Genomic Data Commons provides unprecedented cancer data resource
Launched in 2016 by then-Vice President Biden, the GDC now contains more than 3.3 petabytes of data and serves more than 50,000 unique users each month.
2021-02-26
(Press-News.org) The National Cancer Institute's Genomic Data Commons (GDC), launched in 2016 by then-Vice President Joseph Biden and hosted at the University of Chicago, has become one of the largest and most widely used resources in cancer genomics, with more than 3.3 petabytes of data from more than 65 projects and over 84,000 anonymized patient cases, serving more than 50,000 unique users each month.
In new papers published Feb. 22 in Nature Communications and Nature Genetics, the UChicago-based research team shares new details about the GDC, which is funded by the National Cancer Institute (NCI), via subcontract with the Frederick National Laboratory for Cancer Research, currently operated by Leidos Biomedical Research, Inc. One of the papers describes the design and operation of the GDC. The other describes the pipelines used by the GDC for the harmonization of data submitted to the GDC and the generation of datasets used by the GDC research community.
The goal of the GDC is to provide the cancer research community with a data repository of uniformly processed genomic and associated clinical data that enables data sharing and collaborative analysis in the support of precision medicine.
Data production for what would become the GDC began in June 2015 using a private cloud. After just a year, the GDC had analyzed more than 50,000 raw sequencing data inputs. The GDC includes genomic, transcriptomic, epigenomic, proteomic, clinical, and imaging data. The processing pipelines described in the Nature paper have produced more than 1,660 TB of data on more than two dozen types of primary cancers. These data are stored within the GDC Data Portal, where they are available for viewing and downloading.
Along with the data portal, the GDC also offers additional user resources, including the GDC Data Analysis, Visualization, and Exploration (DAVE) Tools for interactive exploration of data by genomic variant or specific alteration; the GDC Data Submission Portal for submitting data; the GDC Data Transfer Tool (DTT) for downloading large genomic datasets; and the GDC data harmonization system, which allows users to run data submitted to the GDC through the harmonizing processing pipelines.
"These data have a critical role to play," said Robert Grossman, PhD, principal investigator for the GDC and director of the Center for Translational Data Science at UChicago. "As data accumulates, new signals will become easier to identify as important targets for understanding cancer biology. In addition, the data-sharing infrastructure can serve to inform research studies, providing new insight into genetic variation between individuals and how it may affect cancer patient outcomes."
INFORMATION:
To read about the launch of the GDC, visit uchicagomedicine.org.
The Genomic Data Commons project is funded with Federal funds from the National Cancer Institute, National Institutes of Health from the following sources: Leidos Biomedical Research, Inc. Agreement 14X050 and Agreement 17X147, Task Order TO2 under Prime Contract HHSN261200800001E; and Agreement 17X147, Task Orders F07 and F12 under Prime Contract 75N91019D00024, Task Orders 75N91019F0129 and 75N91020F00003.
About the University of Chicago Medicine & Biological Sciences
The University of Chicago Medicine, with a history dating back to 1927, is one of the nation's leading academic health systems. It unites the missions of the University of Chicago Medical Center, Pritzker School of Medicine and the Biological Sciences Division. Twelve Nobel Prize winners in physiology or medicine have been affiliated with the University of Chicago Medicine. Its main Hyde Park campus is home to the Center for Care and Discovery, Bernard Mitchell Hospital, Comer Children's Hospital and the Duchossois Center for Advanced Medicine. It also has ambulatory facilities in Orland Park, South Loop and River East as well as affiliations and partnerships that create a regional network of care. UChicago Medicine offers a full range of specialty-care services for adults and children through more than 40 institutes and centers including an NCI-designated Comprehensive Cancer Center. Together with Harvey-based Ingalls Memorial, UChicago Medicine has 1,296 licensed beds, nearly 1,300 attending physicians, over 2,800 nurses and about 970 residents and fellows.
Visit UChicago Medicine's health and science news blog at http://www.uchicagomedicine.org/forefront.
Twitter @UChicagoMed
Facebook.com/UChicagoMed
Facebook.com/UChicagoMedComer
ELSE PRESS RELEASES FROM THIS DATE:
2021-02-26
Climate alone is not a driver for human behavior. The choices that people make in the face of changing conditions take place in a larger human context. And studies that combine insights from archaeologists and environmental scientists can offer more nuanced lessons about how people have responded -- sometimes successfully -- to long-term environmental changes.
One such study, from researchers at Washington University in St. Louis and the Chinese Academy of Sciences, shows that aridification in the central plains of China during the early Bronze Age did not cause population collapse, a result that highlights the importance of social ...
2021-02-26
URBANA, Ill. - Economists and urban planners generally agree that local pollution sources disproportionally impact racial minorities in the U.S. The reasons for this are largely unclear, but a University of Illinois study provides new insights into the issue.
"Our work finds experimental evidence that racial discrimination in the home-renting process actively sorts minority renters into neighborhoods with higher levels of pollution," says Peter Christensen, assistant professor in the Department of Agricultural and Consumer Economics (ACE) and an affiliate in Center for the Economics of Sustainability at University of Illinois.
Christensen and co-authors Ignacio Sarmiento-Barbieri, U of I, and Christopher Timmins of Duke University conducted an empirical ...
2021-02-26
Challenging the idea that older people with shorter life expectancies should rank lower in coronavirus immunization efforts, new UC Berkeley research shows that giving vaccine priority to those most at risk of dying from COVID-19 will save the maximum number of lives, and their potential or future years of life.
The findings, published Feb. 25 in the journal Proceedings of the National Academy of Sciences, address the ethical dilemma of who should be first in line for a limited supply of vaccine shots amid a contagion that so far has killed 500,000 in the United States and 2.4 million globally.
"Since older age is accompanied by falling life expectancy, it is widely assumed that means we're saving fewer years of life," said study lead author Joshua Goldstein, a UC Berkeley ...
2021-02-26
Scientists at UCL and the IIT -Istituto Italiano di Tecnologia (Italian Institute of Technology) have created a temporary tattoo with light-emitting technology used in TV and smartphone screens, paving the way for a new type of "smart tattoo" with a range of potential uses.
The technology, which uses organic light-emitting diodes (OLEDs), is applied in the same way as water transfer tattoos. That is, the OLEDs are fabricated on to temporary tattoo paper and transferred to a new surface by being pressed on to it and dabbed with water.
The researchers, who ...
2021-02-26
The investigation of Electron-Positron-Ion (EPI) plasma?--?a fully ionised gas of electrons and positrons that includes astrophysical plasmas like solar winds?--?has attracted a great deal of attention over the last twenty years. A new study published in EPJ D by Garston Tiofack, Faculty of Sciences, University of Marousa, Cameroon, and colleagues, assesses the dynamics of positron acoustic waves (PAWS) in EPI plasmas whilst under the influence of magnetic fields, or magnetoplasmas.
The authors studied the changes in PAWs using a framework of Korteweg-de Vries (KdV) and modified Korteweg-de Vries (mKdV) equations finding a former led to compressive positron acoustic solitary waves (PASWs), whilst the latter resulted in the same and additional rarefactive ...
2021-02-26
The total amount of data generated worldwide is expected to reach 175 ZB (Zettabytes; 1 ZB equals 1 billion Terabytes) by 2025. If 175 ZB were stored on Blu-ray disks, the disk stack would be 23 times the distance to the Moon. We face the urgent need to develop storage technologies that can accommodate this enormous amount of data.
The demand to store ever-increasing volumes of information has resulted in the widespread implementation of data centers for Big Data. These centers consume massive amounts of energy (about 3% of global electricity supply) and rely on magnetization-based ...
2021-02-26
IRS refers to the application of insecticide onto the interior walls of houses.
The study, by the Wits Research Institute for Malaria (WRIM) and the London School of Hygiene and Tropical Medicine (LSHTM), was published in The Lancet on 25 February 2021.
Targeted vs blanket Indoor Residual Spraying
Malaria still represents one of the world's largest health crises, particularly on the African continent where 94% of cases and deaths occur (World Health Organization, 2020).
Most countries in southern Africa have set the elimination of malaria within their borders as a policy target.
In ...
2021-02-26
Prior to the emergence of new mutants of the coronavirus, such as the British variant B.1.1.7, the SARS-CoV-2 variant named D614G had already mutated from the original SARS-CoV-2 pathogen that triggered the pandemic. D614G has rapidly spread to become the most abundant variant worldwide and this D614G mutation remains in all the new emerging variants. An international team including researchers from Bern has now been able to demonstrate in both the laboratory and in animal models why the D614G variant was able to gain the upper hand over the original SARS-CoV-2 virus. "Our approach ...
2021-02-26
A study, led by researchers at the Instituto de Astrofísica de Canarias (IAC) and carried out with OSIRIS, an instrument on the Gran Telescopio Canarias (GTC), has found the most densely populated galaxy cluster in formation in the primitive universe. The researchers predict that this structure, which is at a distance of 12.5 billion light years from us, will have evolved becoming a cluster similar to that of Virgo, a neighbour of the Local Group of galaxies to which the Milky Way belongs. The study is published in the specialized journal Monthly Notices of the Royal Astronomical Society (MNRAS).
Clusters of galaxies are groups of galaxies which remain together because of the action of gravity. To understand the evolution of these "cities of galaxies" scientists look ...
2021-02-26
Researchers from the Andalusian Centre for Molecular Biology and Regenerative Medicine (CABIMER), in collaboration with the Swiss Institute for Experimental Cancer Research (ISREC) have studied the mechanisms behind the higher tendency of people with Mulibrey syndrome to develop tumours. Their results point to the important role of the TRIM37 protein, whose absence explains the appearance of tumour cells.
Mulibrey syndrome is a so-called rare disease as it occurs in less than 5 out of every 10,000 inhabitants. Some of these diseases usually have a very definite genetic basis. ...
LAST 30 PRESS RELEASES:
[Press-News.org] Genomic Data Commons provides unprecedented cancer data resource
Launched in 2016 by then-Vice President Biden, the GDC now contains more than 3.3 petabytes of data and serves more than 50,000 unique users each month.
