New method identifies genes that can predict cancer patients' prognoses
Researchers have designed a new method to identify gene sets that can predict prognoses of cancer patients.
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 Montreal (IRCM) saw this as an opportunity to develop 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.
"SAPS makes use of three specific criteria. 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," explained Andrew Beck, MD, Director of the Molecular Epidemiology Research Laboratory at BIDMC, who led the team.
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 published gene expression profiling studies in ovarian cancer (including data from approximately 1700 patients).
When the investigators used SAPS to analyze these previously identified prognostic signatures in breast and ovarian cancer, they found that only a small subset of the signatures that were considered statistically significant by standard measurements also achieved statistical significance when evaluated by SAPS.
"Our work shows that when using prognostic associations to identify biological signatures that drive cancer progression, it is important to not rely solely on a gene set's association with patient survival," said Beck.
"A gene set may appear to be important based on its survival association, when in reality it does not perform significantly better than random genes. This can be a serious problem, as it can lead to false conclusions regarding the biological and clinical significance of a gene set," he added.
By using SAPS, Beck and his colleagues found that they could overcome this problem.
"The SAPS procedure ensures that a significant prognostic gene set is not only associated with patient survival but also performs significantly better than random gene sets," stated Beck.
His team revealed new prognostic signatures in subtypes of breast cancer and ovarian cancer and demonstrated a striking similarity between signatures in estrogen receptor negative breast cancer and ovarian cancer, suggesting new shared therapeutic targets for these aggressive malignancies.
The findings also indicate that the prognostic signatures identified with SAPS will not only help predict patient outcomes but might also help in the development of new anti-cancer drugs.
Their results are reported in journal PLOS Computational Biology.