Statistical Methods for Mapping Multiple QTL

Since Lander and Botstein proposed the interval mapping method for QTL mapping data analysis in 1989, tremendous progress has been made in the last many years to advance new and powerful statistical methods for QTL analysis. Recent research progress has been focused on statistical methods and issues for mapping multiple QTL together. In this article, we review this progress. We focus the discussion on the statistical methods for mapping multiple QTL by maximum likelihood and Bayesian methods and also on determining appropriate thresholds for the analysis.

[1]  Chiara Sabatti,et al.  False discovery rate in linkage and association genome screens for complex disorders. , 2003, Genetics.

[2]  Shizhong Xu.  Estimating polygenic effects using markers of the entire genome. , 2003, Genetics.

[3]  Z B Zeng,et al.  Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Bradley Efron,et al.  Local False Discovery Rates , 2005 .

[5]  E. Lander,et al.  Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. , 1989, Genetics.

[6]  J. Weller,et al.  A new approach to the problem of multiple comparisons in the genetic dissection of complex traits. , 1998, Genetics.

[7]  John D. Storey,et al.  Multiple Locus Linkage Analysis of Genomewide Expression in Yeast , 2005, PLoS biology.

[8]  K. Manly,et al.  Genomics, prior probability, and statistical tests of multiple hypotheses. , 2004, Genome research.

[9]  K. Sax,et al.  The Association of Size Differences with Seed-Coat Pattern and Pigmentation in PHASEOLUS VULGARIS. , 1923, Genetics.

[10]  Z B Zeng,et al.  Estimating the genetic architecture of quantitative traits. , 1999, Genetical research.

[11]  Y. Zuo,et al.  On the Sample Size Requirement in Genetic Association Tests When the Proportion of False Positives Is Controlled , 2006, Genetics.

[12]  C. Haley,et al.  A simple regression method for mapping quantitative trait loci in line crosses using flanking markers , 1992, Heredity.

[13]  Hao Wu,et al.  R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses , 2007, Bioinform..

[14]  Z B Zeng,et al.  Genetic architecture of a morphological shape difference between two Drosophila species. , 2000, Genetics.

[15]  T. Mackay.  The genetic architecture of quantitative traits. , 2001, Annual review of genetics.

[16]  Y. Benjamini,et al.  Resampling-based false discovery rate controlling multiple test procedures for correlated test statistics , 1999 .

[17]  R. Doerge,et al.  Permutation tests for multiple loci affecting a quantitative character. , 1996, Genetics.

[18]  J. Satagopan.  Estimating the number of quantitative trait loci via Bayesian model determination , 1996 .

[19]  R. Doerge,et al.  Empirical threshold values for quantitative trait mapping. , 1994, Genetics.

[20]  Using the False Discovery Rate Approach in the Genetic Dissection of Complex Traits: A Response to Zaykin et al. , 2000 .

[21]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[22]  John D. Storey,et al.  Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[23]  John D. Storey,et al.  Empirical Bayes Analysis of a Microarray Experiment , 2001 .

[24]  John D. Storey.  A direct approach to false discovery rates , 2002 .

[25]  D. Nyholt.  A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other. , 2004, American journal of human genetics.

[26]  Nengjun Yi,et al.  Bayesian model choice and search strategies for mapping interacting quantitative trait Loci. , 2003, Genetics.

[27]  C. Kao,et al.  General formulas for obtaining the MLEs and the asymptotic variance-covariance matrix in mapping quantitative trait loci when using the EM algorithm. , 1997, Biometrics.

[28]  P. Green.  Reversible jump Markov chain Monte Carlo computation and Bayesian model determination , 1995 .

[29]  Fei Zou,et al.  An Efficient Resampling Method for Assessing Genome-Wide Statistical Significance in Mapping Quantitative Trait Loci , 2004, Genetics.

[30]  M A Newton,et al.  A bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo. , 1996, Genetics.

[31]  T. C. Hsiang,et al.  A Bayesian View on Ridge Regression , 1975 .

[32]  Nengjun Yi,et al.  Bayesian Model Selection for Genome-Wide Epistatic Quantitative Trait Loci Analysis , 2005, Genetics.

[33]  G. Churchill,et al.  A statistical framework for quantitative trait mapping. , 2001, Genetics.

[34]  B Müller-Myhsok,et al.  Rapid simulation of P values for product methods and multiple-testing adjustment in association studies. , 2005, American journal of human genetics.

[35]  Nengjun Yi,et al.  A Unified Markov Chain Monte Carlo Framework for Mapping Multiple Quantitative Trait Loci , 2004, Genetics.

[36]  R. Fernando,et al.  Controlling the Proportion of False Positives in Multiple Dependent Tests , 2004, Genetics.

[37]  J. Witte,et al.  On the relative sample size required for multiple comparisons. , 2000, Statistics in medicine.

[38]  M. Boehnke,et al.  So many correlated tests, so little time! Rapid adjustment of P values for multiple correlated tests. , 2007, American journal of human genetics.

[39]  J. Whittaker,et al.  Marker-assisted selection using ridge regression. , 1999, Genetical research.

[40]  D. Balding.  A tutorial on statistical methods for population association studies , 2006, Nature Reviews Genetics.

[41]  Y. Benjamini,et al.  THE CONTROL OF THE FALSE DISCOVERY RATE IN MULTIPLE TESTING UNDER DEPENDENCY , 2001 .

[42]  Z. Zeng,et al.  Multiple interval mapping for quantitative trait loci. , 1999, Genetics.

[43]  L. Kruglyak,et al.  Genetic Dissection of Transcriptional Regulation in Budding Yeast , 2002, Science.

[44]  John D. Storey,et al.  Relaxed Significance Criteria for Linkage Analysis , 2006, Genetics.

[45]  David M. Evans,et al.  Two-Stage Two-Locus Models in Genome-Wide Association , 2006, PLoS genetics.

[46]  F. Schenkel,et al.  Estimation of genetic effects in the presence of multicollinearity in multibreed beef cattle evaluation. , 2005, Journal of animal science.

[47]  Y. Benjamini,et al.  Quantitative Trait Loci Analysis Using the False Discovery Rate , 2005, Genetics.

[48]  John D. Storey.  The positive false discovery rate: a Bayesian interpretation and the q-value , 2003 .