Featured Research

from universities, journals, and other organizations

Next Generation Tool For Visualizing Genomic Data Introduced

Date:
August 6, 2008
Source:
Broad Institute of MIT and Harvard
Summary:
Researchers are collecting vast amounts of genomic data, but ways to visualize these data in an integrated manner have lagged behind the ability to generate them. Researchers have now developed a novel and freely available visualization tool that helps users integrate and analyze different types of genomic data, and gives them the flexibility to zoom in on a specific region of interest or to pan out for a broad, whole genome view.

A genome-wide view of DNA copy number variations in patients with a form of brain cancer.
Credit: Image courtesy of Wendy Winckler, Broad Institute

Researchers are collecting vast amounts of diverse genomic data with ever-increasing speed, but effective ways to visualize these data in an integrated manner have lagged behind the ability to generate them.

To address this growing need, researchers at the Broad Institute have developed the Integrative Genomics Viewer (IGV), a novel and freely available visualization tool that helps users simultaneously integrate and analyze different types of genomic data, and gives them the flexibility to zoom in on a specific genomic region of interest or to pan out for a broad, whole genome view.

"This new tool offers a Google Maps-like view of integrative genomic data," said Jill Mesirov, Chief Informatics Officer and Director of Computational Biology and Bioinformatics at the Broad Institute. "It brings together different kinds of genomic data into a single, holistic view. I'm incredibly proud of our computational scientists for responding so rapidly and effectively to the critical needs of the growing genomics research community."

With IGV, researchers can still choose a Google Maps-like "street view" of the As, Cs, Ts, and Gs that make up the genome, but they can also simultaneously visualize additional layers of complex information about gene expression as well as sequence alterations, or mutations, in the genetic code. Other genomic details, such as copy number variation, chromatin immunoprecipation data, and epigenetic modifications, can also be viewed in IGV. Moreover, all these data types can be overlaid or superimposed to determine how changes at one level will affect another. Users can choose from a variety of display options, viewing their data as a heat map, histogram, scatter plot, or other formats of their choice. This new visualization tool is free and publicly available to researchers via the web.

"Other tools offer detailed, localized views of genomic data, and a few tools are equipped to provide a whole genome view," said Senior Software Engineer Jim Robinson, one of the program's creators. "IGV was designed to integrate both and to provide smooth zooming and panning across all resolution scales. "

"Most visualization tools are limited in their ability to handle multiple types of genomic data and are typically 'retrofitted' to accommodate new data types as they have arisen," said Michael Reich, Director of Cancer Informatics Development at the Broad Institute. "IGV was designed from the ground up to integrate all of these data, and to provide a strong platform for future growth and refinement."

Broad Associate Member John Rinn, an assistant professor at Harvard University and Beth Israel Deaconess Medical Center, has used a variety of visualization tools to sift through different types of genomic data. "Before I was introduced to IGV, I had to use three different programs to visually integrate my data," Rinn said. "But now this one, universal browser allows me to rapidly scan the entire genome and identify promising regions, which has revolutionized my work."

IGV promises to increase the flow of discovery in many areas of biomedical research. "This tool is designed to enable researchers to view many types of genomic data, especially those relevant to human disease," said Reich. "We're particularly excited about its already groundbreaking use in ongoing studies of the cancer genome."

IGV is made publicly available to researchers worldwide and can be accessed at: http://www.broad.mit.edu/igv


Story Source:

The above story is based on materials provided by Broad Institute of MIT and Harvard. Note: Materials may be edited for content and length.


Cite This Page:

Broad Institute of MIT and Harvard. "Next Generation Tool For Visualizing Genomic Data Introduced." ScienceDaily. ScienceDaily, 6 August 2008. <www.sciencedaily.com/releases/2008/08/080804111644.htm>.
Broad Institute of MIT and Harvard. (2008, August 6). Next Generation Tool For Visualizing Genomic Data Introduced. ScienceDaily. Retrieved July 31, 2014 from www.sciencedaily.com/releases/2008/08/080804111644.htm
Broad Institute of MIT and Harvard. "Next Generation Tool For Visualizing Genomic Data Introduced." ScienceDaily. www.sciencedaily.com/releases/2008/08/080804111644.htm (accessed July 31, 2014).

Share This




More Plants & Animals News

Thursday, July 31, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Visitors Feel Part of the Pack at Wolf Preserve

Visitors Feel Part of the Pack at Wolf Preserve

AP (July 31, 2014) — Seacrest Wolf Preserve on the northern Florida panhandle allows more than 10,000 visitors each year to get up close and personal with Arctic and British Columbian Wolves. (July 31) Video provided by AP
Powered by NewsLook.com
Florida Panther Rebound Upsets Ranchers

Florida Panther Rebound Upsets Ranchers

AP (July 31, 2014) — With Florida's panther population rebounding, some ranchers complain the protected predators are once again killing their calves. (July 31) Video provided by AP
Powered by NewsLook.com
Dangerous Bacteria Kills One in Florida

Dangerous Bacteria Kills One in Florida

AP (July 31, 2014) — Sarasota County, Florida health officials have issued a warning against eating raw oysters and exposing open wounds to coastal and inland waters after a dangerous bacteria killed one person and made another sick. (July 31) Video provided by AP
Powered by NewsLook.com
Raw: Thousands Flocking to German Crop Circle

Raw: Thousands Flocking to German Crop Circle

AP (July 30, 2014) — Thousands of people are trekking to a Bavarian farmer's field to check out a mysterious set of crop circles. (July 30) Video provided by AP
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
 
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:  

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



    Save/Print:
    Share:  

    Free Subscriptions


    Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

    Get Social & Mobile


    Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

    Have Feedback?


    Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
    Mobile iPhone Android Web
    Follow Facebook Twitter Google+
    Subscribe RSS Feeds Email Newsletters
    Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins