Featured Research

from universities, journals, and other organizations

Crowdsourcing answer to cancer cell drug sensitivities

Date:
June 1, 2014
Source:
University of Colorado Cancer Center
Summary:
An open challenge to predict which breast cancer cell lines will respond to which drugs, based only on the sum of cells’ genomic data, has released its results. The winning entry was 78 percent accurate in identifying sensitive versus resistant cell lines, and was one of 44 algorithms submitted by groups from around the world.

A study published June 1 in the journal Nature Biotechnology describes the results of an open challenge to predict which breast cancer cell lines will respond to which drugs, based only on the sum of cells' genomic data. The winning entry, from the Helsinki Institute for Information Technology, was 78 percent accurate in identifying sensitive versus resistant cell lines, and was one of 44 algorithms submitted by groups from around the world.

Related Articles


"The idea is simple -- we have this question and anybody can participate in searching for the answer. The question is, do we have enough information from mutations, or gene expression, or methylation, or copy number alterations to predict how cancer cells will respond to drugs," says James Costello, PhD, investigator at the University of Colorado Cancer Center, assistant professor in the Department of Pharmacology at the CU School of Medicine, and Director of Computational and Systems Biology Challenges within the Sage Bionetworks/DREAM organization.

The results of this effort, which mined genomic data provided by the laboratory of Dr. Joe Gray at the Oregon Health Science University, are intended to characterize molecular markers in cancer, which can then be tested against large collections of human samples, such as those of The Cancer Genome Atlas (TCGA), a project by the National Cancer Institute to genomically characterize thousands of human cancers. Now with this massive NCI database, the ongoing challenge is to mine these data to guide drug development and cancer treatment. To incentivize teams of data scientists to work with this data, the NCI partnered with the Dialogue for Reverse Engineering Assessment Methodologies or DREAM project. Prizes include funding support and publication.

"It's an international effort to address fundamental biomedical research questions. The goal is to push open science and access to data, both for researchers and ultimately for doctors and patients," Costello says.

Specifically, the challenge asked groups to submit algorithms -- computerized mathematical strategies -- that could correctly classify 18 breast cancer cell lines from the most "sensitive" to most "resistant" to 28 therapeutic compounds. In this case, challenge organizers including Costello knew the answers and so could check the accuracy of the submitted strategies. The expectation is that algorithms that accurately show what we already know to be true of cancer cells and cancer drugs could then be used to predict sensitivities we don't already know, perhaps suggesting new treatments for known cancer cell lines, or matching a patient's individual cancer cells with the best treatment.

As a corollary, the study was able to show what types of genomic data are most predictive of drug response.

"There are new, great, super flashy technologies we can use to look inside cancer cells, but at least for the time being the data from these new techniques don't tell us how cells will respond to therapy as well as the more established gene expression microarrays," Costello says. The reasons, he suggests, include the 20-year history of microarray analysis that has shaped our ability to accurately generate and use this type of data, and also to the fact that gene expression data is a proxy for many cellular processes. That is, many genomic modifications, such as methylation or mutation, directly affect gene expression and if that modification is a result of a cellular process, gene expression will change accordingly and microarrays measure the results of this effect.

"Data scientists are hungry for new data and new questions and if you can get people from all over the world to work on these challenges, it can drive innovation and we can get to an answer much quicker. If you give smart people interesting questions they frequently come up with highly innovative solutions," Costello says.

Current DREAM project challenges address issues in Alzheimer's disease, rheumatoid arthritis as well as cancer.


Story Source:

The above story is based on materials provided by University of Colorado Cancer Center. The original article was written by Garth Sundem. Note: Materials may be edited for content and length.


Journal Reference:

  1. James C Costello et al. A community effort to assess and improve drug sensitivity prediction algorithms. Nature Biotechnology, 2014; DOI: 10.1038/nbt.2877

Cite This Page:

University of Colorado Cancer Center. "Crowdsourcing answer to cancer cell drug sensitivities." ScienceDaily. ScienceDaily, 1 June 2014. <www.sciencedaily.com/releases/2014/06/140601201901.htm>.
University of Colorado Cancer Center. (2014, June 1). Crowdsourcing answer to cancer cell drug sensitivities. ScienceDaily. Retrieved November 23, 2014 from www.sciencedaily.com/releases/2014/06/140601201901.htm
University of Colorado Cancer Center. "Crowdsourcing answer to cancer cell drug sensitivities." ScienceDaily. www.sciencedaily.com/releases/2014/06/140601201901.htm (accessed November 23, 2014).

Share This


More From ScienceDaily



More Health & Medicine News

Sunday, November 23, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Ebola-Hit Sierra Leone's Late Cocoa Leaves Bitter Taste

Ebola-Hit Sierra Leone's Late Cocoa Leaves Bitter Taste

AFP (Nov. 23, 2014) The arable district of Kenema in Sierra Leone -- at the centre of the Ebola outbreak in May -- has been under quarantine for three months as the cocoa harvest comes in. Duration: 01:32 Video provided by AFP
Powered by NewsLook.com
Don't Fall For Flu Shot Myths

Don't Fall For Flu Shot Myths

Newsy (Nov. 23, 2014) Misconceptions abound when it comes to your annual flu shot. Medical experts say most people older than 6 months should get the shot. Video provided by Newsy
Powered by NewsLook.com
WFP: Ebola Risks Heightened Among Women Throughout Africa

WFP: Ebola Risks Heightened Among Women Throughout Africa

AFP (Nov. 21, 2014) Having children has always been a frightening prospect in Sierra Leone, the world's most dangerous place to give birth, but Ebola has presented an alarming new threat for expectant mothers. Duration: 00:37 Video provided by AFP
Powered by NewsLook.com
Could Your Genes Be The Reason You're Single?

Could Your Genes Be The Reason You're Single?

Newsy (Nov. 21, 2014) Researchers in Beijing discovered a gene called 5-HTA1, and carriers are reportedly 20 percent more likely to be single. Video provided by Newsy
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:

Strange & Offbeat Stories


Health & Medicine

Mind & Brain

Living & Well

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