On the aggregation of multimarker information for marker-set and sequencing data analysis: Genotype collapsing vs. Similarity collapsing

Monnat Pongpanich, Megan L. Neely, Jung Ying Tzeng

研究成果: Article同行評審

9 引文 斯高帕斯(Scopus)

摘要

Methods that collapse information across genetic markers when searching for association signals are gaining momentum in the literature. Although originally developed to achieve a better balance between retaining information and controlling degrees of freedom when performing multimarker association analysis, these methods have recently been proven to be a powerful tool for identifying rare variants that contribute to complex phenotypes. The information among markers can be collapsed at the genotype level, which focuses on the mean of genetic information, or the similarity level, which focuses on the variance of genetic information. The aim of this work is to understand the strengths and weaknesses of these two collapsing strategies. Our results show that neither collapsing strategy outperforms the other across all simulated scenarios. Two factors that dominate the performance of these strategies are the signal-to-noise ratio and the underlying genetic architecture of the causal variants. Genotype collapsing is more sensitive to the marker set being contaminated by noise loci than similarity collapsing. In addition, genotype collapsing performs best when the genetic architecture of the causal variants is not complex (e.g., causal loci with similar effects and similar frequencies). Similarity collapsing is more robust as the complexity of the genetic architecture increases and outperforms genotype collapsing when the genetic architecture of the marker set becomes more sophisticated (e.g., causal loci with various effect sizes or frequencies and potential non-linear or interactive effects). Because the underlying genetic architecture is not known a priori, we also considered a two-stage analysis that combines the two top-performing methods from different collapsing strategies. We find that it is reasonably robust across all simulated scenarios.

原文English
文章編號Article 110
期刊Frontiers in Genetics
2
發行號JAN
DOIs
出版狀態Published - 2012

All Science Journal Classification (ASJC) codes

  • 分子醫學
  • 遺傳學
  • 遺傳學(臨床)

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