The meeting featured: 1) two half-days for working group meetings; 2) two half-day general assembly sessions on; 3) a group dinner; and 4) a joint meeting with ENCODE investigators on Friday.
The CHARGE general assembly sessions included talks on rare variant analysis, sequencing, family studies approaches, as well as presentations from several working groups. The joint session with ENCODE featured formal presentations and hands-on workshops in the use of ENCODE data. The goal of this session was to further develop collaborations between CHARGE and ENCODE investigators.
An overview of the meeting, including links to meeting materials, is provided below.
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Structure / Final Agenda / Meeting Program
CHARGE investigator meetings may include unpublished scientific results that arise from individual efforts put into the CHARGE Consortium and are intended to enabling investigators to share confidential results from their undisclosed and unpublished work. Open discussion is fundamental to the attainment of the aims and goals of the CHARGE Consortium and all attendees will be required to sign a non-disclosure agreement.
The following publications have been recommended for review prior to attending the ENCODE Workshop.
The main ENCODE Project website is at http://www.encodeproject.org
This site includes links to software tools and databases of interest (see lists under http://www.encodeproject.org/ENCODE/softwareTools.html ). Some of the key links from this site are as follows:
The main report of the results to date from ENCODE, published as many papers in several journals simultaneously in 2012, can be navigated at http://www.nature.com/encode
Two commonly used web tools for integrating ENCODE data with GWAS data are:
GENCODE is a catalog of all human and mouse genes and transcripts, including many noncoding RNA genes, developed using ENCODE data ( http://www.gencodegenes.org/ ). Two relevant references are:
The matrix of cell types and data types for which data are available from both ENCODE and the NIH Epigenome Roadmap can be found at http://www.encode-roadmap.org/
Tutorials presented at ASHG 2013 on the use of ENCODE and NIH Epigenome Roadmap data can be found at http://www.genome.gov/27555330 .
The tutorials on “Predicting the Target Gene for a Distal Regulatory Region” and “Predicting Distal Regulatory Regions for a Gene” may be especially useful when you need to link genes to distal regulatory regions.