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Cancer Inform. 2015 Feb 10;13(Suppl 7):85-95. doi: 10.4137/CIN.S16354. eCollection 2014.

Extending information retrieval methods to personalized genomic-based studies of disease.

Author information

1
Department of Statistics, University of Wisconsin, Madison, WI, USA.
2
Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA.

Abstract

Genomic-based studies of disease now involve diverse types of data collected on large groups of patients. A major challenge facing statistical scientists is how best to combine the data, extract important features, and comprehensively characterize the ways in which they affect an individual's disease course and likelihood of response to treatment. We have developed a survival-supervised latent Dirichlet allocation (survLDA) modeling framework to address these challenges. Latent Dirichlet allocation (LDA) models have proven extremely effective at identifying themes common across large collections of text, but applications to genomics have been limited. Our framework extends LDA to the genome by considering each patient as a "document" with "text" detailing his/her clinical events and genomic state. We then further extend the framework to allow for supervision by a time-to-event response. The model enables the efficient identification of collections of clinical and genomic features that co-occur within patient subgroups, and then characterizes each patient by those features. An application of survLDA to The Cancer Genome Atlas ovarian project identifies informative patient subgroups showing differential response to treatment, and validation in an independent cohort demonstrates the potential for patient-specific inference.

KEYWORDS:

cancer; genomics; latent Dirichlet allocation; survival; time-to-event

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