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Accurate eQTL prioritization with an ensemble-based framework

Haoyang Zeng, Matthew D. Edwards, Yuchun Guo, David K. Gifford
doi: https://doi.org/10.1101/069757
Haoyang Zeng
Computer Science and Artificial Intelligence Lab, MIT, Cambridge, MA 02139
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Matthew D. Edwards
Computer Science and Artificial Intelligence Lab, MIT, Cambridge, MA 02139
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Yuchun Guo
Computer Science and Artificial Intelligence Lab, MIT, Cambridge, MA 02139
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David K. Gifford
Computer Science and Artificial Intelligence Lab, MIT, Cambridge, MA 02139
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Abstract

Expression quantitative trait loci (eQTL) analysis links sequence variants with gene expression change and serves as a successful approach to fine-map variants causal for complex traits and understand their pathogenesis. In this work, we present an ensemble-based computational framework, EnsembleExpr, for eQTL prioritization. When trained on data from massively parallel reporter assays (MPRA), EnsembleExpr accurately predicts reporter expression levels from DNA sequence and identifies sequence variants that exhibit significant allele-specific reporter expression. This framework achieved the best performance in the “eQTL-causal SNPs” open challenge in the Fourth Critical Assessment of Genome Interpretation (CAGI 4). We envision EnsembleExpr to be a powerful resource for interpreting non-coding regulatory variants and prioritizing disease-associated mutations for downstream validation.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 16, 2016.
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Accurate eQTL prioritization with an ensemble-based framework
Haoyang Zeng, Matthew D. Edwards, Yuchun Guo, David K. Gifford
bioRxiv 069757; doi: https://doi.org/10.1101/069757
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Accurate eQTL prioritization with an ensemble-based framework
Haoyang Zeng, Matthew D. Edwards, Yuchun Guo, David K. Gifford
bioRxiv 069757; doi: https://doi.org/10.1101/069757

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