Bayesian Multiple Quantitative Trait Loci Mapping for Complex Traits Using Markers of the Entire Genome

Overview

Journal Genetics

Publisher Oxford University Press

Specialty Genetics

Date 2007 May 8

PMID 17483433

Citations 8

Authors

Hanwen Huang

Chevonne D Eversley

David W Threadgill

Fei Zou

Affiliations

Soon will be listed here.

Abstract

A Bayesian methodology has been developed for multiple quantitative trait loci (QTL) mapping of complex binary traits that follow liability threshold models. Unlike most QTL mapping methods where only one or a few markers are used at a time, the proposed method utilizes all markers across the genome simultaneously. The outperformance of our Bayesian method over the traditional single-marker analysis and interval mapping has been illustrated via simulations and real data analysis to identify candidate loci associated with colorectal cancer.

Citing Articles

Empirical Bayesian elastic net for multiple quantitative trait locus mapping.

Huang A, Xu S, Cai X Heredity (Edinb). 2014; 114(1):107-15.

PMID: 25204301 PMC: 4815589. DOI: 10.1038/hdy.2014.79.

Differential expression of miR-1, a putative tumor suppressing microRNA, in cancer resistant and cancer susceptible mice.

Fleming J, Gable D, Samadzadeh-Tarighat S, Cheng L, Yu L, Gillespie J PeerJ. 2013; 1:e68.

PMID: 23646287 PMC: 3642704. DOI: 10.7717/peerj.68.

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

Huang A, Xu S, Cai X BMC Genet. 2013; 14:5.

PMID: 23410082 PMC: 3771412. DOI: 10.1186/1471-2156-14-5.

Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping.

Cai X, Huang A, Xu S BMC Bioinformatics. 2011; 12:211.

PMID: 21615941 PMC: 3125263. DOI: 10.1186/1471-2105-12-211.

Identification of Mom12 and Mom13, two novel modifier loci of Apc (Min) -mediated intestinal tumorigenesis.

Crist R, Roth J, Lisanti M, Siracusa L, Buchberg A Cell Cycle. 2011; 10(7):1092-9.

PMID: 21386660 PMC: 3100885. DOI: 10.4161/cc.10.7.15089.

References

Satagopan J, Yandell B, Newton M, Osborn T . A bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo. Genetics. 1996; 144(2):805-16. PMC: 1207571. DOI: 10.1093/genetics/144.2.805. View

Coffman C, Doerge R, Simonsen K, Nichols K, Duarte C, Wolfinger R . Model selection in binary trait locus mapping. Genetics. 2005; 170(3):1281-97. PMC: 1451193. DOI: 10.1534/genetics.104.033910. View

Hackett C, Weller J . Genetic mapping of quantitative trait loci for traits with ordinal distributions. Biometrics. 1995; 51(4):1252-63. View

Ruivenkamp C, Csikos T, Klous A, van Wezel T, Demant P . Five new mouse susceptibility to colon cancer loci, Scc11-Scc15. Oncogene. 2003; 22(46):7258-60. DOI: 10.1038/sj.onc.1207096. View

Wang H, Zhang Y, Li X, Masinde G, Mohan S, Baylink D . Bayesian shrinkage estimation of quantitative trait loci parameters. Genetics. 2005; 170(1):465-80. PMC: 1449727. DOI: 10.1534/genetics.104.039354. View

Narita A, Sasaki Y . Detection of multiple QTL with epistatic effects under a mixed inheritance model in an outbred population. Genet Sel Evol. 2004; 36(4):415-33. PMC: 2697211. DOI: 10.1186/1297-9686-36-4-415. View

Sillanpaa M, Arjas E . Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics. 1998; 148(3):1373-88. PMC: 1460044. DOI: 10.1093/genetics/148.3.1373. View

Wright S . An Analysis of Variability in Number of Digits in an Inbred Strain of Guinea Pigs. Genetics. 1934; 19(6):506-36. PMC: 1208511. DOI: 10.1093/genetics/19.6.506. View

van de Ven R . Reversible-jump Markov chain Monte Carlo for quantitative trait loci mapping. Genetics. 2004; 167(2):1033-5. PMC: 1470924. DOI: 10.1534/genetics.103.025536. View

10.

Xu S, Atchley W . Mapping quantitative trait loci for complex binary diseases using line crosses. Genetics. 1996; 143(3):1417-24. PMC: 1207409. DOI: 10.1093/genetics/143.3.1417. View

11.

Carlborg O, Andersson L . Use of randomization testing to detect multiple epistatic QTLs. Genet Res. 2002; 79(2):175-84. DOI: 10.1017/s001667230200558x. View

12.

Zeng Z . Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci U S A. 1993; 90(23):10972-6. PMC: 47903. DOI: 10.1073/pnas.90.23.10972. View

13.

Yi N, Xu S . Bayesian mapping of quantitative trait loci under complicated mating designs. Genetics. 2001; 157(4):1759-71. PMC: 1461584. DOI: 10.1093/genetics/157.4.1759. View

14.

Yi N, Xu S . Bayesian mapping of quantitative trait loci for complex binary traits. Genetics. 2000; 155(3):1391-403. PMC: 1461151. DOI: 10.1093/genetics/155.3.1391. View

15.

Yi N, Yandell B, Churchill G, Allison D, Eisen E, Pomp D . Bayesian model selection for genome-wide epistatic quantitative trait loci analysis. Genetics. 2005; 170(3):1333-44. PMC: 1451197. DOI: 10.1534/genetics.104.040386. View

16.

Xu S . Estimating polygenic effects using markers of the entire genome. Genetics. 2003; 163(2):789-801. PMC: 1462468. DOI: 10.1093/genetics/163.2.789. View

17.

Wright S . The Results of Crosses between Inbred Strains of Guinea Pigs, Differing in Number of Digits. Genetics. 1934; 19(6):537-51. PMC: 1208512. DOI: 10.1093/genetics/19.6.537. View

18.

Yi N . A unified Markov chain Monte Carlo framework for mapping multiple quantitative trait loci. Genetics. 2004; 167(2):967-75. PMC: 1470906. DOI: 10.1534/genetics.104.026286. View

19.

Yi N, Xu S . Mapping quantitative trait loci with epistatic effects. Genet Res. 2002; 79(2):185-98. DOI: 10.1017/s0016672301005511. View

20.

Kao C, Zeng Z, Teasdale R . Multiple interval mapping for quantitative trait loci. Genetics. 1999; 152(3):1203-16. PMC: 1460657. DOI: 10.1093/genetics/152.3.1203. View