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Integrative cross-omics and cross-context analysis elucidates molecular links underlying genetic effects on complex traits

Author

Listed:
  • Yihao Lu

    (The University of Chicago)

  • Meritxell Oliva

    (The University of Chicago
    AbbVie)

  • Brandon L. Pierce

    (The University of Chicago)

  • Jin Liu

    (The Chinese University of Hong Kong-Shenzhen)

  • Lin S. Chen

    (The University of Chicago)

Abstract

Genetic effects on functionally related ‘omic’ traits often co-occur in relevant cellular contexts, such as tissues. Motivated by the multi-tissue methylation quantitative trait loci (mQTLs) and expression QTLs (eQTLs) analysis, we propose X-ING (Cross-INtegrative Genomics) for cross-omics and cross-context integrative analysis. X-ING takes as input multiple matrices of association statistics, each obtained from different omics data types across multiple cellular contexts. It models the latent binary association status of each statistic, captures the major association patterns among omics data types and contexts, and outputs the posterior mean and probability for each input statistic. X-ING enables the integration of effects from different omics data with varying effect distributions. In the multi-tissue cis-association analysis, X-ING shows improved detection and replication of mQTLs by integrating eQTL maps. In the trans-association analysis, X-ING reveals an enrichment of trans-associations in many disease/trait-relevant tissues.

Suggested Citation

  • Yihao Lu & Meritxell Oliva & Brandon L. Pierce & Jin Liu & Lin S. Chen, 2024. "Integrative cross-omics and cross-context analysis elucidates molecular links underlying genetic effects on complex traits," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46675-0
    DOI: 10.1038/s41467-024-46675-0
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