Data Coordinating Center
Icahn School of Medicine at Mount Sinai and the University of Chicago

Judy Cho, MD

Principal Investigator, IBDGC Data Coordinating Center

Professor, Icahn School of Medicaine at Mount Sinai

Dr. Cho has served as the Principal Investigator of the NIDDK IBDGC since 2003. She plays a lead role in setting scientific and operational priorities, assessing new sample and analytic approaches, and overseeing internal and external communication.

DCC Objectives

The Data Coordinating Center (DCC) of the NIDDK IBDGC plays a lead role in a) assessing and applying innovative research approaches in genetics and genomics to define pathophysiologic mechanisms, b) operationally unifying the NIDDK IBDGC and assuring rigor and reproducibility at scale, and c) facilitating collaboration with external investigators and groups to maximize the size and scientific value of existing datasets, provide complementary expertise, and develop the next generation of IBD investigators pursuing genetic, cellular and molecular understanding of IBD.


Specific Aims: 2017-2022

Aim 1: To apply new laboratory and computing technologies and collect accurate, detailed data on disease pathogenesis from the clinical all the way down to the cellular level and genetic level, sharing with the broader research community.

  • Expand platforms for collecting detailed, longitudinal cohort collections
  • Efficiently collaborate with top laboratories, operationalizing sample and data flows and linking results to genetics
  • Develop and scale objective assessments of disease activity and treatment including automated methods for extracting information from endoscopy and pathology reports, virtual slides of endoscopic biopsies, endoscopic video and Electronic Medical Records (EMRs)
  • Develop and apply a cloud-based IBD Data Commons, for broad investigator use

Aim 2: To prioritize scientific directions for the Consortium and scale new technologies, sampling strategies and analyses to larger cohorts, including longitudinal data.

  • To fine-map established loci by expanding sample size and diversity. To distinguish credible SNPs between CD and UC
  • Comprehensively define the genetic basis for altered intestinal epithelial gene expression and function in UC. We will analyze sources of variation in mRNA expression from spheroids grown from biopsies taken from inflamed and uninflamed UC colon.
  • Determine the genetic basis for how pathophysiologic mechanisms function over time, including in response to therapeutic interventions

Ongoing and New Directions

New recruitment priorities and approaches

The DCC is piloting methods to facilitate recruitment in non-European populations using single IRBs, alternative reimbursement strategies, biobank-based and direct-to-patient recruitment approaches. The DCC leads a monthly coordinators’ meeting to communicate IBDGC priorities, assess progress and share effective recruiting and sample handling approaches across the Consortium.

New data types and accelerating integration

The DCC is adding to its form-based methods for collecting phenotype data by using electronic medical records and diagnostic imaging and reports. IBDGC investigators are piloting image-based measurements beginning with radiology but likely expanding into both pathology and paraffin-based methods as well. Rapidly developing applications of multi-omic single cell technologies are a high priority, especially for their ability to provide insight into IBD physiology.

Data sharing, data mining, and project acceleration

Common variant, GWAS-based data mapped to traits represents an important, foundation for further studies. Expansions of both chip and sequence-based cohorts will be finalized in 2021-2022 and published via dbGaP and the IBDGC Data Commons. The integration of African-based reference, common variant data substantially improves IBD trait prediction as an important basis for the expansion of non-European cohorts. Tissue-based, bulk RNAseq gene expression linked to important clinical inflection points has provided substantial mechanistic insight, especially when integrated with single cell data. Through the DCC, the IBDGC will utilize the Data Commons to increase the speed of analyses and data sharing in promotion of deeper collaboration.

Training the next generation of IBD researchers

The DCC organizes a rotating schedule of GRC presentations where work from junior investigators is encouraged. In 2020, the DCC initiated a webinar series focusing on data-intensive, translational investigators. Given a) the rapid rate of data expansion in scope and type, and b) the increasingly refined mining capacities of extant clinical collections, the opportunities for training and developing the next generation of translational researchers are highly promising.

 

Personnel

Phil Schumm

Co-Investigator, University of Chicago

Mr. Schumm has served as the central operational architect of the DCC since its inception. He had designed sample and data workflows throughout the IBDGC and internationally, interacting closely with genetic analysts. During this period, he has developed the architecture for the IBDGC website, GitLab-based services and the IBD Data Commons.

John D. Rioux, PhD

Steering Cmte Chair; Director, Laboratory of Genetics and Genomic Medicine of Inflammation

Robert Grossman

Professor, Co-Investigator, University of Chicago

Dr. Grossman is Co-Chief of the Section of Computational Biomedicine and Biomedical Data Science and Chief Research Informatics Officer (CRIO) for the Biological Sciences Division at the University of Chicago. His Center for Translational Data Science has developed the Gen3 platform, upon which the IBDGC Data Commons is based.

Kyle Gettler, PhD

Bioinformatician, Co-Investigator, Icahn School of Medicine at Mount Sinai

Dr. Gettler is leading efforts in genetic association, integration with gene expression and application of polygenic risk scores for trait prediction.

Yuval Itan, PhD

Assistant Professor, Co-Investigator, Icahn School of Medicine at Mount Sinai

Dr. Itan develops and applies methods for rare variant, gene and pathway-based analyses in IBD and primary immunodeficiencies.

Ronald Thisted

Professor, University of Chicago

Dr. Thisted has extensive expertise in biostatistics and epidemiology especially as applied to assessment of therapeutic interventions. He is also an expert in statistical computation. He has advised the DCC on its structure and operations including management of collaborative projects since 2003.

Ksenija Sabic

Research Manager, Icahn School of Medicine at Mount Sinai

Ms. Sabic has extensive industry experience with Next Generation Sequencing, sample management, quality assurance processes and regulatory affairs. She is coordinating efforts and streamlining procedures for biospecimen management and processing, as well as overseeing patient recruitment.

Christopher Tastad

Bioinformatician, Icahn School of Medicine at Mount Sinai

Mr. Tastad is working to elevate analytical capabilities with back-end improvements, lean development, and application of advanced tool sets.

Colleen Chasteau

Clinical Research Coordinator

Ms. Chasteau coordinates the efficient acquisition and processing of patient samples to further our translational research efforts.

Ujunwa Korie, M.D., Ms.P.H.

Clinical Research Coordinator

Dr. Korie aids in the recruitment of patients to our studies, sample processing, and coordinate all of the regulatory efforts including the study IRBs.

Emebet Mengesha

Research Specialist

Talin Haritunians, PhD

Assistant Professor, Cedars-Sinai

Dr. Haritunians participates in multiple IBD genomics studies, with expertise in the management of large-scale genetic datasets. She is a member of the NIDDK IBDGC Steering and DCC Committees, and Chair of the Analytic Committee.