Supplementary Material for: Accounting for Epistasis in Linkage Analysis of General Pedigrees

Complex traits are generally believed to be influenced by multiple loci. Identification of loci involved in complex traits is more difficult for interacting than for additive loci. Here we describe an extension of the program lm_twoqtl in the package MORGAN to handle two quantitative trait loci (QTLs) with gene-gene interaction. We investigate whether parametric linkage analysis that accounts for such epistasis improves prospects for linkage detection and accuracy of localization of QTLs. Through use of simulated data we show that analysis that accounts for epistasis provides higher lod scores and better localization than does analysis without epistasis. In addition, we demonstrate that the difference between lod scores in the presence vs. absence of use of an interaction model in analysis is greater in extended than in nuclear pedigrees.

复杂性状通常被认为受多个基因座（loci）调控。相较于加性基因座，鉴定与复杂性状相关的互作基因座难度更高。本文对MORGAN软件包中的lm_twoqtl程序进行扩展，以处理存在基因-基因互作的双数量性状基因座（QTLs）。本研究探究考虑此类上位性（epistasis）的参数化连锁分析，是否能够提升连锁检测效能以及QTL定位的准确性。通过模拟数据分析，本研究证实，相较于未考虑上位性的分析方法，考虑上位性的分析可获得更高的LOD分值以及更精准的QTL定位结果。此外，本研究还证明，相较于核心家系，在大家系中，分析时使用互作模型与未使用互作模型时的LOD分值差异更为显著。