[PDF] Top 20 Application of the False Discovery Rate to Quantitative Trait Loci Interval Mapping With Multiple Traits

... interval on a chromosome. These cases were, however, conducted at each 1-cM position on the genome. This recorded as evidence for a single QTL. results in a large number of tests with very high correla- As ... See full document

... false discovery rate in multiple testing with independent ...2002 Application of the false discovery rate to quantitative trait Benjamini, ...the ... See full document

... What is common to the above researchers, and to the few other users of FDR ideas in QTL analysis, is their enthusiasm about the important role that these ideas can play in QTL analysis. Since we share this enthusi- asm, ... See full document

... to mapping for QTL controlling endosperm sues of their seeds can have four possible genotypes, traits (Tan et ...Such application implicitly relies on an ered (appendix ...endosperm traits are ... See full document

... two mapping populations (cohorts), treatment combinations for the growth initiation and growth cessation experiments, and sample sizes used in QTL ...among traits that were evaluated during the seasonal ... See full document

... yield traits, or vice ...for trait k of individual j. We assume resistance traits (discrete) with the yield traits (continu- that the residual errors are independent among individ- ous) may ... See full document

... more likely to be eQTL, and annotating SNPs with eQTL scores can be useful for discovering susceptibility loci [12]. However, the eQTL approach is restricted in its applica- tion due to the cost of genome-wide ... See full document

... Varying coefficient models are very useful statistical tools for exploring dynamic effects. The varying coefficient models were introduced by Cleveland et al. (1991), and discussed by Hastie and Tibshirani (1993) in more ... See full document

... of multiple QTL but again there is not strong tween the LOD score and the ...five loci on chromosomes 1, 4, 6, 7, and ...these loci is given in to be a test for linkage wherein the location of the ... See full document

... for multiple testing, 144 SNPs in 10 genes (ADAM12, CNTN1, CNTN6, DTX1, HDAC9, LNX1, NCOR2, RAB6A, TLE1 and E2F3) with false discovery rate (FDR) < ... See full document

... linkage mapping by H aley and K nott (1992) and M artinez and C urnow ...of interval mapping and multiple re- gression on marker genotypes for mapping multiple QTL ... See full document

... We find a major expression regulatory region on chromosome III, affecting more than half of the gene expression levels of individual amino acid biosynthetic genes. Brem et al. (2002) found two transcriptional regulatory ... See full document

... The threshold at each genome-wide significance level was estimated based on 500 permutations. In each permuta- tion cycle, pedigrees of the same size were permuted; within a pedigree, phenotypes were permuted among ... See full document

... Genetic Mapping of Quantitative Trait Loci Controlling Growth and Wood Quality Traits in EucaZyptus grandis Using a Maternal Half-sib Family.. and RAPD Markers.[r] ... See full document

... to traits of foot and leg (FL) structural soundness ...the traits of interest were identified, such as MC4R (for backfat) and IGF2 (for loin muscle area), and a number of novel promising genes were ... See full document

... more false positives (Figure ...lower false-positive rates without loss of power to detect large-effect QTL (Figure ...as false positives according to our stringent defini- tion of true ... See full document

... lower mapping precision. For the 10-trait analysis, the standard deviation of the estimated QTL position (SL) increased from ...in mapping precision can be recovered by a composite interval ... See full document

... A practical example on plant height in an F, progeny of tomato will be used to illustrate the methods de- scribed in the previous section; additional parental and F, dat[r] ... See full document

... of interval mapping, a very common ...quan- loci that influence life span. That information can then titative trait locus (QTL) mapping should be applied provide a basis for more ... See full document

... We evaluate our proposed semiparametric method through simulation studies. The simulation results indicate that our proposed testing procedure will maintain the type I error rate at the specified nominal level, ... See full document