preprint · bioRxiv (Cold Spring Harbor Laboratory) · 2014

LIMIX: genetic analysis of multiple traits

Christoph Lippert, Franceso Paolo Casale, Barbara Rakitsch, Oliver Stegle

Cited by 132Open access

Abstract

Abstract Multi-trait mixed models have emerged as a promising approach for joint analyses of multiple traits. In principle, the mixed model framework is remarkably general. However, current methods implement only a very specific range of tasks to optimize the necessary computations. Here, we present a multi-trait modeling framework that is versatile and fast: LIMIX enables to flexibly adapt mixed models for a broad range of applications with different observed and hidden covariates, and variable study designs. To highlight the novel modeling aspects of LIMIX we performed three vastly different genetic studies: joint GWAS of correlated blood lipid phenotypes, joint analysis of the expression levels of the multiple transcript-isoforms of a gene, and pathway-based modeling of molecular traits across environments. In these applications we show that LIMIX increases GWAS power and phenotype prediction accuracy, in particular when integrating stepwise multi-locus regression into multi-trait models, and when analyzing large numbers of traits. An open source implementation of LIMIX is freely available at: https://github.com/PMBio/limix .

Cite this paper

APA 7

Lippert, C., Casale, F. P., Rakitsch, B., & Stegle, O. (2014). LIMIX: genetic analysis of multiple traits. bioRxiv (Cold Spring Harbor Laboratory). https://doi.org/10.1101/003905

MLA 9

Lippert, Christoph, et al. “LIMIX: genetic analysis of multiple traits.” bioRxiv (Cold Spring Harbor Laboratory), 2014, https://doi.org/10.1101/003905.

Chicago

Lippert, Christoph, Franceso Paolo Casale, Barbara Rakitsch, and Oliver Stegle. 2014. “LIMIX: genetic analysis of multiple traits.” bioRxiv (Cold Spring Harbor Laboratory). https://doi.org/10.1101/003905.

Harvard

Lippert, C. et al. (2014) ‘LIMIX: genetic analysis of multiple traits’, bioRxiv (Cold Spring Harbor Laboratory). Available at: https://doi.org/10.1101/003905.

BibTeX

@misc{lippert2014limix,
  title = {{LIMIX: genetic analysis of multiple traits}},
  author = {Lippert, Christoph and Casale, Franceso Paolo and Rakitsch, Barbara and Stegle, Oliver},
  journal = {bioRxiv (Cold Spring Harbor Laboratory)},
  year = {2014},
  doi = {10.1101/003905}
}

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