Influence analysis in quantitative trait loci detection

• Published in: Biometrical journal Vol. 56; no. 4; pp. 697 - 719
• Main Authors: Dou, Xiaoling, Kuriki, Satoshi, Maeno, Akiteru, Takada, Toyoyuki, Shiroishi, Toshihiko
• Format: Journal Article
• Language: English
• Published: Germany Blackwell Publishing Ltd 01-07-2014; Wiley - VCH Verlag GmbH & Co. KGaA; BlackWell Publishing Ltd
• Subjects: Animals; Biometry - methods; Chromosome Mapping - methods; Chromosomes, Mammalian - genetics; Gene loci; Genomics; Influence score vector; Likelihood Functions; Methods; Mice; Models, Statistical; Performance Analysis via Receiver Operating Characteristics; Profile likelihood; Quantitative Trait Loci - genetics; ROC analysis; ROC Curve; Shape of LOD score curve; Standardized empirical influence function; Profile likelihood; Standardized empirical influence function; Influence score vector; ROC analysis; Shape of LOD score curve
• ISSN: 0323-3847; 1521-4036
• DOI: 10.1002/bimj.201200178

This paper presents systematic methods for the detection of influential individuals that affect the log odds (LOD) score curve. We derive general formulas of influence functions for profile likelihoods and introduce them into two standard quantitative trait locus detection methods—the interval mapping method and single marker analysis. Besides influence analysis on specific LOD scores, we also develop influence analysis methods on the shape of the LOD score curves. A simulation‐based method is proposed to assess the significance of the influence of the individuals. These methods are shown useful in the influence analysis of a real dataset of an experimental population from an F2 mouse cross. By receiver operating characteristic analysis, we confirm that the proposed methods show better performance than existing diagnostics.