Evaluation of transethnic fine mapping with population-specific and cosmopolitan imputation reference panels in diverse Asian populations (original) (raw)
McCarthy MI, Abecasis GR, Cardon LR et al: Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 2008; 9: 356–369. ArticleCAS Google Scholar
Manolio TA, Collins FS, Cox NJ et al: Finding the missing heritability of complex diseases. Nature 2009; 461: 747–753. ArticleCAS Google Scholar
Abecasis GR, Auton A, Brooks LD et al: An integrated map of genetic variation from 1,092 human genomes. Nature 2012; 491: 56–65. Article Google Scholar
Durbin RM, Abecasis GR, Altshuler DL et al: A map of human genome variation from population-scale sequencing. Nature 2010; 467: 1061–1073. ArticleCAS Google Scholar
Jallow M, Teo YY, Small KS et al: Genome-wide and fine-resolution association analysis of malaria in West Africa. Nat Genet 2009; 41: 657–665. ArticleCAS Google Scholar
Teo YY, Small KS, Kwiatkowski DP : Methodological challenges of genome-wide association analysis in Africa. Nat Rev Genet 2010; 11: 149–160. ArticleCAS Google Scholar
Rosenberg NA, Huang L, Jewett EM, Szpiech ZA, Jankovic I, Boehnke M : Genome-wide association studies in diverse populations. Nat Rev Genet 2010; 11: 356–366. ArticleCAS Google Scholar
Twee-Hee Ong R, Wang X, Liu X, Teo YY : Efficiency of trans-ethnic genome-wide meta-analysis and fine-mapping. Eur J Hum Genet 2012; 20: 1300–1307. Article Google Scholar
Teo YY, Ong RT, Sim X, Tai ES, Chia KS : Identifying candidate causal variants via trans-population fine-mapping. Genet Epidemiol 2010; 34: 653–664. Article Google Scholar
Morris AP : Transethnic meta-analysis of genomewide association studies. Genet Epidemiol 2011; 35: 809–822. Article Google Scholar
Mahajan A, Go MJ, Zhang W et al: Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nat Genet 2014; 46: 234–244. ArticleCAS Google Scholar
Howie B, Marchini J, Stephens M : Genotype imputation with thousands of genomes. G3 (Bethesda, MD) 2011; 1: 457–470. Article Google Scholar
Marchini J, Howie B : Genotype imputation for genome-wide association studies. Nat Rev Genet 2010; 11: 499–511. ArticleCAS Google Scholar
Howie BN, Donnelly P, Marchini J : A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 2009; 5: e1000529. Article Google Scholar
Marchini J, Howie B, Myers S, McVean G, Donnelly P : A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 2007; 39: 906–913. ArticleCAS Google Scholar
Wong LP, Ong RT, Poh WT et al: Deep whole-genome sequencing of 100 southeast Asian Malays. Am J Hum Genet 2013; 92: 52–66. ArticleCAS Google Scholar
Wong LP, Lai JK, Saw WY et al: Insights into the genetic structure and diversity of 38 South Asian Indians from deep whole-genome sequencing. PLoS Genet 2014; 10: e1004377. Article Google Scholar
Hindorff LA, Mehta J, Wise A _et al_European Bioinformatics Institute.: A catalog of Published Genome-Wide Association Studies; Available at: www.genome.gov/gwastudies (last access date September 2014).
Lopes MC, Hysi PG, Verhoeven VJ et al: Identification of a candidate gene for astigmatism. Invest Ophthalmol Vis Sci 2013; 54: 1260–1267. ArticleCAS Google Scholar
Fan Q, Zhou X, Khor CC et al: Genome-wide meta-analysis of five Asian cohorts identifies PDGFRA as a susceptibility locus for corneal astigmatism. PLoS Genet 2011; 7: e1002402. ArticleCAS Google Scholar
Khor CC, Ramdas WD, Vithana EN et al: Genome-wide association studies in Asians confirm the involvement of ATOH7 and TGFBR3, and further identify CARD10 as a novel locus influencing optic disc area. Hum Mol Genet 2011; 20: 1864–1872. ArticleCAS Google Scholar
Ramdas WD, van Koolwijk LM, Ikram MK et al: A genome-wide association study of optic disc parameters. PLoS Genet 2010; 6: e1000978. Article Google Scholar
Guggenheim JA, McMahon G, Kemp JP et al: A genome-wide association study for corneal curvature identifies the platelet-derived growth factor receptor alpha gene as a quantitative trait locus for eye size in white Europeans. Mol Vis 2013; 19: 243–253. CASPubMedPubMed Central Google Scholar
Mishra A, Yazar S, Hewitt AW et al: Genetic variants near PDGFRA are associated with corneal curvature in Australians. Invest Ophthalmol Vis Sci 2012; 53: 7131–7136. ArticleCAS Google Scholar
Han S, Chen P, Fan Q et al: Association of variants in FRAP1 and PDGFRA with corneal curvature in Asian populations from Singapore. Hum Mol Genet 2011; 20: 3693–3698. ArticleCAS Google Scholar
Kathiresan S, Melander O, Guiducci C et al: Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nat Genet 2008; 40: 189–197. ArticleCAS Google Scholar
Willer CJ, Sanna S, Jackson AU et al: Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat Genet 2008; 40: 161–169. ArticleCAS Google Scholar
Aulchenko YS, Ripatti S, Lindqvist I et al: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. Nat Genet 2009; 41: 47–55. ArticleCAS Google Scholar
Kathiresan S, Willer CJ, Peloso GM et al: Common variants at 30 loci contribute to polygenic dyslipidemia. Nat Genet 2009; 41: 56–65. ArticleCAS Google Scholar
Teslovich TM, Musunuru K, Smith AV et al: Biological, clinical and population relevance of 95 loci for blood lipids. Nature 2010; 466: 707–713. ArticleCAS Google Scholar
Spencer CC, Su Z, Donnelly P, Marchini J : Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip. PLoS Genet 2009; 5: e1000477. Article Google Scholar
Frazer KA, Ballinger DG, Cox DR et al: A second generation human haplotype map of over 3.1 million SNPs. Nature 2007; 449: 851–861. ArticleCAS Google Scholar
Cho YS, Chen CH, Hu C et al: Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians. Nat Genet 2012; 44: 67–72. ArticleCAS Google Scholar
Sim X, Ong RT, Suo C et al: Transferability of type 2 diabetes implicated loci in multi-ethnic cohorts from Southeast Asia. PLoS Genet 2011; 7: e1001363. ArticleCAS Google Scholar
de Bakker PI, Ferreira MA, Jia X, Neale BM, Raychaudhuri S, Voight BF : Practical aspects of imputation-driven meta-analysis of genome-wide association studies. Hum Mol Genet 2008; 17: R122–R128. ArticleCAS Google Scholar
Zeggini E, Scott LJ, Saxena R et al: Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet 2008; 40: 638–645. ArticleCAS Google Scholar
Vithana EN, Aung T, Khor CC et al: Collagen-related genes influence the glaucoma risk factor, central corneal thickness. Hum Mol Genet 2011; 20: 649–658. ArticleCAS Google Scholar
Wang X, Chua HX, Chen P et al: Comparing methods for performing trans-ethnic meta-analysis of genome-wide association studies. Hum Mol Genet 2013; 22: 2303–2311. ArticleCAS Google Scholar
Franceschini N, van Rooij FJ, Prins BP et al: Discovery and fine mapping of serum protein loci through transethnic meta-analysis. Am J Hum Genet 2012; 91: 744–753. ArticleCAS Google Scholar
Rasmussen-Torvik LJ, Pacheco JA, Wilke RA et al: High density GWAS for LDL cholesterol in African Americans using electronic medical records reveals a strong protective variant in APOE. Clin Transl Sci 2012; 5: 394–399. ArticleCAS Google Scholar
Conrad DF, Jakobsson M, Coop G et al: A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet 2006; 38: 1251–1260. ArticleCAS Google Scholar
Hanchard N, Elzein A, Trafford C et al: Classical sickle beta-globin haplotypes exhibit a high degree of long-range haplotype similarity in African and Afro-Caribbean populations. BMC Genet 2007; 8: 52. Article Google Scholar
Deelen P, Menelaou A, van Leeuwen EM et al: Improved imputation quality of low-frequency and rare variants in European samples using the 'Genome of The Netherlands'. Eur J Hum Genet 2014; 22: 1321–1326. ArticleCAS Google Scholar
Gao X, Haritunians T, Marjoram P et al: Genotype Imputation for Latinos Using the HapMap and 1000 Genomes Project Reference Panels. Front Genet 2012; 3: 117. ArticleCAS Google Scholar
Huang L, Li Y, Singleton AB et al: Genotype-imputation accuracy across worldwide human populations. Am J Hum Genet 2009; 84: 235–250. ArticleCAS Google Scholar
Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR : MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 2010; 34: 816–834. Article Google Scholar