admixed populations. Bioinformatics. 2011, 27: 670-677. 10.1093/bioinformatics/btq709.
9. Almasy L, Dyer T, Peralta JM, Jun G, Fuchsberger C, Almeida MA, Kent JW, Fowler S, Duggirala R, Blangero J: Data for Genetic Analysis Workshop 18: human whole genome sequence, blood pressure, and simulated phenotypes in extended pedigrees. BMC Proceedings. 2014, 8 (Suppl 1): S2-
10. Winkler CA, Nelson GW, Smith MW: Admixture mapping comes of age. Annu Rev Genomics Hum Genet. 2010, 11: 65-89. 10.1146/annurev-genom-082509-141523.
11. Baran Y, Pasaniuc B, Sankararaman S, Torgerson DG, Gignoux C, Eng C, Rodriguez-Cintron W, Chapela R, Ford JG, Avila PC, et al: Fast and accurate inference of local ancestry in Latino populations. Bioinformatics. 2012, 28: 1359-1367. 10.1093/bioinformatics/bts144.
12. Manichaikul A, Palmas W, Rodriguez CJ, Peralta CA, Divers J, Guo X, Chen W-M, Wong Q, Williams K, Kerr KF, et al: Population structure of Hispanics in the United States: the multi-ethnic study of atherosclerosis. PLoS Genet. 2012, 8: e1002640-10.1371/journal.pgen.1002640.
13. Johnson NA, Coram MA, Shriver MD, Romieu I, Barsh GS, London SJ, Tang H: Ancestral components of admixed genomes in a Mexican cohort. PLoS Genet. 2011, 7: e1002410-10.1371/journal.pgen.1002410.
14. Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L, et al: Integrating common and rare genetic variation in diverse human populations. Nature. 2010, 467: 52-58. 10.1038/nature09298.
15. Rosenberg NA: Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives. Ann Hum Genet. 2006, 70: 841-847. 10.1111/j.1469-1809.2006.00285.x.
16. Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, et al: Worldwide human relationships inferred from genome-wide patterns of variation. Science. 2008, 319: 1100-1104. 10.1126/science.1153717.
17. Delaneau O, Marchini J, Zagury J-F: A linear complexity phasing method for thousands of genomes. Nat Methods. 2012, 9: 179-181.
18. McKeigue PM: Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in admixed populations, by conditioning on parental admixture. Am J Hum Genet. 1998, 63: 241-251. 10.1086/301908.