Wednesday, October 25, 2017

New phenotypes and physical activity stratification available in the T2DKP

We’ve recently updated one dataset and added another in the Type 2 Diabetes Knowledge Portal. Associations with multiple new phenotypes are now available for the BioMe AMP T2D GWAS dataset, and the new dataset "GIANT GWAS - stratified by physical activity" adds associations with anthropometric traits for cohorts stratified by gender and physical activity levels.

The BioMe AMP T2D GWAS dataset was first added to the T2DKP in early 2017, initially with three phenotypes (T2D, fasting glucose levels, and HbA1c levels). Deposition and analysis 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. This dataset was the first to be entirely produced within the AMP T2D project, including the deposition, analysis, quality control, and presentation of the data.

The 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 dataset adds significant ethnic diversity to the Portal’s genetic association data.

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. In this second phase of analysis, associations with seven traits were calculated: systolic and diastolic blood pressure; HDL and LDL cholesterol levels; creatinine levels and eGFR-creat; and BMI. A detailed analysis report for these associations may be downloaded from the BioMe AMP T2D GWAS section of our Data page.

The new GIANT dataset was generated by the GIANT (Genetic Investigation of Anthropometric Traits) consortium via a meta-analysis of genetic associations for BMI, waist-hip ratio, and waist circumference from more than 200,000 adults. Samples are stratified by sex, ancestry, and physical activity level (active or inactive). This work was published in a recent paper by Graff et al.

Data from both the BioMe and GIANT studies are available at these locations in the Portal:
  • On Gene pages (see an example) in the Common variants and High-impact variants tables and in LocusZoom static plots
  • On Variant pages  (see an example) in the Associations at a glance section and in the Association statistics across traits table, and in LocusZoom static plots 
  • Via the Variant Finder tool
  • "Manhattan plots" of associations across the genome may be seen by selecting one of the phenotypes analyzed in these datasets in the View full genetic association results for a phenotype scroll box on the Portal home page
  • Additionally, the BioMe data are available for sample filtering and custom association analysis via the Genetic Association Interactive Tool (GAIT) on Variant pages.

Please check out the new data and contact us with any questions, comments, or suggestions.

Monday, October 16, 2017

Learn about complex disease knowledge portals at ASHG 2017

Members of the Knowledge Portal team will be attending the American Society of Human Genetics meeting this week in Orlando, FL.

We'll be talking about the continuing progress of the Type 2 Diabetes Knowledge Portal, which has grown dramatically since ASHG 2016, with loads of new data and many new features. We'll also present our work towards expanding the T2DKP framework to other complex diseases, with the recent release of a new sibling portal for stroke genetics, the Cerebrovascular Disease Knowledge Portal.

You can catch us nearly every day of the meeting:

Wednesday 10/18

10 AM - 5 PM: Find us in the exhibit hall at booth #863. We’ll be there to answer your questions and give tours and tutorials on the Knowledge Portal Network.

10-10:30 AM: Demonstration of the Type 2 Diabetes Knowledge Portal at our booth, #863.
10:30-11 AM: Demonstration of the Cerebrovascular Disease Knowledge Portal at our booth, #863.

2 PM - 4 PM: Ben Alexander will present poster #1186: The Type 2 Diabetes Knowledge Portal: Clearing a path from genetic associations to disease biology.

Thursday 10/19

10 AM - 5 PM: We will again be in the exhibit hall at booth #863.

10:30 - 11:30 AM: Portal team members will be available at the Broad Institute booth (#1037) for demonstrations and tutorials.

2-2:30 PM: Demonstration of the Type 2 Diabetes Knowledge Portal at our booth, #863.
2:30-3 PM: Demonstration of the Cerebrovascular Disease Knowledge Portal at our booth, #863.

4:15 PM–6:15 PM: Portal team members will be participating in Concurrent Invited Session #49:

Data Sharing, Analysis, and Tools to Catalyze Translation from Genomic to Clinical Knowledge
Room 330C, Level 3, Convention Center
Moderators: Benjamin Neale and Noël Burtt
Serving genetic data and tools to the world - Jason Flannick.
The EGA as a platform for effective data sharing of human genetic and phenotype data -Thomas Keane.
Converting sequence data from over 140,000 people into rare disease diagnoses - Daniel MacArthur.
Assessing the phenome-wide consequences of genetically regulated molecular traits - Hae Kyung Im.

Friday 10/20

10 AM - 2:30 PM: This is our last day in the exhibit hall at booth #863.

We look forward to meeting you at ASHG! If you have questions and cannot meet us any of these times, or if you won’t be at ASHG, our mailbox is always open at

Thursday, October 5, 2017

Portal team presents at Festival of Genomics

The Festival of Genomics was held in Boston on October 3-4, and the Type 2 Diabetes Knowledge Portal was well represented. This meeting brings together multiple stakeholders in genomics and health care, using innovative formats to educate, promote connections, and spark conversations.

On the first day of the meeting, Nöel Burtt presented a talk focusing on the T2DKP: "The Type 2 Diabetes Knowledge Portal: accelerating action from data."

Nöel Burtt speaking at the Festival of Genomics

The next day, T2DKP team members participated in a session with an unusual format, designed to stimulate interaction and conversation: "In the Loop."  Jason Flannick, Senior Group Leader for the Portal project, chaired the session, which was entitled "Complex data, complex solutions: tackling the challenges of genetic data sharing, interpretation, and representation." "Loop leaders," all from the Broad Institute, included:

  • Sean Simmons, speaking on "Technological solutions to privacy concerns around data access and utilization";
  • Moran Cabili, speaking on "Ethical and technical challenges to genetic data access";
  • David Siedzik, speaking on "Analysis tools for genetic data and their scalability"; and
  • Maria Costanzo, speaking on "Representing and democratizing access to genetic association results."

Left to right: Jason Flannick, Sean Simmons, Moran Cabili, David Siedzik, and Maria Costanzo participate in an "In the Loop" session
The session began with an introduction from the chair and speakers, and then the audience broke into four groups for discussion with each of the Loop leaders. Each leader facilitated a discussion among two different groups, and then the entire group convened again to sum up the discussions. The group may not have come up with any breakthrough ideas, but participants definitely emerged with a clearer picture of the many challenges around aggregating and representing genetic data.

The T2DKP team is headed next to the American Society of Human Genetics meeting. Stay tuned for a preview of our participation there in the next blog post!