Scope:

The Omics WG ensures the availability of high-quality omics datasets harmonized across Affiliate Cohorts to Consortium-wide and prioritized Consortium projects in DEFINE-T2D. Initial focus for this WG is to inventory existing data and formulate a quality control (QC) and harmonization plan for genetic and metabolomic data.

Priorities:

• Maintain list of ‘omics data availability
• Provide guidance on QC and harmonization of ‘omics data
• Summarize imputation panels/methods across cohorts and provide guidance on imputation methods
• Address ancestry considerations in genetic and other omics analyses
• Provide guidance on the use of polygenic risk scores (PRS)

Co-conveners:

• Nichole Allred
• Eric Gamazon

Members:

• Alisa Manning
• Casey Marchek 
• Garrett Kaas
• Iain Konigsberg
• Ivana Yang
• Jerome Rotter
• Joanne Cole
• Joohyun Kim
• Josep Mercader
• Kent Taylor
• Kevin Lu
• Laura Brenner
• Lukasz Szczerbinski
• Magdalena (Magda) Sevilla
• Maggie Ng
• Mary Rooney
• Miriam Udler
• Nicholette Allred 
• Qibin Qi
• Ravi Shah
• Swapan K. Das
• Tamar Sofer
• Varinderpal (Vicky) Kaur
• Zanetta Toomata
• Zsu-Zsu Chen

NIH Project Scientist:

• Norann Zaghloul

BRC Project Manager:

• Aastha Kakar
• Luciana Vargas

Scope:

The Phenotypes WG is responsible for defining data format and documentation requirements for Study Site and Affiliate Cohort-provided phenotype data to be used in Consortium-side and prioritized Consortium projects in DEFINE-T2D. This WG will inventory existing data, coordinate and prioritize harmonization efforts, establish and document harmonization best practices, and define consortium phenotype data standards.

Priorities:

• Across cohorts, identify and summarize important variables for diabetes identification (e.g., glucose), complications, and other related outcomes, in addition to any variables required for diabetes subtyping, including informed GWAS clustering
• Provide guidance on QC and harmonization of all variables above
• Provide guidance on the definition and harmonization of race, ethnicity and ancestry variables

Co-Conveners:

• Leslie Lange
• Shy Srinivasan

Members:

• Aaron Leong
• Alisa Manning
• Allison Bebo
• Alain Bertoni
• Casey Marchek
• Dana Dabelea
• Eric Gamazon
• Josephine Li
• Kristen Boyle
• Kristen Nadeau
• Kristina Utzschneider
• Maggie Ng
• Mark Goodarzi
• Mary Rooney
• Megan Shuey
• Melanie Cree
• Mike Bancks
• Monique Hedderson
• Peter Liu
• Ravi Shah
• Sarah Hsu
• Steven Kahn
• Xue Zhong
• Zsu-Zsu Chen

NIH Project Scientist:

• Norann Zaghloul

BRC Project Manager:

• Aastha Kakar

EHR Subgroup of the Phenotypic WG

The Phenotype WG EHR sub-group began in Year 2 of the study and is focused on curating and harmonizing T2D-related phenotypes and medications across the EHR-based data sources in DEFINE-T2D.

The main sub-group meets monthly (second Mondays), and a “analyst” subset of the groups meet on third and fourth Mondays. Megan Shuey (Vanderbilt site) chairs these calls.

The group has focused on collecting information about overall data models and medications for each EHR data set (BioVu, Mass General Brigham Biobank, Atrium Health Wake Forest Baptist, Colorado Center for Personalized Medicine Biobank, and All of Us).

Initial harmonization of diabetes related phenotypes has occurred for approximately 16 continuous traits and eight binary conditions across three sites (BioVU, Mass General Brigham Biobank, and All of Us) for the genetic clustering projects, which aligns with the goals of this working group to support larger consortium related projects.

The data curation pipeline for these phenotypes has been developed and shared with the analysts. Additional phenotypes and medication specific variables are in progress and the related data curation pipelines will be made available over the next few months.

In the coming year, this group will continue to meet monthly to discuss EHR analysis details,  provide a springboard to discuss ideas for EHR-focused data, and engage other consortia project to identify potential collaborative efforts. 

Scope:

Publications and Presentations (P&P) Committee oversees the life cycle of Consortium papers from proposal development and approval to publication in scholarly journals and presentations at conferences.  As part of this process, the P&P WG will also provide guidance on authorship practices, and facilitate dissemination of findings to the scientific community and key stakeholders.

Priorities:

• Develop a process for project proposal and tracking.
• Develop tracking and review process for papers within the consortium, from concept/analysis proposal through publication. 
• Ensure appropriate utilization and interpretation of race, ethnicity and ancestry in products produced by the Consortium.
• Maintain list of established processes for publications & presentations that are specific to cohorts in the Consortium and develop a process tailored for the Consortium

Co-conveners:

• Mark Espeland
• Alisa Manning

Members:

• Anna Bellatorre
• Heidi Krause-Steinrauf
• Iain Konigsberg
• Kristina Utzschneider
• Lynne Wagenknecht
• Maggie Ng
• Steven Kahn
• Wei Perng

NIH Project Scientist:

• Norann Zaghloul

BRC Project Manager:

• Kyle Salmon
• Lynn Dexter