Tuesday, January 17, 2017

New Year, New Data: BioMe AMP T2D GWAS

We’re happy to announce the first addition of data to the Type 2 Diabetes Knowledge Portal in 2017: the BioMe AMP T2D GWAS data set. The generation of these data was funded by the Accelerating Medicines Partnership in Type 2 Diabetes (AMP T2D), a collaboration between multiple stakeholders that aims to catalyze the clinical translation of genetic discoveries by producing and aggregating data, developing and implementing novel analytical methods and tools, and building infrastructure for data storage and presentation.

The BioMe AMP T2D GWAS data set is the first set to be entirely produced by the AMP T2D project, which supplied the funding and carried out every step of its production, from data generation to analysis, quality control, and presentation. Its immediate availability in the Portal, prior to publication, fulfills the mission of AMP T2D to speed up access to and utilization of new data.

These data were generated at the Charles Bronfman Institute for Personalized Medicine BioMe BioBank, a biorepository located at the Mount Sinai Medical Center (MSMC) in the upper Manhattan area of New York City. MSMC serves a diverse population of over 800,000 outpatients each year. Importantly, since many BioMe participants are African American or Hispanic Latino, this data set adds significant ethnic diversity to the Portal’s genetic association data.

The BioMe AMP T2D GWAS data set is comprised of about 13,000 unique individuals, 41.5% of whom are admixed American, 38% African American, and 20% European. Subjects were genotyped using at least one of three platforms: the Illumina Exome Array, the Illumina GWAS array, or the Affymetrix GWAS array. Their T2D status was assessed by an algorithm, and many additional traits were also measured.

The data were subjected to quality control and association analysis by the Analysis Team at the AMP Data Coordinating Center (DCC) at the Broad Institute. Variant associations with T2D, fasting glucose levels, and HbA1c levels were analyzed. The top results included both previously known and novel variants, with only a single variant reaching genome-wide significance: T2D association of the variant rs7903146, within the well-established T2D risk gene TCF7L2. Now that these results are available in the T2D Knowledge Portal, the ability to analyze them further in the context of all other available T2D association data may lead to additional insights.

The BioMe AMP T2D GWAS data currently has the “Early Access Phase 1” status that is assigned to new data. This status denotes that although analysis and quality control checks have been performed, the data are not yet considered to be in their final state. During the early access period, users may analyze the data but may not submit the results of these analyses for publication. Find the full details about the different phases of data release on our Policies page. More information about the data set, along with links to download even more detailed reports on its quality control and analysis, may be found in the BioMe AMP T2D GWAS section of our Data page.

BioMe AMP T2D GWAS data are available at these locations in the Portal:

  • On Gene Pages (see an example) in the Variants & Associations table and the Minor allele frequencies across data sets table
  • On Variant Pages  (see an example) in the Associations at a glance section and in the Association statistics across traits table
  • Via the Variant Finder tool, for these phenotypes: type 2 diabetes; fasting glucose adjusted for age and sex; HbA1c adjusted for age and sex; and HbA1c adjusted for age, sex, and body mass index
  • A "Manhattan plot" of associations across the genome may be seen by selecting one of the phenotypes above in the View full genetic association results for a phenotype scroll box on the Portal home page, and then selecting the BioMe AMP T2D GWAS data set.

As always, please contact us with any questions, comments, or suggestions.

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