Tuesday, October 18, 2016

New and updated data in the T2D Knowledge Portal

As members of the T2D Knowledge Portal team arrive in Vancouver for the American Society of Human Genetics meeting, we are pleased to announce that we have added a new data set to the Portal and made extensive updates to existing data sets. 

The new data set, named “CAMP GWAS” in the Portal, comes from the MGH Cardiology and Metabolic Patient Cohort (CAMP). These data were contributed by Pfizer, Inc. as part of a public-private partnership to generate genotype data for a cardiometabolic and prediabetic cohort, and were analyzed by the Analysis Team of the Accelerating Medicines Partnership Data Coordinating Center (AMP-DCC) at the Broad Institute. The set adds individual-level genetic association data for type 2 diabetes (T2D), fasting glucose levels, and fasting insulin levels from nearly 3,500 samples to the Portal knowledgebase, and association data for more phenotypes will be added in the future.

CAMP data may be accessed on Gene and Variant pages in the Portal and via the Variant Finder, and may also be filtered and queried using the Genetic Association Interactive tool (GAIT).

Several other data sets in the Portal have been updated and improved:
  • The size of the CARDIoGRAM GWAS data set has nearly doubled, now consisting of 184,305 samples, and the data analysis has been updated.
  • The size of the CKDGen GWAS data set has also nearly doubled, to 133,814 samples; the data analysis has been updated; new subsets have been added that stratify serum creatinine associations by African American ancestry and stratify both serum creatinine and urinary albumin-to-creatinine ratio by the presence or absence of T2D.
  • The data set previously named “DIAGRAM GWAS” in the Portal has been updated and re-named “DIAGRAM Trans-ethnic meta-analysis;” its sample size has increased to 149,821. Several new subsets have been added, including gender-stratified, MetaboChip, and fine mapping data.
  • The GIANT GWAS data have been updated and European cohorts have been added for BMI and height traits.
  • The GLGC GWAS data set has increased in size to 188,577 samples and has been updated.
  • The number of samples in the MAGIC GWAS dataset has more than doubled, to 133,010; the data have been updated, and associations with 2 hour glucose, fasting glucose, and fasting insulin have been added for MetaboChip data.
Full details about all of these data sets are available on our Data page.

Because of compatibility issues with the updated data, we have temporarily removed the “GWAS results summary” section from Gene pages of the Portal. This feature will be restored within the next week.

As always with major updates, issues or bugs may have been introduced and we may not have found all of them during our routine testing. We encourage you to let us know of any problems that you encounter in using the Portal, and we welcome your questions and suggestions.

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