Spring 2020 newsletter

Contents

Introducing the Common Metabolic Diseases Knowledge Portal, coming Summer 2020

Currently, four separate Knowledge Portals offer genetic and genomic results, tools, and workflows to help researchers understand and treat diabetes, cardiovascular and cerebrovascular disease, and sleep disorders. Yet all of these conditions are related, and insights into any one of these disease areas may be relevant for the others. We are now merging the four portals to create the Common Metabolic Diseases Knowledge Portal (CMDKP), which will take advantage of the breadth of these results and the relationships between these cardiometabolic diseases and traits. The CMDKP has a flexible, modular design that allows rapid updates, and is based on a new infrastructure with greatly improved performance and speed. Each of the four disease-area specific portals has been retained within the CMDKP, so that the next iteration of the T2DKP and other Knowledge Portals will also benefit from the improved speed and new visualizations.

An in-progress beta version of the CMDKP is now available for testing. Please try it out and send us your comments and suggestions!

In development: a new Type 1 Diabetes Knowledge Portal

The NIDDK has supported the T2DKP from its inception. Now, further extending its commitment to diabetes research, NIDDK is enabling the Knowledge Portal team, along with scientific collaborators Drs. Stephen Rich and Kyle Gaulton, to build a resource for type 1 diabetes researchers. The T1DKP, scheduled for release during summer 2020, will be powered by the Human Genetics Amplifier (HuGeAMP) software platform, developed at the Broad Institute with support from the AMP-T2D program.

Multiple datasets added to the T2DKP

With our last release, the T2DKP now includes 99 datasets with genetic associations for 234 traits. We have recently added the following datasets. Asterisks indicate that in addition to integration in the T2DKP interfaces and tools, full summary statistic files are also available for download.

Glycemic phenotypes and diabetic complications

  • AGEN and DIAMANTE GWAS*: T2D associations for over 433,000 individuals of East Asian ancestry
  • MAGIC fasting glucose change over time GWAS: associations for the rate of change in fasting glucose levels over time (up to 14 years) in nearly 14,000 non-diabetic European ancestry subjects
  • BioMe AMP T2D GWAS: the Phase 2 complications analysis performed by the AMP DCC analysis team determined associations for 5 complication phenotypes in type 2 diabetics, in over 9,300 subjects of multiple ancestries
  • Diabetic retinopathy GWAS*: two ancestry-specific datasets include associations for diabetic retinopathy and its sub-types, with or without adjustments (8 phenotypes total), from over 3,200 European ancestry participants and 2,600 African American participants
  • IAMDGC 2013 AMD GWAS: associations for age-related macular degeneration and 2 sub-types, for over 57,000 subjects of multiple ancestries
  • Primary angle closure glaucoma GWAS: associations for PAGC from over 26,000 participants of multiple ancestries

Anthropometric measures

  • GIANT-UK Biobank GWAS Meta-analysis: meta-analysis of body fat distribution associations in nearly 700,000 European subjects
  • GIANT 2017 smoking-adjusted GWAS: meta-analysis of anthropometric measures accounting for smoking behavior in over 241,000 participants of multiple ancestries

Cardiovascular phenotypes

  • UK Biobank Cardiac MRI LV GWAS*: associations for 7 MRI measures of left ventricle function from over 36,000 European subjects
  • PR interval 1000G GWAS*: associations for PR interval, an ECG measure, from over 293,000 participants of multiple ancestries
  • UK Biobank atrial fibrillation exome sequence analysis: single-variant associations for atrial fibrillation from 43,000 European subjects are integrated into the T2KP, and gene-level association scores are available for download
  • CARDIoGRAMplusC4D-UK Biobank CAD GWAS Meta-analysis: meta-analysis of coronary artery disease associations in nearly 550,000 individuals of European ancestry
  • Hypertension exome chip analysis: blood pressure associations for over 192,000 European and South Asian participants

Multiple phenotypes from biobank analyses

  • FinnGen GWAS: associations for 15 cardiometabolic and diabetic complication phenotypes from 96,000 Finnish individuals
  • UK Biobank dietary habit GWAS*: associations for 3 dietary preferences and 2 diet patterns from a study of almost 450,000 European individuals are integrated into the T2DKP; full summary statistics for 170 phenotypes are available for download
  • UK Biobank Mendelian trait GWAS: associations for 5 metabolic quantitative traits, which can each be affected by single-gene mutations; these represent positive control data underlying a new method for predicting effector genes for a given phenotype (results from this method will be represented on the CMDKP in the near future)
  • UK Biobank 409K GWAS: associations for blood pressure and hypothyroidism phenotypes in 408,000 Europeans; these associations represent part of the data underlying a new method for predicting effector genes for a given phenotype (results from this method will be represented on the CMDKP in the near future)

Musculoskeletal Knowledge Portal (MSK-KP) launched

In March, with support from the International Federation of Musculoskeletal Research Societies (IFMRS) we launched the MSK-KP, a new open-access resource that aggregates, integrates, analyzes, and displays 'omic results relevant to musculoskeletal traits and diseases. The MSK-KP will facilitate and accelerate musculoskeletal disease research by comprehensively amassing and distilling "big data" to make them accessible to all researchers. Like the other Knowledge Portals, the MSK-KP is powered by the Human Genetics Amplifier (HuGeAMP) software platform, developed at the Broad Institute with support from the AMP-T2D program.

Diabetes Epigenome Atlas news

In its most recent release, the Diabetes Epigenome Atlas (DGA) added 143 RNA-seq datasets and 50 ChIP-seq assays relevant to T2D, along with chromatin accessibility annotations for 289 tissues from ChIP-Atlas. The epigenomic and functional data that will be coming to the Common Metabolic Diseases Knowledge Portal will be loaded and processed initially at DGA and then transferred to the CMDKP. The CMDKP and DGA teams will be collaborating closely in the coming months in order to prioritize, load, track, and document these datasets.

New video resources

 

Follow these links to view our most recent videos:

Upcoming webinars

Our next webinars are scheduled for Thursday July 16, Thursday September 16, and Thursday, November 12, all at noon ET. Watch our home page for announcements and connection information!

Stay in touch!

Contact us with questions or suggestions; follow us on Twitter; join our LinkedIn group; or watch our videos on the Broad Institute YouTube channel.

Portals
all