Wednesday, May 3, 2017

Explore new datasets and phenotypes in the T2D Knowledge Portal

We are releasing multiple new datasets in the Portal and have updated existing sets with associations for new phenotypes. To make it even easier to browse and explore these sets, we've also updated our Data page and added new functionality. Here's an overview of what's new in the Portal today.

17K exome sequence analysis dataset has grown to 19K
The Data Coordinating Center (DCC) of the Accelerating Medicines Partnership in Type 2 Diabetes (AMP T2D) analyzes exome sequence data contributed by AMP T2D consortium members to find variant associations with T2D and related traits. The exome sequencing dataset available in the Portal has until now consisted of exome sequences from about 17,000 individuals. Today, we have added exome sequencing performed on 2,000 Danish subjects by the LuCamp (Lubeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention and Care) consortium, making a total of nearly 19,000 exomes. This is just a taste of things to come: at the AMP T2D DCC we are currently analyzing additional exome sequences that will bring the total up to 52,000!

New community-contributed datasets: GENESIS GWAS and 70KforT2D GWAS

We are grateful to two groups from the larger T2D research community who have shared data that will make the T2D Knowledge Portal even more valuable to worldwide T2D researchers.

The GENEticS of Insulin Sensitivity (GENESIS) consortium performed GWAS on over 2,700 nondiabetic participants, finding genetic associations with direct measures of insulin sensitivity.

The 70KforT2D project collected, harmonized, and re-analyzed public GWAS data from over 70,000 individuals to find T2D genetic associations.

New public dataset: VATGen GWAS

The VATGen GWAS consortium performed meta-analysis of GWAS data from a mixed-ancestry group of more than 18,000 people to identify genetic associations with the localization of body fat deposition, leading to insights into adipocyte development.

Updated dataset: glucose-stimulated insulin secretion phenotypes in MAGIC GWAS

A study by Prokopenko et al. analyzed genetic associations with insulin secretion. Associations of variants with nine different measures of insulin secretion, among them corrected insulin response (CIR) and disposition index (DI), have now been added to the MAGIC GWAS dataset.

ExAC updated to gnomAD exomes and whole genomes
The Exome Aggregation Consortium (ExAC) has more than doubled in size and has morphed into the Genome Aggregation Database (gnomAD). More than 120,000 exome sequences and 15,000 whole genome sequences are now available, and these data are accessible via several tools and interfaces in the T2D Knowledge Portal.

New Data page: explore datasets using new filters

As our collection of data grows, it becomes more difficult to understand the differences between datasets and to find those of interest. To address this challenge, we've reorganized and streamlined our Data page.

A section of the Data page, expanded to show phenotype selection.

At the top of the Data page, you can choose to filter the dataset table by data type, phenotype category, or both. When you click on a phenotype category, the phenotypes within that category are available for selection. Clicking on the name of any dataset expands a section with details and references for each. 

In the coming days, watch this space for more details about each of these new developments. And as always, please contact us if you have any comments or questions.

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