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Quantitative Trait Loci Analysis Using The False Discovery Rate

Y. Benjamini, D. Yekutieli
Published 2005 · Biology, Medicine

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False discovery rate control has become an essential tool in any study that has a very large multiplicity problem. False discovery rate-controlling procedures have also been found to be very effective in QTL analysis, ensuring reproducible results with few falsely discovered linkages and offering increased power to discover QTL, although their acceptance has been slower than in microarray analysis, for example. The reason is partly because the methodological aspects of applying the false discovery rate to QTL mapping are not well developed. Our aim in this work is to lay a solid foundation for the use of the false discovery rate in QTL mapping. We review the false discovery rate criterion, the appropriate interpretation of the FDR, and alternative formulations of the FDR that appeared in the statistical and genetics literature. We discuss important features of the FDR approach, some stemming from new developments in FDR theory and methodology, which deem it especially useful in linkage analysis. We review false discovery rate-controlling procedures—the BH, the resampling procedure, and the adaptive two-stage procedure—and discuss the validity of these procedures in single- and multiple-trait QTL mapping. Finally we argue that the control of the false discovery rate has an important role in suggesting, indicating the significance of, and confirming QTL and present guidelines for its use.
This paper references
Mapping mendelian factors underlying quantitative traits using RFLP linkage maps.
E. Lander (1989)
10.1038/hdy.1992.131
A simple regression method for mapping quantitative trait loci in line crosses using flanking markers
C. Haley (1992)
Empirical threshold values for quantitative trait mapping.
G. Churchill (1994)
10.1038/NG1195-241
Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results
E. Lander (1995)
10.1111/J.2517-6161.1995.TB02031.X
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Y. Benjamini (1995)
10.1080/01621459.1997.10473627
Multiple Testing of General Contrasts Using Logical Constraints and Correlations
P. Westfall (1997)
A new approach to the problem of multiple comparisons in the genetic dissection of complex traits.
J. Weller (1998)
10.1016/S0378-3758(99)00041-5
Resampling-based false discovery rate controlling multiple test procedures for correlated test statistics
D. Yekutieli (1999)
Resampling based false discovery rate controlling procedure for dependent test statistics
D Yekutieli (1999)
10.3102/10769986025001060
On the Adaptive Control of the False Discovery Rate in Multiple Testing With Independent Statistics
Y. Benjamini (2000)
Using the False Discovery Rate Approach in the Genetic Dissection of Complex Traits: A Response to Zaykin et al.
J. Weller (2000)
Using the False Discovery Rate in the genetic dissection of complex traits: A response to Weller et al
D V Zaykin (2000)
Using the False Discovery Rate in the genetic dissection of complex traits: A response to Weller et al.
D V.Zaykin (2000)
The adaptive control of the false discovery rate in multiple comparison problems
Y Benjamini (2000)
10.1214/AOS/1013699998
THE CONTROL OF THE FALSE DISCOVERY RATE IN MULTIPLE TESTING UNDER DEPENDENCY
Y. Benjamini (2001)
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.
M. O. Mosig (2001)
10.1073/pnas.091062498
Significance analysis of microarrays applied to the ionizing radiation response
V. G. Tusher (2001)
Theoretical results needed for applying the False Discovery Rate in statistical problems
D Yekutieli (2001)
Significance Analysis of Microarrays Applied to Transcriptional Responses to Ionizing Radiation
V Tusher (2001)
Application of the false discovery rate to quantitative trait loci interval mapping with multiple traits.
H. Lee (2002)
10.1111/1467-9868.00346
A direct approach to false discovery rates
John D. Storey (2002)
Hierarchical FDR testing of trees of hypotheses
Y Benjamini (2002)
Genomic Analysis of Transcriptional Networks: Combining Microarrays with Complex Trait Analysis
R W Williams (2002)
Genomic Analysis of Transcriptional Networks: Combining Microarrays with Complex Trait Analysis”, abstract in the First Annual CTC
R WWilliams (2002)
Yekutieli D.,(2002) ”Hierarchical FDR testing of trees of hypotheses ”, Research Paper 02-02 the Department of Statistics and OR
Y. Benjamini (2002)
False discovery rate in linkage and association genome screens for complex disorders.
C. Sabatti (2003)
10.1534/genetics.166.1.611
Controlling the Proportion of False Positives in Multiple Dependent Tests
R. Fernando (2004)
10.1111/J.1467-9868.2004.00439.X
Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach
John D. Storey (2004)
10.1111/J.1369-7412.2003.05527.X
A note on the adaptive control of false discovery rates
M. Black (2004)
10.1214/009053604000000283
A stochastic process approach to false discovery control
C. Genovese (2004)
10.1093/BIOMET/93.3.491
Adaptive linear step-up procedures that control the false discovery rate
Y. Benjamini (2006)



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10.1101/2020.09.03.282343
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10.1111/acel.13232
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Y. Fang (2020)
10.1101/719336
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10.1093/ajcn/nqz152
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10.14814/phy2.13952
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10.1016/j.ijporl.2019.109664
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10.1016/J.JNUTBIO.2019.03.004
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