Thursday, January 19, 2017

CAMP GWAS data set moves to Early Access Phase 2

Three months ago, we incorporated a data set from the MGH Cardiology and Metabolic Patient Cohort (CAMP) into the T2D Knowledge Portal. These data were contributed by Pfizer, Inc. as part of a public-private partnership to generate genotype data for a cardiometabolic and prediabetic cohort; they add individual-level genetic association data for type 2 diabetes (T2D), fasting glucose levels, and fasting insulin levels from more than 3,500 samples to the Portal knowledgebase. Now, the CAMP GWAS data set has transitioned to Early Access Phase 2 status in the Portal.

The CAMP GWAS data set was the first to be included in the Portal with “Early Access” status, which is assigned to new data. As described on our Policies page, all newly added data sets have Early Access status for the first six months that they are in the Portal. In the first three months, Phase 1 of the Early Access period, the data have undergone quality control checks but they are not considered to be in their final form. The purpose of Phase 1 is to allow Portal users to review and analyze the data in order to identify any potential problems or areas needing further analysis. After this three-month period, data sets move to Phase 2, indicating that the data are in final form and are fully integrated into the Portal.

Portal users must not submit manuscripts concerning new data until both Phase 1 and Phase 2 of the Early Access period have passed, and any results of analyses or proposed publications are subject to the "Fort Lauderdale Principles" articulated for the sharing of genomic data.

In three months, the CAMP GWAS data set will become Open Access, meaning that it may be freely used for research as long as Portal users comply with our guidelines on user responsibilities and proper citation. It is important to note that in order to protect patient privacy, individual-level data in the Portal are never directly accessible to users. Rather, the Portal makes available summary statistics derived from the data, and also provides tools (such as the Genetic Association Interactive Tool (GAIT) and the Interactive Burden Test) that allow users to perform custom analyses based on individual-level data while protecting the security and privacy of those data.

Find CAMP data at all of these locations in the Portal:

  • On Gene Pages (e.g.,  HLA-C) in the Variants & Associations table.
  • On Variant Pages (e.g., rs9468919) in the Associations at a glance section and in the Association statistics across traits table.
  • Via the Variant Finder tool, for the phenotypes T2D, fasting glucose, and fasting insulin.
  • Via the Genetic Association Interactive Tool (GAIT), which enables custom association analysis for either single variants (available on Variant Pages) or for the set of variants in and near a gene (Interactive burden test, available on Gene Pages).
  • A "Manhattan plot" of genetic associations across the genome may be accessed by selecting the phenotype T2D, fasting glucose, or fasting insulin in the "View full genetic association results for a phenotype" selection box on our home page, and then choosing the CAMP GWAS data set.

Find many more details about the CAMP GWAS data set on our Data page, or read a summary in this blog post.

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