GDC Workshop on Oct 23

Date: Thursday, October 12, 2017

Time: 12:00 PM - 1:00 PM (EDT)

Location: Web Conference (See WebEx information below)

Speaker: Michael Fitzsimons, Ph.D, GDC User Services Manager, University of Chicago


Abstract

The Analyzing Data using GDC Data Analysis, Visualization, and Exploration (DAVE) Tools workshop will help introduce users to GDC tools for analyzing data from cancer genomic studies. As an example, we will explore most frequently mutated genes and mutations and perform a survival analysis for cases with and without these mutations, view the distribution of particular mutations and mutated genes across the GDC and visualize associated transcripts in a protein viewer, build custom gene sets for targeted analysis, perform integrated analysis on the most mutated cases in an OncoGrid, and analyze cases within and across projects.

Included Topics

  • Visualize most frequently mutated genes and view most frequent somatic mutations for a project
  • Perform a survival analysis for cases with a mutated form of a certain gene and cases without the mutation
  • Visualize mutations and their frequencies across protein domains
  • Build custom gene sets for targeted analysis
  • Plot all cases for a project in an OncoGrid and visualize the top 50 mutated genes affected by high impact mutations
  • View the number of cases affected by particular mutation across all projects

New platform for children's health issues

Investigators from the University of Chicago Medicine will play a central role in a five-year, $14.8 million effort by the National Institutes of Health, contingent upon available funding, to improve the understanding of inherited diseases.

The project, known as the Gabriella Miller Kids First pediatric data resource center, will be a multi-centered effort led by investigators at the Center for Data Driven Discovery in Biomedicine at the Children’s Hospital of Philadelphia (CHOP).

Two crucial components of the Kids First project, however, are the teams led by Robert L. Grossman, PhD, and Sam Volchenboum, MD, PhD, at the University of Chicago. Grossman and Volchenboum will play a central role in the technical underpinnings of the large-scale processing and sharing of genomic and clinical data for this important initiative.

Grossman, the Frederick H. Rawson Professor in Medicine and Computer Science and director of the Center for Data Intensive Science at the University of Chicago, heads up an operations center that runs numerous data commons, supporting more than 20,000 researchers across the world every month.

“Platforms that enable researchers to analyze securely large amounts of de-identified clinical and genomic data are one of our most powerful tools for making discoveries that improve children’s lives,” Grossman said.

Grossman’s team is known for its work on the NCI’s Genomic Data Commons (GDC), a federally funded, unified data system that promotes sharing of cancer genomic and clinical data between researchers. The GDC is a core component of the National Institutes of Health’s Precision Medicine Initiative.

Grossman will work closely with Volchenboum, an expert in pediatric cancers and director of the Center for Research Informatics at UChicago. Volchenboum’s team developed the world’s first international pediatric cancer data commons, housing data on more than 19,000 neuroblastoma patients from around the world.

Under their leadership, the Chicago team of engineers and scientists will design and operate the cloud-based, open-source software needed to establish the data coordination center within the Kids First data resource center.

“This is a critical step forward for the pediatric oncology community,” Volchenboum said. “The Kids First data resource center will provide a much-needed resource for pediatric researchers to leverage a large set of genomic and clinical data on children. These data will help us understand why some children develop cancer and how to best stratify and treat their disease

Read more at https://sciencelife.uchospitals.edu/2017/08/15/new-genomic-data-platform-to-focus-on-childrens-health-issues/

Engine for Precision Medicine

The NCI Genomic Data Commons as an engine for precision medicine

Jensen MA, Ferretti V, Grossman RL, Staudt LM. (2017). The NCI Genomic Data Commons as an engine for precision medicine. Blood. 130(4), 453-459. doi:10.1182/blood-2017-03-735654.

Abstract

The National Cancer Institute Genomic Data Commons (GDC) is an information system for storing, analyzing, and sharing genomic and clinical data from patients with cancer. The recent high-throughput sequencing of cancer genomes and transcriptomes has produced a big data problem that precludes many cancer biologists and oncologists from gleaning knowledge from these data regarding the nature of malignant processes and the relationship between tumor genomic profiles and treatment response. The GDC aims to democratize access to cancer genomic data and to foster the sharing of these data to promote precision medicine approaches to the diagnosis and treatment of cancer.

Figure 3. 

User workflow. Diagram indicating user steps to authenticate and download GDC data. Red panels indicate the 3 means for accessing data: the Web-based Data Portal, the standalone Data Transfer Tools, and the programmatic API. “Token” is a short text file provided to an authenticated user that acts like a password to enable secure transfer of authorized controlled data, such as sequence alignments.

GOES-16 Data Now Available

Provisional data from the GOES-16 satellite from NOAA is now available through the OCC Environmental Data Commons (EDC).  This is a joint project using datasharing technology developed by the CDIS team at the University of Chicago.

The GOES-16 data is generated from three types of instruments: Earth sensing, solar imaging, and space environment measuring. In addition to the data, Docker images, Python notebooks and GDAL tools have also been made available as community tools.  

Learn more at http://edc.occ-data.org.

New GDC Data Analysis Tools

The latest Genomic Data Commons release now allows you to look at mutations and other genomic variants across all data in the GDC.  This new set of tools is transforming the GDC from a cancer genomics data repository into an interactive knowledge base.  Users can now interact intuitively with the data, and no downloading is necessary!

ASCO Annual Meeting 2017

The GDC team was at the ASCO Annual Meeting again this year, engaging feedback from oncologists and offering demonstrations of the Genomic Data Commons.  The GDC was showcased along with numerous other innovations in the field to over 30,000 oncology professionals from around the world that come together for this meeting every year.  Michael Fitzsimons gave a Meet the Experts talk and showed an early preview of the upcoming data analysis, visualization, and exploration tools.

Learn more at https://am.asco.org.

BioIT World '17

We'll be at the annual BioIT World Conference again this year talking about our work building digital ecosystems to use and share biomedical data at scale.  Michael Fitzsimons, PhD will be speaking on the Data Commons panel on Thursday, May 25th.

Bio-IT World Conference & Expo is building a global network for precision medicine by uniting the BioIT community.  They bring together more than 3,300 attendees from 41 countries to navigate the new era of precision medicine and build collaboration across the industry.

Learn more

Translational Data Science Workshop

The TDS17 Workshop is an important step towards developing a community around translational data science.  Translational data science is a new term that is being used for an emerging field that applies data science principles, techniques, and technologies to challenging scientific problems that hold the promise of having an important impact on human or societal welfare.  The term is also used when data science principles, techniques and technologies are applied to problems in different domains in general, including—but not restricted to—science and engineering research.   The workshop will bring together a group focus on this field and collaborate to write a white paper on translational data science.

Learn more

BloodPAC Milestone

We recently achieved a milestone in building out data commons technology for the Blood Profiling Atlas in Cancer (BloodPAC) by adding the first set of users.  BloodPAC is a consortium effort working to accelerate the development and validation of liquid biopsy assays to improve the outcomes of patients with cancer.   We are contributing our data commons technology to build out a collaborative infrastructure that enables sharing of information between stakeholders in industry, academia, and regulatory agencies. 

AACR Annual Meeting April 1-5

GDC Demonstrations

We will be at the AACR Annual Meeting again this year offering demonstrations of the Genomic Data Commons at the NCI Exhibit #1407.  Stop by and see we've been working on!

Meet the Expert Session

Date: Monday, April 3rd

Time: 10:15AM – 10:45AM ET

Location: Exhibit Booth #1407

Title: Genomic Data Commons Live Demonstration

Presenter: Michael Fitzsimons, Genomic Data Commons

Joe Biden highlights accomplishments of the GDC

Vice President Biden outlines his plans for a Biden cancer initiative, calling on attendees at SXSW to join him to take on cancer. In his remarks, he reflects on the progress made under his leadership of the White House Cancer Moonshot, including the work of the NCI Genomic Data Commons.  He called for innovative solutions to tackle the barriers that prevent faster gains against cancer, and described how he plans to remain in the fight.

Christina Yung joins CDIS as Director of Data Commons

Christina Yung, PhD recently joined CDIS as the Director of Data Commons for the GDC.  Christina has a PhD in Biomedical Engineering from Johns Hopkins University.  She was most recently at the Ontario Institute for Cancer Research, leading the technical working groups for the ICGC PanCancer Analysis of Whole Genomes project.  During her time there, she managed a team of software developers and bioinformaticians from 15 institutes to develop 5 analytical pipelines; runthe pipelines on 700TB of sequencing data in 14 compute environments, and coordinate data dissemination to over 300 researchers. 

Doug Lowy recognizes GDC as a signature achievement

As administrations change, cancer research stands in an unusually strong position, NCI Acting Director Douglas Lowy said in an interview with The Cancer Letter. “We’re very fortunate that both Republicans and Democrats strongly support biomedical research in general, and cancer research in particular,” said Lowy said in a wide-ranging interview. “The leadership of the House and Senate appropriations subcommittees was responsible for the increase in FY16 for the NIH appropriation.” Lowy spoke with Paul Goldberg, editor and publisher of The Cancer Letter, and Matthew Ong, a reporter with The Cancer Letter. Read the full story on The Cancer Letter: http://cancerletter.com/articles/20170106_1

https://vimeo.com/198356746