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CHS Meta-Analysis Policy

 

CHS Meta-Analysis Policy – as of April 15, 2014

Please see the table below to determine the level of CHS review required for your meta-analysis.

Overview:

A meta-analysis manuscript uses CHS data in conjunction with data from one or more other cohort or case-control studies. Like regular CHS manuscript proposals, all meta-analyses require the analysis of individual level CHS data. In most cases, meta-analyses require CHS review of both manuscript proposal and the penultimate draft manuscript.

Because genetic studies have typically been meta-analyses, CHS has provided some simplifying methods for their review and approval. For a meta-analysis of a new phenotype in genome-wide association studies, for instance, the use of standard methods can be summarized in an abbreviated ms (one page for part II). For multiple new analyses that use a common set of genotypes (such as the exome chip or the exome sequencing in ESP), an omnibus manuscript proposal can serve as the basis of analysis for multiple phenotypes.

Examples of Omnibus Proposals (Requires Internal site access):

  • CHARGE GWAS Omnibus #3998: Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium: Design of prospective meta-analyses of genome-wide association studies from 5 cohorts.
  • CHARGE-S omnibus #6016: Omnibus CHARGE-S proposal for meta-analysis of sequence data.
  • ESP-Go omnibus #4798: Omnibus ESP-GO proposal for analysis of sequence data
  • Exome chip omnibus #6015: Omnibus proposal for meta-analyses of exome-chip rare-variant data and various phenotypes in CHS

The papers published from these analyses will be associated with a fixed set of association results. Some but not all association results will appear in the final paper. On occasion, the full set of association results is posted on a website (subject to approval by the CHS Steering Committee).

Criteria for manuscript proposals:

The publication of a genetic association study is often followed by other work, sometimes participation in a larger meta-analysis, sometime a request for replication from another group, sometimes an expanded analysis. In general, new or additional analyses, even analyses for a few genetic variants, will require a new manuscript proposal. Simple look-ups from already-analyzed association results for published papers will not generally require a new manuscript proposal. If the expanded analysis is within the scope of the original request--for instance, whites and blacks were to be included, but the first manuscript focused only on whites, then no new paper proposal is required for a new analysis of the same phenotype in blacks, but the penultimate draft manuscript must be reviewed by the P&P (Publications) Committee.

Criteria for review of penultimate draft manuscripts:

Manuscripts of meta-analyses that use CHS genetic data in major discovery or replication efforts, whether or not new analyses were required, should be submitted to the CHS Publications Committee for review and approval. Manuscripts that use "look-ups" of a few associations from an approved and published meta-analysis, if no new analyses are needed, do not require review by CHS. The same goes for manuscripts that use population allele frequencies. If possible, these manuscripts should cite the original paper, and acknowledge the CHS funding sources.

Expedited Review of Penultimate Draft Manuscripts:

All requirements governing the review of penultimate drafts of CHS manuscripts also apply to the review of meta-analysis draft manuscripts, with the following exception:

There is no distributed P&P Committee review by expertise. The CHS Sponsor serves as the primary internal reviewer for CHS. Along with the standard criteria for submission of a penultimate draft manuscript, the sponsor needs to provide a brief summary of the paper and confirm that CHS is correctly represented and that CHS data have been accurately characterized. This cover note will accompany the draft through a combined, expedited 1-week review by the P&P and Steering Committees.

Sample Cover note
 

 

CHS REVIEW REQUIREMENTS FOR META-ANALYSES:

 

 

Specific Meta-Analysis Situation

Level of CHS Review Needed

Example

Use of Unpublished data

1.

New Meta-analysis that is NOT from a genetic consortium

  • MS proposal
  • Penultimate Draft MS

 

2.

New Meta-analysis on a genetic association with a specific phenotype (one of many papers from a single genetic study that all use similar methods)

  • Proposal
  • Penultimate Draft MS

CARe (unless proposal was already approved by CARe P&P Committee)

3.

Multiple new analyses on a common theme, all with the same methods - WITH NO NEW DATA NEEDED

  • Single project “omnibus” MS proposal (1-time only)
  • Separate Penultimate Draft MSS

CHARGE GWAS (unless a proposal was previously submitted), CHARGE-S, ESP, ERFC, FSC

4.

Multiple new analyses on a common theme, all with the same methods - WITH NEW DATA NEEDED

  • MS proposal
  • Penultimate Draft MS

Some CHARGE, PAGE metabochip

5.

Splitoff : separate meta-analysis resulting from division of a previously approved proposal

  • Penultimate Draft MS

 

 

6.

Re-use of previously analyzed data from an approved ms proposal for use in a  new analysis, such as:

  • Replications
  • expanded or new consortia
  • imputations to a different panel
  • different part of the same cohort

 

  • Penultimate Draft MS

 

Use of Previously Published data or results

10.

Re-use of previously published  summary data in a new analysis (we do not publish individual level data)

 

  • Penultimate Draft MS

 

11.

Re-use of previously published data for an in-silico look-up and replication (no new analyses)

 

  • No review required, but counts as a CHS paper
  • Authors should if possible acknowledge CHS funding and forward to CHS

 

12.

Use of published population allele frequencies from prior CHS meta-analyses (no phenotypic data used)

 

  • No review required
  • Not tracked as CHS papers

 

13.

Re-use of previously published results in a new analysis

  • No review required
  • Not tracked as CHS papers

 

 

Related Links

General Guidelines for Publications and Presentations
Objectives of the CHS Publications and Presentations Committee
Classification of CHS Manuscripts
Funding of CHS Manuscripts