ISB News

ISB Co-Authored Nature Paper Featured in the New York Times

The Ilya Shmulevich Group at ISB has been participating in The Cancer Genome Atlas (TCGA) project as a Genome Data Analysis Center. The first paper resulting from the main phase of the TCGA project – "Comprehensive molecular characterization of human colon and rectal cancer" – was published in the July 19, 2012, issue of Nature and also featured on the front page of the New York Times. ISB teamed up with the MD Anderson Cancer Center to contribute analysis and we were co-authors of the paper in Nature. Here's a YouTube video, featuring ISB senior research scientist Vesteinn Thorsson, that explains our work.

One of ISB's unique contributions to the project was a web tool that allows researchers – and the public – to explore the molecular signatures that were found to be associated with aggressive colorectal cancer. This web tool, the CRC Aggressiveness Explorer, is part of the Regulome Explorer, which was designed and developed at the ISB to facilitate the integrative exploration of associations in clinical and molecular data from the TCGA. The Regulome Explorer technology also was featured in the June 28 keynote presentation at the Google I/O developers conference.

Here's a more detailed description the ISB's contribution to the TCGA publication on colorectal cancer:

Collaborating with Timothy A. Chan, MD, PhD, of the Memorial Sloan-Kettering Cancer Center (mskcc.org) we identified a set of six clinical measurements that are indicative of aggressive colorectal cancer. This includes whether the tumor has found its way into the bloodstream or into neighboring lymph nodes, whether the tumor has metastasized, and what stage the tumor has reached. We scored each of the thousands of molecular features available to us in the TCGA data set to indicate the degree of association with tumor aggressiveness. The score results from combining results from individual statistical association tests (p-values) between molecular variable and the six clinical variables using a weighted form of Fisher's method. This yielded ranked lists of genes whose expression may be indicative of aggressive or less aggressive tumors. It also yielded corresponding lists for other kinds of colorectal tumor data generated by the TCGA: DNA mutations, DNA copy number variation, methylation of gene promoters, and the expression of microRNAs. To examine the molecular features associated with tumor aggressiveness in the context of the cancer genome, we used the CRC Aggressiveness Explorer, developed at the ISB.

Recent Articles

  • New Research Unveils Effective STEM Program Models for High School Students from Historically Marginalized Communities

    An ISB-led study has unveiled important insights and actionable protocols into providing equitable STEM experiences for high school students from historically marginalized communities. The research highlights the transformative power of informal STEM learning in addressing societal challenges and the ease with which many organizations could provide these important opportunities.

  • Common Immune Response Protective Across Many Diseases

    Combined, infection, autoimmunity and cancer account for 40 percent of deaths worldwide and represent major global health challenges. In a Cell Reports paper, ISB researchers detail how the human immune system works in common ways across diseases. Their findings offer promising avenues for exploring multi-disease therapeutic strategies.

  • Spotlight on ISB Education graphic

    2023-24 School Year ISB Education Highlights

    Each month throughout the 2023-2024 academic year, we will highlight some of the top projects the ISB Education team is working on.