Optimized prediction of extreme treatment outcomes in ovarian cancer

Burook Misganaw, Eren Ahsen, Nitin Singh, Keith A. Baggerly, Anna Unruh, Michael A. White, M. Vidyasagar

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

The TCGA ovarian cancer database shows that about 10% of patients respond poorly to platinum-based chemotherapy, with tumors relapsing in seven months or less. At the other extreme, another 10% or so enjoy disease-free survival of three years or more [1]. At present there are more than a dozen prognostic signatures that claim to predict the survival prospects of a patient based on her genetic profile. Yet, according to [2], none of these signatures performs significantly better than pure guessing. Accordingly, in this paper the objective is to propose and validate another gene-based signature. TCGA ovarian cancer data is analyzed using the lone star algorithm [3] that is specifically developed for identifying a small number of highly predictive features from a very large set. Using this algorithm, we are able to identify a biomarker panel of 25 genes (out of 12,000) that can be used to classify patients into one of three groups: super-responders (SR), medium responders (MR), and non-responders (NR). We are also able to determine a discriminant function that can divide patients into two classes, such that there is a clear survival advantage of one group over the other. This signature is developed using the TCGA Agilent platform data, and cross-validated on the TCGA Affymetrix platform data, as well as entirely independent data due to Tothill et al. [4]. The P-value on the training data is below machine zero, while the P-values on cross-validation are well below the widely accepted threshold of 0.05.

Original languageEnglish (US)
Title of host publicationProceedings of the IEEE Conference on Decision and Control
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1254-1258
Number of pages5
Volume2016-February
ISBN (Print)9781479978861
DOIs
StatePublished - Feb 8 2016
Event54th IEEE Conference on Decision and Control, CDC 2015 - Osaka, Japan
Duration: Dec 15 2015Dec 18 2015

Other

Other54th IEEE Conference on Decision and Control, CDC 2015
CountryJapan
CityOsaka
Period12/15/1512/18/15

ASJC Scopus subject areas

  • Control and Systems Engineering
  • Modeling and Simulation
  • Control and Optimization

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  • Cite this

    Misganaw, B., Ahsen, E., Singh, N., Baggerly, K. A., Unruh, A., White, M. A., & Vidyasagar, M. (2016). Optimized prediction of extreme treatment outcomes in ovarian cancer. In Proceedings of the IEEE Conference on Decision and Control (Vol. 2016-February, pp. 1254-1258). [7402383] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CDC.2015.7402383