CONTENTS CONTENTS NEW DATA

This is the inaugural issue of the Type 2 Diabetes Knowledge Portal (T2DKP) newsletter. Each quarter, it will keep you informed about recent updates to the T2DKP, upcoming conferences, and other news. You are receiving it because you signed up for email updates via a link on the T2DKP home page. To unsubscribe, please email us at [email protected].

CONTENTS New data • New datasets and phenotypes added to T2DKP • Epigenomic data integrated into T2DKP • EBI Federated node now provides access to more data

New features and tools • Interactive burden test is now more versatile than ever • New Gene pages distill and summarize information for individual genes

Other T2DKP news • T2DKP presence at ADA 2017

Upcoming conferences 1.

CONTENTS NEW DATA

New datasets and phenotypes added to T2DKP We added lots of new data: 2,000 additional exome sequences from LuCamp, growing our 17K exome sequence analysis dataset to 19K; GENESIS GWAS for insulin sensitivity; 70KforT2D re-analysis and metaanalysis of T2D associations for 70,000 individuals; VATGen GWAS for fat deposition traits; and glucosestimulated insulin secretion associations from the MAGIC GWAS dataset. We also integrated gnomAD exome and whole genome sequences. And,to help you navigate and explore all these datasets, we added an interactive Data page. (See more details.)

Epigenomic data integrated into T2DKP Genetic association data are the necessary foundation for understanding complex disease, but they don’t tell the whole story by themselves. Patterns of epigenomic features, such as chromatin modifications, can suggest whether DNA regions have a regulatory role and are particularly important for interpreting the effects of variants that lie outside protein-coding regions. Chromatin state predictions based on several different histone modifications, generated with the ChromHMM algorithm, are now available on both the Variant and Gene pages of the T2DKP. (See more details.)

www.type2diabetesgenetics.org T2DKP Newsletter, Summer 2017

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Contact us: [email protected] Twitter: @T2DKP

EBI Federated node now provides access to more data The T2DKP now draws on data housed in two locations: the Data Coordinating Center (DCC) at the Broad institute in Cambridge, MA, USA, and the European Bioinformatics Institute in Hinxton, UK. This federation means that T2DKP users can interact with a much wider range of data, including data that may not be transferred to the DCC. The first dataset to be accessible via federation is an exome chip analysis of associations with glycemic phenotypes, from the Oxford BioBank. (See more details.)

NEW FEATURES AND TOOLS Interactive burden test is now more versatile than ever Our interactive burden test, available on Gene pages, tests the aggregate contribution to disease risk of the variants within a gene. We’ve been continually adding features to this test, making it increasingly customizable and versatile. It previously allowed you to choose custom sets of variants, to filter samples by phenotypic range (such as individuals with a certain BMI, fasting glucose level, or cholesterol level) and/or by ancestry, and to select specific covariates. This quarter, we updated the variant effect filters to correspond to those widely used in the field, and also made it easier to add and select multiple variants. (See more details.)

New Gene pages distill and summarize information for individual genes The T2DKP brings together hundreds of thousands of genetic associations, and our mission is to facilitate the translation of those associations into actionable knowledge for T2D treatment. In order to do that, we need to develop methods to integrate and interpret the data. We’ve taken a big step towards this goal with a new, totally redesigned Gene page that provides a “bottom line” summary for each gene, giving an immediate indication of its possible significance for T2D and other traits. (See more details.)

OTHER T2DKP NEWS T2DKP presence at ADA 2017 The T2DKP team enjoyed attending the 77th Scientific Sessions of the American Diabetes Association in early June. With a mini-symposium, a moderated poster discussion, and three days of exhibiting at our booth, we were able to reach out to many T2D researchers and clinicians. (See a summary.)

UPCOMING CONFERENCES This section lists upcoming conferences that are relevant to T2D and human genetics; asterisks indicate attendance by T2DKP team members. The Genomics of Common Diseases September 6-9, 2017, Hinxton, UK Abstract deadline: July 11 European Association for the Study of Diabetes (EASD) September 11-14, 2017, Lisbon, Portugal Festival of Genomics* October 3-4, 2017, Boston, MA


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Abstract deadline: September 14 American Society of Human Genetics* October 17-21, 2017, Orlando, FL Genome Informatics November 1-4, 2017, Cold Spring Harbor, NY Abstract deadline: August 18 American Heart Association Scientific Sessions 2017* November 11-15, Anaheim, CA Epigenomics of Common Diseases November 14-17, 2017, Hinxton, UK Abstract deadline: September 19 Epigenetics and Epigenomics: Implications for Diabetes and Obesity November 17-19, 2017, Cambridge, MA Abstract deadline: August 18 Advances in Genome Biology and Technology (AGBT) February 12-15, Orlando, FL Abstract deadline: September 30 Please let us know of conferences that should be added to this list.

STAY IN TOUCH! Follow us on Twitter: @T2DKP Join our LinkedIn group: Type 2 Diabetes Knowledge Portal Sign up to receive this newsletter by email We’re always interested in your comments, suggestions, and questions. Please email us at [email protected].


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