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BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

View ORCID ProfileInes de Santiago, Wei Liu, Martin O’Reilly, View ORCID ProfileKe Yuan, Chandra Sekhar Reddy Chilamakuri, Bruce A.J. Ponder, Kerstin B. Meyer, View ORCID ProfileFlorian Markowetz
doi: https://doi.org/10.1101/093393
Ines de Santiago
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Wei Liu
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Martin O’Reilly
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Ke Yuan
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Chandra Sekhar Reddy Chilamakuri
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Bruce A.J. Ponder
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Kerstin B. Meyer
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Florian Markowetz
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  • For correspondence: florian.markowetz@cruk.cam.ac.uk
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Abstract

Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most methods to detect allelic imbalance assume diploid genomes.This assumption severely limits their applicability to cancer samples with frequent DNA copy number changes.Here we present a Bayesian statistical approach called BaalChIP to correct for the effect of backgroundallele frequency on the observed ChIP-seq read counts. BaalChIP allows the joint analysis of multiple ChIP-seq samples across a single variant and outperforms competing approaches in simulations. Using 548 ENCODE ChIP-seq and 6 targeted FAIRE-seq samples we show that BaalChIP effectively corrects allele-specific analysis for copy number variation and increases the power to detect putative cis-acting regulatory variants in cancer genomes.

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Posted December 12, 2016.
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BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
Ines de Santiago, Wei Liu, Martin O’Reilly, Ke Yuan, Chandra Sekhar Reddy Chilamakuri, Bruce A.J. Ponder, Kerstin B. Meyer, Florian Markowetz
bioRxiv 093393; doi: https://doi.org/10.1101/093393
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BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
Ines de Santiago, Wei Liu, Martin O’Reilly, Ke Yuan, Chandra Sekhar Reddy Chilamakuri, Bruce A.J. Ponder, Kerstin B. Meyer, Florian Markowetz
bioRxiv 093393; doi: https://doi.org/10.1101/093393

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