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New method identifies genes that can predict prognoses of cancer patients
Date:1/25/2013

BOSTON In recent years, it has been thought that select sets of genes might reveal cancer patients' prognoses. However, a study published last year examining breast cancer cases found that most of these "prognostic signatures" were no more accurate than random gene sets in determining cancer prognoses. While many saw this as a disappointment, investigators at Beth Israel Deaconess Medical Center (BIDMC), the Dana-Farber Cancer Institute, and the Institut de Recherches Cliniques de Montral (IRCM) saw this as an opportunity to design a new method to identify gene sets that could yield more significant prognostic value.

Led by Andrew Beck, MD, Director of the Molecular Epidemiology Research Laboratory at BIDMC, the team has developed SAPS (Significance Analysis of Prognostic Signatures), a new algorithm that makes use of three specific criteria to more accurately identify prognostic signatures associated with patient survival.

Their results, the largest analysis of its kind ever performed, are reported in the January 24 on-line issue of the journal PLOS Computational Biology.

"SAPS makes use of three specific criteria," explains Beck, who is also an Assistant Professor of Pathology at Harvard Medical School. "First, the gene set must be enriched for genes that are associated with survival. In addition, the gene set must separate patients into groups that show survival differences. Lastly, it must also perform significantly better than sets of random genes at these tasks."

In the new study, the scientific team applied the SAPS algorithm to gene expression profiling data from the study's senior author Benjamin Haibe-Kains, PhD, Director of the Bioinformatics and Computational Genomics Laboratory at IRCM and an Assistant Research Professor at the University of Montreal. The first collection of data was obtained from 19 published breast cancer studies (including approximately 3800 patients), and the second included 12 publ
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Contact: Bonnie Prescott
bprescot@bidmc.harvard.edu
617-667-7306
Beth Israel Deaconess Medical Center
Source:Eurekalert

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