Initiatives

1000 Chicago Cancer Genome Project

Cancer is, at it heart, a genetic disease, driven by the acquisition of mutations in important genes.  Although these mutations produce cancer, recent results in several tumors suggest that these mutations may also represent cancer’s Achilles heel. Over the last several years, several new successful chemotherapeutic drugs have been developed that directly target specific cancer mutations.  Thus, the identification of mutations that drive carcinogenesis will allow the development of new, more effective therapies for cancer. However, these drugs only work in a small percentage of cancers.  Cancer is extremely complex and heterogeneous, and the identification of which mutations are present in a tumor and should be targeted by chemotherapeutic therapy is not obvious.

The recent development of novel “next-generation” sequencing technologies now make it possible to identify every mutation in a cancer cell.  Over the last 18 months, the Institute for Genomics and Systems Biology at the University of Chicago has developed significant experience in this emerging technology.  Thus, the IGSB, in conjunction with the University of Chicago Medical Center, is proud to announce the launch of the 1000 Cancer Transcriptomes Project.  Over the next 2 years, the IGSB and UCMC will sequence the transcriptomes of 1000 tumors at the UCMC.  We combine this data with a series of sophisticated analyses and high throughput experiments to identify new targets for therapy, in some of the most common and deadly cancers.

Metabolic Diseases and Diabetes

In partnership with the IGSB, Mark Ratain, MD (Department of Medicine, Section of Hematology / Oncology) and colleagues are analyzing genome wide variation in DNA sequence and gene expression in a large collection of human livers to discover patterns of genomic variation and expression. This comprehensive study, never before conducted, will provide the basis for evaluating potential outcomes of drug therapy in individual cancer patients.

About 75% of the top 200 drugs prescribed are eliminated from the body through the metabolic enzymes in the liver. In addition to receiving seed funding as part of the IGSB Metabolic Diseases and Diabetes Initiative, Ratain and colleagues are using the resources of the High Throughput Genome Analysis Core (HGAC) to perform their study.

As part of the same Initiative, Chris Rhodes, PhD (Department of Medicine, Section of Endocrinology, Diabetes and Metabolism) is performing drug and genome screening of insulin-secreting cells in the Celluar Screening Center (CSC) to identify therapies which promote insulin production in diabetes patients.

Inflammatory Bowel Disease

Eugene Chang, MD (Department of Medicine, Section of Gastroenterology) has partnered with IGSB Core Member Dion Antonopoulos, PhD (IGSB, Argonne) to sequence patient gut contents, containing thousands of different bacterial species, to determine the relationship between specific bacteria and inflammatory bowel disease.

This metagenomics project has been supported by seed funding from the Institute’s Inflammatory Bowel Disease Initiative and takes advantage of the next generation sequencing technology within the High-Throughput Genome Analysis Core (HGAC), as well as the computational expertise at Argonne.

 

 

Funding Opportunities

The primary sources of grant funding for nonprofit organizations (such as the University of Chicago) include the government and private foundations. These grantors will vary greatly in terms of the specificity, subject matter, amount of funding provided, and the desired scope of submitted proposals.  To locate sources of funding, some good starting points are the many funding portals for federal government agencies and non-federal foundations.  These searchable databases will provide you with the opportunity/announcement, required materials, important deadlines and, in many cases, the forms necessary for submission.  Again, it is imperative to contact both IGSB and the University Research Administration (URA) offices to help guide you through the submission process.

Throughout the year, there may be several major grant announcements that could potentially impact the goals for the IGSB and its members.  We will list any such announcements on this webpage when they become available.  We will also be listing specific opportunities for IGSB members on the tabbed pages for faculty, postdocs and students.  However, for the most current announcement information, a portal query may provide information sooner.

To inquire about participating in or submitting for any of the announcements or opportunities listed to the right, please contact the IGSB Business Administrator, Liza Herendeen at 4-3913 or lherend1@bsd.uchicago.edu

Inflammatory Bowel Disease

Bowel Eugene Chang, MD (Department of Medicine, Section of Gastroenterology) has partnered with IGSB Core Member Dion Antonopoulos, PhD (IGSB, Argonne) to sequence patient gut contents, containing thousands of different bacterial species, to determine the relationship between specific bacteria and inflammatory bowel disease.

This metagenomics project has been supported by seed funding from the Institute’s Inflammatory Bowel Disease Initiative and takes advantage of the next generation sequencing technology within the High-Throughput Genome Analysis Core (HGAC), as well as the computational expertise at Argonne.

Metabolic Diseases and Diabetes

In partnership with the IGSB, Mark Ratain, MD (Department of Medicine, Section of Hematology / Oncology) and colleagues are analyzing genome wide variation in DNA sequence and gene expression in a large collection of human livers to discover patterns of genomic variation and expression. This comprehensive study, never before conducted, will provide the basis for evaluating potential outcomes of drug therapy in individual cancer patients.

About 75% of the top 200 drugs prescribed are eliminated from the body through the metabolic enzymes in the liver. In addition to receiving seed funding as part of the IGSB Metabolic Diseases and Diabetes Initiative, Ratain and colleagues are using the resources of the High Throughput Genome Analysis Core (HGAC) to perform their study.

As part of the same Initiative, Chris Rhodes, PhD (Department of Medicine, Section of Endocrinology, Diabetes and Metabolism) is performing drug and genome screening of insulin-secreting cells in the Celluar Screening Center (CSC) to identify therapies which promote insulin production in diabetes patients.

1000 Chicago Cancer Genome Project

Cancer is, at it heart, a genetic disease, driven by the acquisition of mutations in important genes.  Although these mutations produce cancer, recent results in several tumors suggest that these mutations may also represent medical’s Achilles heel. Over the last several years, several new successful chemotherapeutic drugs have been developed that directly target specific cancer mutations.  Thus, the identification of mutations that drive carcinogenesis will allow the development of new, more effective therapies for cancer. However, these drugs only work in a small percentage of cancers.  Cancer is extremely complex and heterogeneous, and the identification of which mutations are present in a tumor and should be targeted by chemotherapeutic therapy is not obvious.

The recent development of novel “next-generation” sequencing technologies now make it possible to identify every mutation in a cancer cell.  Over the last 18 months, the Institute for Genomics and Systems Biology at the University of Chicago has developed significant experience in this emerging technology.  Thus, the IGSB, in conjunction with the University of Chicago Medical Center, is proud to announce the launch of the 1000 Cancer Transcriptomes Project.  Over the next 2 years, the IGSB and UCMC will sequence the transcriptomes of 1000 tumors at the UCMC.  We combine this data with a series of sophisticated analyses and high throughput experiments to identify new targets for therapy, in some of the most common and deadly cancers.

Research

IGSB research at the University of Chicago is focused on genomics and systems biology projects to discover new mechanisms, diagnostic tools, and therapeutic targets to help improve human health, implement models to predict disease dynamics, and ascertain genomic functions that control homeostasis in living matter.  Resources promote research initiatives aligned with the Institute’s thematic framework: Discover, Predict, and Improve: Advancing Human and Environmental Health.

DISCOVER

  • Genetic Mechanisms of Health and Disease, Such as Cancer and Diabetes
  • Annotations of Human and Model Organism Genomes
  • Proteomics and Signaling Networks in Health and Disease
  • Genomics and Cellular Molecular Networks That Control Development
  • Role of Microbes in the Planet’s Carbon Cycle
  • Microbial Systems Biology Networks
  • Genomic & Environment Interactions By Mining Clinical Records
  • Cellular Signaling Networks and Evolutionary Genomics
  • Relationships Between Population Genomics and Complex Diseases

PREDICT

  • Patient Outcomes With Computational Biology, Informatics and Modeling
  • Which Molecules Are The Best Drug Targets
  • Molecular Behavior of Interacting Components in Biological Systems That Help Investigators Design New Therapies
  • Behavior of Gene Networks that Regulate Living Matter
  • Emergence of Biological Properties and Behaviors in Complex Systems

IMPROVE

  • Human Health
  • Biological Engineering & Technology Development of Biotech Tools
  • Diagnostic Markers for Molecular Medicine
  • Computational Approaches to Analyze Complex Systems-Wide Data
  • Predictive Models for Transcriptional Robustness Systems in Model Organisms and Humans