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Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser

Nature Biotechnology volume 33, pages 345–346 (2015)Cite this article

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Advances in next-generation sequencing platforms have reshaped the landscape of functional genomic and epigenomic research as well as human genetics studies. Annotation of noncoding regions in the genome with genomic and epigenomic data has facilitated the generation of new, testable hypotheses regarding the functional consequences of genetic variants associated with human complex traits1,2. Large consortia, such as the US National Institutes of Health (NIH) Roadmap Epigenomics Consortium3 and ENCODE4, have generated tens of thousands of sequencing-based genome-wide data sets, creating a useful resource for the scientific community5. The WashU Epigenome Browser6,7,8 continues to provide a platform for investigators to effectively engage with this resource in the context of analyzing their own data. Here, we describe the Roadmap Epigenome Browser (http://epigenomegateway.wustl.edu/browser/roadmap/), which is based on the WashU Epigenome Browser and integrates data from both the NIH Roadmap Epigenomics Consortium and ENCODE in a visualization and bioinformatics tool that enables researchers to explore the tissue-specific regulatory roles of genetic variants in the context of disease.

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Figure 1: Epigenomic annotation of SNPs.

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Authors and Affiliations

  1. Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA

    Xin Zhou, Daofeng Li, Bo Zhang, Rebecca F Lowdon, Nicole B Rockweiler, Renee L Sears & Ting Wang

  2. Department of Psychiatry, Washington University in St. Louis, St. Louis, Missouri, USA

    Xin Zhou & Pamela A F Madden

  3. Department of Neurosurgery, Brain Tumor Research Center, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA

    Ivan Smirnov & Joseph F Costello

Authors
  1. Xin Zhou
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  2. Daofeng Li
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  3. Bo Zhang
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  4. Rebecca F Lowdon
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  5. Nicole B Rockweiler
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  6. Renee L Sears
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  7. Pamela A F Madden
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  8. Ivan Smirnov
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  9. Joseph F Costello
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  10. Ting Wang
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Corresponding authors

Correspondence to Joseph F Costello or Ting Wang.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Notes and Supplementary Figures 1–9 (PDF 3621 kb)

Supplementary Tutorial 1

Tutorial: Using the Roadmap EpiGenome Browser to explore integrated human epigenomics resources and annotate genetic variants (PDF 6659 kb)

Supplementary Tutorial 2

Tutorial: Cloning the Roadmap EpiGenome Browser on Amazon Cloud (PDF 2010 kb)

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Zhou, X., Li, D., Zhang, B. et al. Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser. Nat Biotechnol 33, 345–346 (2015). https://doi.org/10.1038/nbt.3158

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