Request for Information (RFI): Research Needs to Facilitate Broad Community Use of the Roadmap Epigenomics Program Data Resource

Notice Number: NOT-RM-13-011

Key Dates
Release Date: February 22, 2013
Response Date: March 29, 2013

Issued by
National Institutes of Health (NIH)
Office of Strategic Coordination (Common Fund)

Purpose

The purpose of this Request for Information (RFI) is to solicit feedback from the community in an effort to identify the highest priority areas to pursue to facilitate broad use of the public data resource developed by the Roadmap Epigenomics Program, funded as part of the NIH Common Fund. 

Background

The Roadmap Epigenomics Program was established to further our understanding of the critical role epigenetic mechanisms play in normal human development, and in disease. A key component of this program are the Reference Epigenome Mapping Centers, a consortium focused on creating a public database of reference epigenomic maps for a variety of normal, primary human cells and tissues, including pluripotent lineages.  To date, over 2300 datasets are available for download at NCBI (http://www.ncbi.nlm.nih.gov/geo/roadmap/epigenomics/), spanning over 150 unique cell and tissue types. More than 50 of these cell/tissue types can be considered “complete epigenomes”, i.e. they contain data for a broad set of modifications/features including DNA methylation, a panel of histone modifications, RNA expression, and in many cases DNase I hypersensitivity mapping (see http://www.roadmapepigenomics.org/complete_epigenomes for a detailed view of the four classes of complete epigenome). As the field has continued to develop and technologies for mapping have improved, the methods used by the consortium have also changed. For example, the resource includes DNA methylation data generated using reduced-representation bisulfite sequencing (RRBS), a combination of MeDIP-seq/MRE-seq, and whole-genome bisulfite sequencing; mRNA expression data has been generated using microarrays or RNA-seq.

As the Reference Epigenome Mapping Center's mapping efforts near completion, the program continues its efforts to ensure that the data generated is broadly used by the scientific community. The purpose of this Request for Information is to solicit feedback from the community in an effort to identify the highest priority areas to pursue to facilitate broad use of the resource.

Information requested

In order to maximize the impact of this valuable community resource, and facilitate its use by scientists with a broad range of expertise, we seek input on several topics and issues. We request feedback from the scientific community to assist in identifying and prioritizing research needs and gaps, especially in the following areas:

Data presentation/accessibility: What challenges have you faced when using reference epigenome data generated by the Roadmap Epigenomics Program? What additional tools or information are needed to make these and other similar datasets useful to the broader research community (e.g. tools for data mining)? 

Data analysis: What biological questions can now be addressed using reference epigenome datasets produced by the consortium? What methods or tools would facilitate analysis of user-generated datasets relative to reference epigenomic data?

Data integration: What roadblocks prevent integration of reference epigenome data with other kinds of data, such as other public or user-generated epigenomic datasets (e.g. ENCODE), genome-wide association studies (GWAS) and genotype data, transcriptomic, metabolomic, or other –omic data sets? Are new analytical methods or tools needed to facilitate such integrative analyses? What methods are needed to integrate different epigenomic data types? What methods are needed to enable integrated analyses of related data types, i.e. those generated by different platforms (such as Illumina 450K arrays), with different levels of coverage, or from multiple individuals or time points?

Submitting a response

This RFI is for planning purposes only, and is not a solicitation for applications or an obligation to provide support for any of the ideas identified in response to it. Response to this RFI is voluntary. Responders are free to address any or all of the categories listed above.

Please include the following information in your response:
1. Your name
2. Your email address
3. Your organization
4. Your main area of research interest

To ensure consideration, your response must be sent to epigenomics@niehs.nih.gov and received by midnight on March 29, 2013.

No basis for claims against the U.S. Government shall arise as a result of a response to this request for information or from the Government’s use of such information.

Inquiries

Please direct all inquiries to:

Lisa Helbling Chadwick, Ph.D.
National Institute of Environmental Health Sciences
Phone: (850) 727-7218
Email: chadwickL@niehs.nih.gov


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