Multi-population GWA mapping via multi-task regularized regression

Bioinformatics

Volumn 26, Issue 12, 2010, Pages

  Puniyani, Kriti ^a   Kim, Seyoung ^a   Xing, Eric P ^a  

^a Carnegie Mellon University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CHROMOSOME MAP; ETHNIC AND RACIAL GROUPS; GENETIC ASSOCIATION; GENETIC MARKER; GENOME; HUMAN; METHODOLOGY; PHENOTYPE; REGRESSION ANALYSIS;

ALGORITHMS; CHROMOSOME MAPPING; GENETIC MARKERS; GENOME; GENOME-WIDE ASSOCIATION STUDY; HUMANS; PHENOTYPE; POPULATION GROUPS; REGRESSION ANALYSIS;

EID: 77954194620     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq191     Document Type: Article

References (31)

1. Bersaglieri, T. et al. (2004) Genetic signatures of strong recent positive selection at the lactase gene. Am. J. Hum. Genet., 74, 1111-1120.
2. Bertsekas, D.P. (1982) Constrained Optimization and Lagrange Multiplier Methods. Academic Press, Boston.
3. Devlin, B. and Roeder, K. (1999) Genomic control for association studies. Biometrics, 55, 997-1004.
4. Devlin, B. et al. (2004) Genomic control to the extreme. Nat. Genet., 36, 1129-1130.
5. Enattah, N.S. et al. (2002) Identification of a variant associated with adult-type hypolactasia. Nat. Genet., 30, 233-37.
6. Epstein, M.P. et al. (2007) Asimple and improved correction for population stratification in case-control studies. Am. J. Hum. Genet., 80, 921-930.
7. Hartigan, J.A. (1975) Clustering Algorithms. John Wiley & Sons, Inc., New York, NY, USA.
8. Hastie, T. et al. (2003) The Elements of Statistical Learning. Springer, New York.
9. Hoggart, C. et al. (2003) Control of confounding of genetic associations in stratified populations. Am. J. Hum. Genet., 72, 1492-1504.
10. Hoggart, C.J. et al. (2008) Simultaneous analysis of all snps in genome-wide and re-sequencing association studies. PLoS Genet., 4, e1000130.
11. Hubisz, M.J. et al. (2009) Inferring weak population structure with the assistance of sample group information. Mol. Ecol. Res.
12. Kimmel, G. et al. (2007) A randomization test for controlling population stratification in whole-genome association studies. Am. J. Hum. Genet., 81, 895-905.
13. Malo, N. et al. (2008) Accommodating linkage disequilibrium in genetic-association analyses via ridge regression. Am. J. Hum. Genet., 82, 375-85.
14. Meier, L. et al. (2008) The group lasso for logistic regression. J. Roy. Stat. Soc. B, 70, 53-71.
15. Obozinski, G. et al. (2008) High-dimensional union support recovery in multivariate regression. In Advances in Neural Information Processing Systems 21. Vancouver, B.C., Canada.
16. Price, A.L. et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet., 38, 904-909.
17. Pritchard, J. et al. (2000) Association mapping in structured populations. Am. J. Hum. Genet., 67, 170-181.
18. Purcell, S. and Shamb, P. (2004) Properties of structured association approaches to detecting population stratification. Hum. Heredity, 58, 93-107.
19. Shi, W. et al. (2007) Detecting disease-causing genes by LASSO-Patternsearch algorithm. BMC Proceedings, 1(Suppl. 1), S60.
20. Shringarpure, S. and Xing, E.P. (2009) mstruct: inference of population structure in light of both genetic admixing and allele mutations. Genetics, 182, 575-593.
21. The International HapMap Consortium. (2005) Ahaplotype map of the human genome. Nature, 437, 1399-1320.
22. Tishkoff, S.A. et al. (2006) Convergent adaptation of human lactase persistence in africa and europe. Nat. Genet., 39, 31-40.
23. Tomioka, R. and Sugiyama, M. (2009) Dual augmented lagrangian method for efficient sparse reconstruction. IEEE Signal Proccesing Lett., 16, 1067-1070.
24. Turlach, B. et al. (2005) Simultaneous variable selection. Technometrics, 47, 349-363.
25. Wasserman, L. and Roeder, K. (2009) High-dimensional variable selection. Ann. Stat., 37, 2178-2201.
26. Wellcome Trust Case Control Consortium. (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447, 661-678.
27. Wu, T.T. et al. (2009) Genome-wide association analysis by lasso penalized logistic regression. Bioinformatics, 25, 714-721.
28. Yu, J. et al. (2005) Aunified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet., 38, 203-208.
29. Yuan, M. and Lin, Y. (2006) Model selection and estimation in regression with grouped variables. J. Roy. Stat. Soc. B, 68, 49-67.
30. Zhao, P. et al. (2008) Grouped and hierarchical model selection through composite absolute penalties. Technical Report 703, Department of Statistics, University of California, Berkeley.
31. Zhu, X. et al. (2002) Association mapping, using a mixture model for complex traits. Genetic Epidemiol., 23, 181-196.