Adapt-Mix: Learning local genetic correlation structure improves summary statistics-based analyses

Bioinformatics

Volumn 31, Issue 12, 2015, Pages i181-i189

  Park, Danny S ^a   Brown, Brielin ^b   Eng, Celeste ^c   Huntsman, Scott ^c   Hu, Donglei ^c   Torgerson, Dara G ^c   Burchard, Esteban G ^a,c   Zaitlen, Noah ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; COMPUTER PROGRAM; CORONARY ARTERY DISEASE; EVALUATION STUDY; GENETIC ASSOCIATION; GENETICS; GENOTYPE; HUMAN; PHENOTYPE; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS;

ALGORITHMS; CORONARY ARTERY DISEASE; DATA INTERPRETATION, STATISTICAL; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 84931050631     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv230     Document Type: Conference Paper

References (26)

1. 1000 Genomes Project Consortium, et al. (2012). An integrated map of genetic variation from 1 092 human genomes. Nature, 491, 56-65
2. Baran Y., et al. (2012). Fast and accurate inference of local ancestry in Latino populations. Bioinformatics, 28, 1359-1367
3. Borrell L.N., et al. (2013). Childhood Obesity and Asthma Control in the GALA II and SAGE II Studies. Am J Respir Crit Care Med., 187, 697-702
4. Bryc K., et al. (2010). Genome-wide patterns of population structure and admixture in West Africans and African Americans. Proc. Natl. Acad. Sci. USA., 107, 786-791
5. Bulik-Sullivan B., et al. (2014). LD score regression distinguishes confounding from polygenicity in genome-wide association studies. Technical report, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
6. Byrd R.H., et al. (2006). A limited memory algorithm for bound constrained optimization. SIAM Journal on Scientific Computing, 16, 1190-1208
7. Coronary Artery Disease (C4D) Genetics Consortium. (2011). A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease. Nat. Genet., 43, 339-344
8. Galarneau G., et al. (2010). Fine-mapping at three loci known to affect fetal hemoglobin levels explains additional genetic variation. Nat. Genet., 42, 1049-1051
9. Gymrek M., et al. (2013). Identifying personal genomes by surname inference. Science, 339, 321-324
10. Han B., et al. (2011). Postassociation cleaning using linkage disequilibrium information. Genet. Epidemiol., 35, 1-10
11. Hormozdiari F., et al. (2014). Identifying causal variants at loci with multiple signals of association. Genetics, 198, 497-508
12. Howie B.N., et al. (2009). A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet., 5, e1000529
13. Kichaev G., et al. (2014). Integrating functional data to prioritize causal variants in statistical fine-mapping studies. PLoS Genet., 10, e1004722
14. Liu J.Z., et al. (2010). A versatile gene-based test for genome-wide association studies. Am. J. Hum. Genet., 87, 139-145
15. Moorjani P., et al. (2013). Genetic evidence for recent population mixture in India. Am. J. Hum. Genet. 93, 422-438
16. Pasaniuc B., et al. (2013). Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation. Bioinformatics, 29, 1407-1415
17. Pasaniuc B., et al. (2014). Fast and accurate imputation of summary statistics enhances evidence of functional enrichment. Bioinformatics, 30, 2906-2914
18. Reich D., et al. (2009). Reconstructing Indian population history. Nature, 461, 489-494
19. Sanna S., et al. (2011). Fine mapping of five loci associated with low-density lipoprotein cholesterol detects variants that double the explained heritability. PLoS Genet., 7, e1002198
20. Schork A.J., et al. (2013). All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs. PLoS Genet., 9, e1003449
21. Schunkert H., et al. (2011). Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nat. Genet., 43, 333-338
22. Silva-Zolezzi I., et al. (2009). Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico. Proc. Natl. Acad. Sci. USA., 106, 8611-8616
23. Speliotes E.K., et al. (2010). Association analyses of 249 796 individuals reveal 18 new loci associated with body mass index. Nat. Genet., 42, 937-948
24. Wang S., et al. (2008). Geographic patterns of genome admixture in Latin American Mestizos. PLoS Genet., 4, e1000037
25. Yang J., et al. (2012). Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. Nat. Genet., 44, 369-375
26. Zaitlen N., et al. (2009). Linkage effects and analysis of finite sample errors in the HapMap. Hum. Hered., 68, 73-86