Wednesday, September 26, 2018

New datasets and many new phenotypes in the T2DKP

Today we release several new datasets, including associations for many new phenotypes and individual-level data for secure interactive analysis, to the Type 2 Diabetes Knowledge Portal.

The AAGILE GWAS dataset, from the African American Glucose and Insulin Genetic Epidemiology (AAGILE) Consortium, brings more diversity of ancestry to the T2DKP, with meta-analysis of fasting glucose and BMI-adjusted fasting insulin associations from over 20,000 African American individuals. These results were combined with associations for over 57,000 individuals of European ancestry from the Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC) in a trans-ethnic meta-analysis.

This release also adds two new diabetic kidney disease datasets from the SUMMIT (SUrrogate markers for Micro- and Macro-vascular hard endpoints for Innovative diabetes Tools) consortium. All of the more than 40,000 subjects in the "Diabetic Kidney Disease GWAS: subjects with T1D or T2D" dataset had either type 1 or type 2 diabetes. The study measured seven different renal phenotypes in these subjects, including four that are new to the T2DKP. Summary association results are available for the entire group and for sub-cohorts that separate T1D from T2D and European from Asian ancestry. A separate dataset from SUMMIT, "Diabetic Kidney Disease GWAS: subjects with T1D or T2D, ESRD vs. controls" is comprised of more than 5,600 diabetics, nearly 1,200 of whom had end-stage renal disease. These two datasets greatly expand the range of diabetic complications for which genetic association data are available in the T2DKP.

The T2DKP is federated, meaning that in addition to the Data Coordinating Center at the Broad Institute, some results are drawn from a sister site at the European Bioinformatics Institute (EMBL-EBI). This system allows data that may not leave Europe to be represented in the T2DKP. Six of the new datasets in this release are housed at the T2DKP Federated Node at EMBL-EBI.

The Hoorn Diabetes Care System (DCS) dataset includes associations for 12 different anthropometric, blood lipid, blood pressure, and liver and kidney function measures for a cohort of over 3,400 type 2 diabetics in the Netherlands.

The GoDarts project (Genetics of Diabetes Audit and Research in Tayside Scotland) recruits type 2 diabetics and matching controls in the Tayside region of Scotland. This release includes five new datasets from GoDarts, representing experiments performed using different arrays. Each experiment determined genetic associations for a wide variety of phenotypes, including two that are new to the T2DKP: levels of adiponectin and leptin, hormones that are associated with risk of T2D and obesity.

Results from all of these datasets may be searched using the Variant Finder tool and may be browsed:

• On Gene Pages in the Common variants and High-impact variants tables and in LocusZoom plots;

• On Variant Pages in the Associations at a glance section, the Associations across all datasets section, and in LocusZoom plots;

• From the View full genetic association results for a phenotype search on the home page: first select a phenotype, then select a dataset on the resulting page.

Individual-level data from the Hoorn DCS and GoDarts datasets also power secure interactive analyses using the Genetic Association Interactive Tool (GAIT) on Variant Pages. With the new additional data, nearly 61,000 individual-level samples are now available for custom association analysis.

Please take a look at the new results and contact us any time with questions or suggestions!