The first CHARGE Investigator Meeting of 2013 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.

Meeting Information

Structure / Final Agenda / Meeting Program 


CHARGE

ENCODE


Wednesday

January 22

Thursday

January 23

Friday

January 24

Morning

(8am-noon)

Working Group Meetings

50 minute blocks / 
concurrent sessions

 8:00- Blood Pressure
- Adiposity
- Stroke 
 8:50- Hemostasis
- Gene-Lifestyle
- Dementia
10:00- Gene Expression
- Subclinical/CHD
- Cognition
10:50- Commons
- Microbiome
- Hearing

Main Assembly

Rare Variants

Analysis Presentations

Working Group Presentations

Population vs. Family Study

Rare Variants in Rare Disorders

Main Assembly

Intro to ENCODE

Chromatin/regulation data

RNA data

Integrating ENCODE & GWAS

Specific Examples

Q&A / Panel

Afternoon

(1-5:30pm)


Main Assembly

Cloud Computing

Working Group Presentations

Tissues & Organelles

Family Studies


Working Group Meetings

50 minute blocks / 
concurrent sessions

2:00- Analysis/Bioinfo
- Bone
- DM/Glycemia 
2:50- ExomeChip/ENCODE
- Social Science
- Insulin-like GF
4:00- Pharmacogenetics
- Lipids
- Pulmonary
4:50- Family Studies
- Nutrition
- Epigenetics

Workshop

Introduction to Metadata

3 blocks / 8 concurrent

  1. Browsing the Metadata

  2. Computing on the metadata* 

  3. RNASeq and GENCODE

  4. ChIP-Seq and DNase-Seq (intro)

  5. RNA-Seq* 

  6. DNasel-Seq and ChIP-Seq (adv)*

  7. HaploReg, RegulomeDB, and ENSEMBL VEP

  8. BEDOPS/BEDTOOLS w/GWAS*

Evening

    

Poster Session / Reception

--

Dinner (on your own)

Jr. Investigator Informal Dinner @ BALEEN

Social Drinks @ Hudson House 

Group Dinner/Activity

"California Dreaming" @Crowne Plaza

Reception


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CHARGE investigator meetings may include unpublished scientific results that arise from individual efforts put into the CHARGE Consortium and are intended to enabling investigators to share confidential results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


Hotel

Directions

 From Los Angeles International Airport (LAX): From the 405 Freeway North:
  • Take Sepulveda Blvd. South for 7 miles
  • Right on Beryl St.
  • LEFT on Harbor Drive (Hotel is on the left)
  • Take the Western. Exit and go LEFT.
  • Go under the Freeway, then immediately
  • Right on 190th St. to the end.
  • LEFT on Harbor Drive (Hotel is on the left)
  From Los Angeles (Downtown):  From 405 Freeway South:
  • Take the Harbor Freeway 110 South to the 105 West.
  • Take Sepulveda Blvd. South for 7 miles
  • Right on Beryl St.
  • LEFT on Harbor Drive (Hotel is on the left)
  • Take the Inglewood Ave. Exit, Take a RIGHT.
  •  Right on 190th St. to the End
  • LEFT on Harbor Drive (Hotel is on the left)


ENCODE Workshop

The following publications have been recommended for review prior to attending the ENCODE Workshop.

 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 

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

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

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:

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:

 

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 

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.

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