Bailey Swneke D, Virtanen Carl, Haibe-Kains Benjamin, Lupien Mathieu
Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and Ontario Institute for Cancer Research, Toronto, ON, Canada Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and Ontario Institute for Cancer Research, Toronto, ON, Canada.
Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and Ontario Institute for Cancer Research, Toronto, ON, Canada.
Bioinformatics. 2015 Sep 15;31(18):3057-9. doi: 10.1093/bioinformatics/btv321. Epub 2015 May 20.
Detection of allelic imbalances in ChIP-Seq reads is a powerful approach to identify functional non-coding single nucleotide variants (SNVs), either polymorphisms or mutations, which modulate the affinity of transcription factors for chromatin. We present ABC, a computational tool that identifies allele-specific binding of transcription factors from aligned ChIP-Seq reads at heterozygous SNVs. ABC controls for potential false positives resulting from biases introduced by the use of short sequencing reads in ChIP-Seq and can efficiently process a large number of heterozygous SNVs.
ABC successfully identifies previously characterized functional SNVs, such as the rs4784227 breast cancer risk associated SNP that modulates the affinity of FOXA1 for the chromatin.
The code is open-source under an Artistic-2.0 license and versioned on GitHub (https://github.com/mlupien/ABC/). ABC is written in PERL and can be run on any platform with both PERL (≥5.18.1) and R (≥3.1.1) installed. The script requires the PERL Statistics::R module.
Supplementary data are available at Bioinformatics online.
检测ChIP-Seq reads中的等位基因失衡是一种强大的方法，可用于识别功能性非编码单核苷酸变异（SNV），包括多态性或突变，这些变异可调节转录因子对染色质的亲和力。我们提出了ABC，这是一种计算工具，可从杂合SNV处比对的ChIP-Seq reads中识别转录因子的等位基因特异性结合。ABC可控制因在ChIP-Seq中使用短测序reads而引入的偏差导致的潜在假阳性，并能有效处理大量杂合SNV。
ABC成功识别了先前已表征的功能性SNV，例如与乳腺癌风险相关的rs4784227 SNP，它可调节FOXA1对染色质的亲和力。
代码在Artistic-2.0许可下开源，并在GitHub（https://github.com/mlupien/ABC/）上进行版本管理。ABC用PERL编写，可在任何安装了PERL（≥5.18.1）和R（≥3.1.1）的平台上运行。该脚本需要PERL Statistics::R模块。
补充数据可在《生物信息学》在线获取。
