Featured Research

from universities, journals, and other organizations

Study Identifies Common Flaws In Oncology Microarray Studies

Date:
January 17, 2007
Source:
Journal of the National Cancer Institute
Summary:
A substantial percentage of microarray-based studies in oncology contain critical flaws in analysis or in their conclusions, reports a study in the Jan. 17 issue of the Journal of the National Cancer Institute. The study's authors provide a checklist and a set of guidelines for performing and reporting such studies.

A substantial percentage of microarray-based studies in oncology contain critical flaws in analysis or in their conclusions, reports a study in the January 17 issue of the Journal of the National Cancer Institute. The study's authors provide a checklist and a set of guidelines for performing and reporting such studies.

Microarrays are a tool used to study gene expression. Researchers can study thousands of genes at a time, all on a single glass slide. In oncology, scientists have used microarrays to study unique gene expression patterns of specific tumor types, to discover new drug targets, and to categorize unique characteristics of a particular tumor to help doctors tailor treatments to an individual patient. However, such studies produce volumes of data that is easily misinterpreted. It has been difficult to replicate such studies, which is considered the best way to validate scientific findings.

To study the statistical methods used in cancer-focused microarray studies, Alain Dupuy, M.D., and Richard M. Simon, D.Sc., of the National Cancer Institute in Bethesda, Md., reviewed 90 studies published through the end of 2004 that related microarray expression profiling to clinical outcome. The most common cancers in those studies were hematologic malignancies (24 studies), lung cancer (12 studies), and breast cancer (12 studies). The studies fell into three general categories: an outcome-related gene finding, such as searching for specific genes that are expressed differently in people who have a good versus bad prognosis; a class discovery, where researchers cluster together tumors with similar gene expression profiles; and supervised prediction, in which the gene expression profiles are used to generate an algorithm or set of rules that will predict clinical outcomes for patients based on their individual gene expression profiles.

The authors closely scrutinized the statistical methods and reporting in 42 studies published in 2004. Half of these studies (21) contained at least one basic flaw. In the 23 studies with an outcome-related gene finding, nine of them had inadequate, unclear, or unstated methods to take into account false-positive findings. In 13 of the 28 studies focused on class discovery, there were spurious claims of meaningful classifications of outcomes, in which the authors did not perform adequate analyses to reach their conclusions. Among the 28 studies reporting supervised prediction, Dupuy and Simon found that 12 of those studies used biased estimates of the accuracy of their predictions.

"...Microarray studies are a fast-growing area for both basic and clinical research with an exponentially growing number of publications," the authors write. "As demonstrated by our results, common mistakes and misunderstandings are pervasive in studies published in good-quality, peer-reviewed journals." To avoid such errors, Dupuy and Simon provide guidelines in the form of a list of "Do's and Don'ts" for researchers. "We believe that following these guidelines should substantially improve the quality of analysis and reporting of microarray investigations," the authors write.

Citation: Dupuy A, Simon RM. Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J Natl Cancer Inst 2006; 99:148-58.

Note: The Journal of the National Cancer Institute is published by Oxford University Press and is not affiliated with the National Cancer Institute. Attribution to the Journal of the National Cancer Institute is requested in all news coverage. Visit the Journal online at http://jnci.oxfordjournals.org/.


Story Source:

The above story is based on materials provided by Journal of the National Cancer Institute. Note: Materials may be edited for content and length.


Cite This Page:

Journal of the National Cancer Institute. "Study Identifies Common Flaws In Oncology Microarray Studies." ScienceDaily. ScienceDaily, 17 January 2007. <www.sciencedaily.com/releases/2007/01/070116205601.htm>.
Journal of the National Cancer Institute. (2007, January 17). Study Identifies Common Flaws In Oncology Microarray Studies. ScienceDaily. Retrieved April 25, 2014 from www.sciencedaily.com/releases/2007/01/070116205601.htm
Journal of the National Cancer Institute. "Study Identifies Common Flaws In Oncology Microarray Studies." ScienceDaily. www.sciencedaily.com/releases/2007/01/070116205601.htm (accessed April 25, 2014).

Share This



More Health & Medicine News

Friday, April 25, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Deadly Fungus Killing Bats, Spreading in US

Deadly Fungus Killing Bats, Spreading in US

AP (Apr. 24, 2014) A disease that has killed more than six million cave-dwelling bats in the United States is on the move and wildlife biologists are worried. White Nose Syndrome, discovered in New York in 2006, has now spread to 25 states. (April 24) Video provided by AP
Powered by NewsLook.com
Companies Ramp Up Wellness to Lower Health Costs

Companies Ramp Up Wellness to Lower Health Costs

AP (Apr. 24, 2014) That little voice telling you to exercise, get in shape and get healthy is probably coming from your boss. More companies are beefing up wellness programs to try and cut down their health care costs. (April 24) Video provided by AP
Powered by NewsLook.com
Blood From World's Oldest Woman Suggests Life Limit

Blood From World's Oldest Woman Suggests Life Limit

Newsy (Apr. 24, 2014) Scientists say for the extremely elderly, their stem cells might reach a state of exhaustion. This could limit one's life span. Video provided by Newsy
Powered by NewsLook.com
FDA Wants To Ban Sales Of E-Cigarettes To Minors

FDA Wants To Ban Sales Of E-Cigarettes To Minors

Newsy (Apr. 24, 2014) The Food and Drug Administration wants to crack down on the use of e-cigarettes, banning the sale of the product to minors. 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:
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