Empirical Bayesian LASSO-logistic regression for multiple binary trait locus mapping

BMC Genetics

Volumn 14, Issue , 2013, Pages

  Huang, Anhui ^a   Xu, Shizhong ^b   Cai, Xiaodong ^a  

^a University of Miami College of Engineering   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Bayesian shrinkage; Binary traits; Epistatic effects; Logistic regression; QTL mapping

Indexed keywords

ALGORITHM; ARTICLE; BAYES THEOREM; COMPUTER PROGRAM; CONTROLLED STUDY; EPISTASIS; FALSE POSITIVE RESULT; GENETIC MARKER; GENETIC TRAIT; GENOTYPE; LOGISTIC REGRESSION ANALYSIS; MICROCOMPUTER; QUANTITATIVE TRAIT LOCUS MAPPING; SIMULATION;

ALGORITHMS; BAYES THEOREM; CHROMOSOME MAPPING; COMPUTER SIMULATION; EPISTASIS, GENETIC; HUMANS; LOGISTIC MODELS; QUANTITATIVE TRAIT LOCI;

EID: 84873739129     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-14-5     Document Type: Article

References (49)

1. Falconer DS, Mackay TFC. Introduction to Quantitative Genetics 1996, Boston: Addison-Wesley, 4.
2. Hackett CA, Weller JI. Genetic mapping of quantitative trait loci for traits with ordinal distributions. Biometrics 1995, 51(4):1252-1263. 10.2307/2533257, 8589221.
3. Xu S, Atchley WR. Mapping quantitative trait loci for complex binary diseases using line crosses. Genetics 1996, 143(3):1417-1424. 1207409, 8807312.
4. Rao S, Xu S. Mapping quantitative trait loci for ordered categorical traits in four-way crosses. Heredity 1998, 81(2):214-224. 10.1046/j.1365-2540.1998.00378.x, 9750263.
5. Xu S, Yi N, Burke D, Galecki A, Miller RA. An EM algorithm for mapping binary disease loci: application to fibrosarcoma in a four-way cross mouse family. Genet Res 2003, 82(2):127-138. 10.1017/S0016672303006414, 14768897.
6. Xu C, Zhang YM, Xu S. An EM algorithm for mapping quantitative resistance loci. Heredity 2004, 94(1):119-128.
7. Xu C, Li Z, Xu S. Joint mapping of quantitative trait loci for multiple binary characters. Genetics 2005, 169(2):1045-1059. 10.1534/genetics.103.019406, 1449126, 15489509.
8. Deng W, Chen H, Li Z. A logistic regression mixture model for interval mapping of genetic trait loci affecting binary phenotypes. Genetics 2006, 172(2):1349-1358. 1456231, 16272416.
9. Haley CS, Knott SA. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 1992, 69(4):315-324. 10.1038/hdy.1992.131, 16718932.
10. Martínez O, Curnow RN. Estimating the locations and the sizes of the effects of quantitative trait loci using flanking markers. Theor Appl Genet 1992, 85(4):480-488.
11. Yi N, Xu S. Bayesian mapping of quantitative trait loci for complex binary traits. Genetics 2000, 155(3):1391-1403. 1461151, 10880497.
12. Yi N, Xu S. Mapping quantitative trait loci with epistatic effects. Genet Res 2002, 79(2):185-198.
13. Yi N, Xu S, George V, Allison DB. Mapping multiple quantitative trait loci for ordinal traits. Behav Genet 2004, 34(1):3-15.
14. Yi N, Banerjee S, Pomp D, Yandell BS. Bayesian mapping of genomewide interacting quantitative trait loci for ordinal traits. Genetics 2007, 176(3):1855-1864. 10.1534/genetics.107.071142, 1931535, 17507680.
15. Huang H, Eversley CD, Threadgill DW, Zou F. Bayesian multiple quantitative trait loci mapping for complex traits using markers of the entire genome. Genetics 2007, 176(4):2529-2540. 10.1534/genetics.106.064980, 1950652, 17483433.
16. Yang R, Li J, Wang X, Zhou X. Bayesian functional mapping of dynamic quantitative traits. Theor Appl Genet 2011, 123(3):483-492. 10.1007/s00122-011-1601-0, 21573763.
17. Chen Z, Liu J. Mixture generalized linear models for multiple interval mapping of quantitative trait loci in experimental crosses. Biometrics 2009, 65(2):470-477. 10.1111/j.1541-0420.2008.01100.x, 18647293.
18. Li J, Wang S, Zeng ZB. Multiple-interval mapping for ordinal traits. Genetics 2006, 173(3):1649-1663. 10.1534/genetics.105.054619, 1526652, 16585135.
19. Coffman CJ, Doerge RW, Simonsen KL, Nichols KM, Duarte CK, Wolfinger RD, McIntyre LM. Model selection in binary trait locus mapping. Genetics 2005, 170(3):1281-1297. 10.1534/genetics.104.033910, 1451193, 15834149.
20. Xu S. Estimating polygenic effects using markers of the entire genome. Genetics 2003, 163(2):789-801. 1462468, 12618414.
21. Wang H, Zhang YM, Li X, Masinde GL, Mohan S, Baylink DJ, Xu S. Bayesian shrinkage estimation of quantitative trait loci parameters. Genetics 2005, 170:465-480. 10.1534/genetics.104.039354, 1449727, 15781696.
22. Hoti F, Sillanpää MJ. Bayesian mapping of genotype x expression interactions in quantitative and qualitative traits. Heredity 2006, 97(1):4-18. 10.1038/sj.hdy.6800817, 16670709.
23. Yi N, Xu S. Bayesian LASSO for quantitative trait loci mapping. Genetics 2008, 179(2):1045-1055. 10.1534/genetics.107.085589, 2429858, 18505874.
24. Xu S. An empirical Bayes method for estimating epistatic effects of quantitative trait loci. Biometrics 2007, 63(2):513-521. 10.1111/j.1541-0420.2006.00711.x, 17688503.
25. Hoggart CJ, Whittaker JC, De Iorio M, Balding DJ. Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies. PLoS Genet 2008, 4(7):e1000130. 10.1371/journal.pgen.1000130, 2464715, 18654633.
26. Yi N, Banerjee S. Hierachical generalized linear models for multiple quantitative trait locus mapping. Genetics 2009, 181:1101-1133. 10.1534/genetics.108.099556, 2651046, 19139143.
27. Tibshirani R. Regression shrinkage and selection via the lasso. J R Stat Soc Series B Stat Methodol 1996, 58(1):267-288.
28. Wu TT, Chen YF, Hastie T, Sobel E, Lange K. Genome-wide association analysis by lasso penalized logistic regression. Bioinformatics 2009, 25:714-721. 10.1093/bioinformatics/btp041, 2732298, 19176549.
29. Ayers KL, Cordell HJ. SNP selection in genome-wide and candidate gene studies via penalized logistic regression. Genet Epidemiol 2010, 34(8):879-891. 10.1002/gepi.20543, 3410531, 21104890.
30. Cai X, Huang A, Xu S. Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping. BMC Bioinformatics 2011, 12(1):211. 10.1186/1471-2105-12-211, 3125263, 21615941.
31. Park T, Casella G. The Bayesian lasso. J Am Stat Assoc 2008, 103(482):681-686.
32. Tipping ME. Sparse Bayesian learning and the relevance vector machine. J Mach Learn Res 2001, 1(3):211-244.
33. Tipping ME, Faul AC. Fast marginal likelihood maximisation for sparse Bayesian models 2003, Key West, FL: Proc 9th International Workshop on Artificial Intelligence and Statistics.
34. Cockerham CC. An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives when epistasis is present. Genetics 1954, 39(6):859-882. 1209694, 17247525.
35. Griffin JE, Brown PJ. Bayesian hyper-lassos with non-convex penalization. Aust N Z J Stat 2011, 53(4):423-442.
36. Carlin BP, Louis TA. Bayesian methods for data analysis 2008, London/New York: Chapman & Hall/CRC, 3.
37. Bishop CM. Pattern recognition and machine learning 2006, New York: Springer.
38. MacKay DJC. The evidence framework applied to classification networks. Neural Comput 1992, 4(5):720-736.
39. Hastie T, Tibshirani R, Friedman JH. The elements of statistical learning: data mining, inference, and prediction 2009, New York: Springer, 2.
40. Wu R, Ma CX, Casella G. Statistical genetics of quantitative traits: linkage, maps, and QTL 2007, LLC: Springer Science + Business Media.
41. R Development Core Team A language and environment for statistical computing 2012, Vienna, Austria: R Foundation for Statistical Computing, R Development Core Team.
42. Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat software 2010, 33(1):1-22.
43. Masinde GL, Li X, Gu W, Davidson H, Mohan S, Baylink DJ. Identification of wound healing/regeneration Quantitative Trait Loci (QTL) at multiple time points that explain seventy percent of variance in (MRL/MpJ and SJL/J) mice F2 population. Genome Res 2001, 11(12):2027-2033. 10.1101/gr.203701, 311224, 11731492.
44. Li X, Mohan S, Gu W, Baylink DJ. Analysis of gene expression in the wound repair/regeneration process. Mamm Genome 2001, 12(1):52-59. 10.1007/s003350010230, 11178744.
45. Kunimoto BT. Growth factors in wound healing: the next great innovation?. Ostomy Wound Manage 1999, 45(8):56-64.
46. Xu S. An expectation maximization algorithm for the Lasso estimation of quantitative trait locus effects. Heredity 2010, 2010:1-12.
47. Yi N, Shriner D, Banerjee S, Mehta T, Pomp D, Yandell BS. An efficient Bayesian model selection approach for interacting quantitative trait loci models with many effects. Genetics 2007, 176(3):1865-1877. 10.1534/genetics.107.071365, 1931520, 17483424.
48. Fan J, Song R. Sure independence screening in generalized linear models with NP-dimensionality. Ann Stat 2010, 38(6):3567-3604.
49. Fan J, Lv J. Sure independence screening for ultrahigh dimensional feature space. J R Stat Soc Series B Stat Methodol 2008, 70(5):849-911. 10.1111/j.1467-9868.2008.00674.x, 2709408, 19603084.