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The first CHARGE Investigator Meeting of 2014 was held in Los Angeles California on, Wednesday–Friday, January 22-24, 2014. 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.
Wednesday
January 22
Working Group Meetings
Afternoon
Afternoon
(1-5:30pm)
(1-5:30pm)
Main Assembly
Cloud Computing
Working Group Presentations
Tissues & Organelles
Family Studies
Poster Session / Reception
--
Dinner (on your own)
Jr. Investigator Informal Dinner @ BALEEN
Social Drinks @ Hudson House
Thursday
January 23
Main Assembly
Rare Variants
Analysis Presentations
Working Group Presentations
Population vs. Family Study
Rare Variants in Rare Disorders
Working Group Meetings
50 minute blocks /
concurrent sessions
Group Dinner/Activity
"California Dreaming" @Crowne Plaza
Friday
January 24
Main Assembly
Intro to ENCODE
Chromatin/regulation data
RNA data
Integrating ENCODE & GWAS
Specific Examples
Q&A / Panel
ENCODE Workshop
Introduction to Metadata
3 blocks / 8 concurrent
Browsing the Metadata
Computing on the metadata*
RNASeq and GENCODE
ChIP-Seq and DNase-Seq (intro)
RNA-Seq*
DNasel-Seq and ChIP-Seq (adv)*
HaploReg, RegulomeDB, and ENSEMBL VEP
BEDOPS/BEDTOOLS w/GWAS*
Reception
Confidentiality
Confidentiality
CHARGE investigator meetings may include unpublished scientific results that arise from individual efforts put into the CHARGE Consortium and are intended to enabling investigators to share confidential results from their undisclosed and unpublished work.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.
Location
Location
ENCODE Workshop
ENCODE Workshop
The following publications have been recommended for review prior to attending the ENCODE Workshop.
Recommended reading
Recommended reading
Beyond GWASs: illuminating the dark road from association to function.
Edwards SL, Beesley J, French JD, Dunning AM. Am J Hum Genet. 2013 Nov 7;93(5):779-97. doi: 10.1016/j.ajhg.2013.10.012. Review. PMID: 24210251
Systematic localization of common disease-associated variation in regulatory DNA.
Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, Stamatoyannopoulos JA. Science. 2012 Sep 7;337(6099):1190-5. doi: 10.1126/science.1222794. Epub 2012 Sep 5. PMID: 22955828 Free PMC Article
A user's guide to the encyclopedia of DNA elements (ENCODE).
ENCODE Project Consortium. PLoS Biol. 2011 Apr;9(4):e1001046. doi: 10.1371/journal.pbio.1001046. Epub 2011 Apr 19. PMID: 21526222 Free PMC Article
Additional references and web links
Additional references and web links
The ENCODE Project
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:
HaploReg: http://www.broadinstitute.org/mammals/haploreg/haploreg.php
RegulomeDB: http://regulome.stanford.edu/
Regulatory Elements Database: http://dnase.genome.duke.edu/
BEDOPS software: http://code.google.com/p/bedops/
BEDTOOLS software: http://code.google.com/p/bedtools/
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
Web Tools
Two commonly used web tools for integrating ENCODE data with GWAS data are:
HaploReg: Ward and Kellis, HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants, Nucleic Acids Res 40:D930-4 (2012). http://nar.oxfordjournals.org/content/40/D1/D930.long
RegulomeDB: Boyle et al, Annotation of functional variation in personal genomes using RegulomeDB, Genome Res 22:1790-7 (2012). http://genome.cshlp.org/content/22/9/1790.long
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:
Harrow et al, GENCODE: The reference human genome annotation for The ENCODE Project. Genome Res 22:1760-74 (2012). http://genome.cshlp.org/content/22/9/1760.long
Derrien et al, The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res 22:1775-89 (2012). http://genome.cshlp.org/content/22/9/1775.long
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
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.
Meeting Materials:
Meeting Materials:
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