Open AccessApplication of the False Discovery Rate to Quantitative Trait Loci Interval Mapping With Multiple Traits
Author(s) -
Hak-Kyo Lee,
Jack C. M. Dekkers,
M. Soller,
Massoud Malek,
Rohan L. Fernando,
Max F. Rothschild
Publication year - 2002
Publication title -
genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.792
H-Index - 246
eISSN - 1943-2631
pISSN - 0016-6731
DOI - 10.1093/genetics/161.2.905
Subject(s) - false discovery rate , quantitative trait locus , multiple comparisons problem , biology , trait , type i and type ii errors , statistics , family based qtl mapping , false positive rate , genetics , context (archaeology) , statistic , interval (graph theory) , test statistic , inclusive composite interval mapping , statistical hypothesis testing , mathematics , gene mapping , computer science , gene , paleontology , combinatorics , chromosome , programming language
Controlling the false discovery rate (FDR) has been proposed as an alternative to controlling the genome-wise 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.