EMADS

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EMADS thumb5.png

Welcome! This is an informational page devoted to the EMADS consortium, the exome meta-analysis of drinking and smoking.

If you're looking for the analysis plan see this page: Analysis Plan.

Contact

If you are interested in contributing to the consortium please email Scott Vrieze or Goncalo Abecasis.

Description and Rationale

EMADS is a collaborative effort of many studies to investigate the potential role of rare exomic variation on drinking and smoking phenotypes. Through the effort we hope to extend results of previous GWAS meta-analyses of drinking and smoking as well as identify novel genetic associations. As of this writing over 20 studies plan to contribute a total of 120,000 samples. Several other studies hope to contribute but, given the novelty of the exome chip genotyping array, are awaiting completion of genotyping.

We use the exome chip as the primary genotyping technology because larger samples have been genotyped on the exome chip (compared to sequencing). However, studies with sequences are more than welcome and can easily be included in our current analysis efforts.

Organization

Primary Call

We have a primary teleconference on a monthly basis. Senior and junior investigators from each site contribute to consortium planning.

The next primary call will take place on August 16 2013 at 11am EDT (4pm BST).

Analysis Projects

Exome-Wide Meta-Analysis

The current primary goal of the EMADS consortium is an exome-wide analysis of nonsynonymous variation in smoking and drinking phenotypes.

Please see the Analysis Plan.

Detailed Evaluation of Chromosome 15 Region

We hope to expand the list of possible projects using the data available through our consortium. These may include a project headed by LiShiun Chen, Nancy Saccone and Laura Bierut on detailed analysis of the chromosome 15 region and smoking.

Guidelines for participation

While we have no strict policies or procedures, there are a few best practices guidelines to consider.

  • We believe it’s best if participants refrain from contribution to similar meta-anlayses that duplicate our efforts. Ideally, similar meta-analyses would join efforts.
  • Any work that uses data from EMADS should, at the very least, include the consortium name in the list of authors. Depending on the extent of involvement of individuals in EMADS, individual contributors should also be included in the author list.

Authorship

While authorship is decided on an individual basis for each paper (depending on contribution), typically, authorship is arranged in groups. We hope the GIANT investigators will forgive us for adopting their authorship guidelines.

  1. A group of 6 or fewer junior investigators who strongly led the efforts, usually starred to denote equal contribution, followed by additional junior investigators who played key, central roles.
  2. In alphabetical order, junior investigators who had substantial individual contributions but not as much as those in Group 1. Typically, these might be lead analysts or other junior investigators who made a sizable contribution such as GWA analyses performed specifically for the paper.
  3. In alphabetical order, junior investigators who had notable individual contributions but not as much as those in Groups 1 or 2. Typically, these might be lead analysts for replication cohorts, providing results for a group of top hits.
  4. In alphabetical order, junior and senior investigators who had contributions worthy of authorship (participating in analysis, phenotype collection, genotyping, oversight of cohorts, etc. that was specific to the paper) but not as much as those in the other groups.
  5. In alphabetical order, senior investigators who had contributions worthy of authorship and contributed more than those in group 4. Typically, these might be a lead PI of a participating cohort who did not participate as strongly in EMADS activities as those in group 6.
  6. In alphabetical order, senior investigators who participated strongly in EMADS activities but did not strongly lead/oversee the writing and/or analysis for the paper. Typically, these might be members of the EMADS steering committee or leaders of other key EMADS activities.
  7. The senior investigators who strongly led/oversaw the writing and/or analysis of the paper, including a subset that are co-corresponding authors (usually 6 or fewer).

Guidelines for Handling Proposals for Additional Analysis of EMADS Data

In consultation with Goncalo, Scott will receive and coordinate proposals for discussion during regular conference calls.

Categories of Proposals

Secondary Analyses of Existing Summary Data

At the time of this writing (5/7/2013), all summary statistics will be protected on University of Michigan servers, and curated by Scott and Goncalo. Proposals that call for analysis of existing data will be discussed by local site principal investigators. Note that some principal investigators may have to obtain permission from committees overseeing their study before sharing summary statistics from that study (e.g., for very large and/or complex cohorts). If approved, these proposals will be granted access to selected portions of the summary statistics. Any manuscript generated from these secondary analyses must not be submitted for publication until the primary EMADS manuscript has been accepted for publication.

In general, we expect most if not all proposals for secondary analysis of existing summary data to be approved.

Proposal that Require Site Investigators to Perform Additional Analysis

Proposals that request local sites to perform additional analysis will be more difficult to implement. In the end, such proposals will be "at the mercy" of local sites, who may or may not agree to conduct the proposed analyses. Such proposals can be discussed on conference calls and local sites may volunteer to participate.

Authorship for Publications Resulting from Proposals

The EMADS consortium should be listed as an author, if possible, in any resulting publication. If listing a consortium is not possible, for example due to journal guidelines, then individual EMADS investigators may be listed. Further, depending on the level of involvement from EMADS members in facilitating fulfillment of the proposal's aims, individual investigators may be named as well.

Data Security

Summary statistics of genetic variants are not truly de-identified, as they can still be used by a sufficiently sophisticated and motivated person to re-identify individuals. This concern must be taken very seriously, and any proposal to use EMADS data, even if only summary statistics, must have a plan to assure the safety and security of the data, protect against its re-release, and must guarantee that there will be no attempt to re-identify the data.

Submitting Proposals

Please submit proposals to use EMADS summary data, or to suggest additional analysis, to Scott Vrieze. Please include the following information:

  • Names of investigators, institutions, contact info, etc.
  • The data you need
  • Description of the experiment
  • If requiring additional analysis from local sites, an analysis plan
  • Timeline to completion of project
  • Authorship credit for EMADS investigators