scholarly journals Quantitative Trait Loci Analysis Using the False Discovery Rate

Genetics ◽  
2005 ◽  
Vol 171 (2) ◽  
pp. 783-790 ◽  
Author(s):  
Yoav Benjamini ◽  
Daniel Yekutieli
Keyword(s):  
Quantitative Trait Loci ◽  
False Discovery Rate ◽  
Quantitative Trait ◽  
False Discovery ◽  
Trait Loci

Application of the False Discovery Rate to Quantitative Trait Loci Interval Mapping With Multiple Traits

Genetics ◽  
2002 ◽  
Vol 161 (2) ◽  
pp. 905-914 ◽  
Author(s):  
Hakkyo Lee ◽  
Jack C M Dekkers ◽  
M Soller ◽  
Massoud Malek ◽  
Rohan L Fernando ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
False Discovery Rate ◽  
Error Rate ◽  
Quantitative Trait ◽  
Interval Mapping ◽  
Error Rates ◽  
Multiple Traits ◽  
Test Statistic ◽  
False Discovery ◽  
Trait Loci

Abstract Controlling the false discovery rate (FDR) has been proposed as an alternative to controlling the genomewise error rate (GWER) for detecting quantitative trait loci (QTL) in genome scans. The objective here was to implement FDR in the context of regression interval mapping for multiple traits. Data on five traits from an F2 swine breed cross were used. FDR was implemented using tests at every 1 cM (FDR1) and using tests with the highest test statistic for each marker interval (FDRm). For the latter, a method was developed to predict comparison-wise error rates. At low error rates, FDR1 behaved erratically; FDRm was more stable but gave similar significance thresholds and number of QTL detected. At the same error rate, methods to control FDR gave less stringent significance thresholds and more QTL detected than methods to control GWER. Although testing across traits had limited impact on FDR, single-trait testing was recommended because there is no theoretical reason to pool tests across traits for FDR. FDR based on FDRm was recommended for QTL detection in interval mapping because it provides significance tests that are meaningful, yet not overly stringent, such that a more complete picture of QTL is revealed.

scholarly journals Multiple Quantitative Trait Loci Mapping With Cofactors and Application of Alternative Variants of the False Discovery Rate in an Enlarged Granddaughter Design

Genetics ◽  
2004 ◽  
Vol 168 (2) ◽  
pp. 1019-1027 ◽  
Author(s):  
Jörn Bennewitz ◽  
Norbert Reinsch ◽  
Volker Guiard ◽  
Sebastien Fritz ◽  
Hauke Thomsen ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
False Discovery Rate ◽  
Quantitative Trait ◽  
Quantitative Trait Loci Mapping ◽  
False Discovery ◽  
Trait Loci

scholarly journals A Whole Genome Scan for Quantitative Trait Loci Affecting Milk Protein Percentage in Israeli-Holstein Cattle, by Means of Selective Milk DNA Pooling in a Daughter Design, Using an Adjusted False Discovery Rate Criterion

Genetics ◽  
2001 ◽  
Vol 157 (4) ◽  
pp. 1683-1698 ◽  
Author(s):  
Mathias O Mosig ◽  
Ehud Lipkin ◽  
Galina Khutoreskaya ◽  
Elena Tchourzyna ◽  
Morris Soller ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
False Discovery Rate ◽  
Quantitative Trait ◽  
Milk Protein ◽  
Dna Pooling ◽  
Protein Percentage ◽  
False Discovery ◽  
Data Points ◽  
Selective Dna Pooling ◽  
Daughter Design

Abstract Selective DNA pooling was employed in a daughter design to screen all bovine autosomes for quantitative trait loci (QTL) affecting estimated breeding value for milk protein percentage (EBVP%). Milk pools prepared from high and low daughters of each of seven sires were genotyped for 138 dinucleotide microsatellites. Shadow-corrected estimates of sire allele frequencies were compared between high and low pools. An adjusted false discovery rate (FDR) method was employed to calculate experimentwise significance levels and empirical power. Significant associations with milk protein percentage were found for 61 of the markers (adjusted FDR = 0.10; estimated power, 0.68). The significant markers appear to be linked to 19–28 QTL. Mean allele substitution effects of the putative QTL averaged 0.016 (0.009–0.028) in units of the within-sire family standard deviation of EBVP% and summed to 0.460 EBVP%. Overall QTL heterozygosity was 0.40. The identified QTL appear to account for all of the variation in EBVP% in the population. Through use of selective DNA pooling, 4400 pool data points provided the statistical power of 600,000 individual data points.

Identification of cis-regulated genes in quantitative trait loci driving liver fibrosis

2012 ◽  
Vol 50 (08) ◽  
Author(s):  
R Hall ◽  
R Müllenbach ◽  
S Huss ◽  
R Alberts ◽  
K Schughart ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Liver Fibrosis ◽  
Quantitative Trait ◽  
Trait Loci
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