Inference of Tumor Phylogenies from Genomic Assays on Heterogeneous Samples
Joint Authors
Shackney, Stanley
Schwartz, Russell
Subramanian, Ayshwarya
Source
Journal of Biomedicine and Biotechnology
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-16, 16 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-05-13
Country of Publication
Egypt
No. of Pages
16
Main Subjects
Abstract EN
Tumorigenesis can in principle result from many combinations of mutations, but only a few roughly equivalent sequences of mutations, or “progression pathways,” seem to account for most human tumors.
Phylogenetics provides a promising way to identify common progression pathways and markers of those pathways.
This approach, however, can be confounded by the high heterogeneity within and between tumors, which makes it difficult to identify conserved progression stages or organize them into robust progression pathways.
To tackle this problem, we previously developed methods for inferring progression stages from heterogeneous tumor profiles through computational unmixing.
In this paper, we develop a novel pipeline for building trees of tumor evolution from the unmixed tumor data.
The pipeline implements a statistical approach for identifying robust progression markers from unmixed tumor data and calling those markers in inferred cell states.
The result is a set of phylogenetic characters and their assignments in progression states to which we apply maximum parsimony phylogenetic inference to infer tumor progression pathways.
We demonstrate the full pipeline on simulated and real comparative genomic hybridization (CGH) data, validating its effectiveness and making novel predictions of major progression pathways and ancestral cell states in breast cancers.
American Psychological Association (APA)
Subramanian, Ayshwarya& Shackney, Stanley& Schwartz, Russell. 2012. Inference of Tumor Phylogenies from Genomic Assays on Heterogeneous Samples. Journal of Biomedicine and Biotechnology،Vol. 2012, no. 2012, pp.1-16.
https://search.emarefa.net/detail/BIM-498959
Modern Language Association (MLA)
Subramanian, Ayshwarya…[et al.]. Inference of Tumor Phylogenies from Genomic Assays on Heterogeneous Samples. Journal of Biomedicine and Biotechnology No. 2012 (2012), pp.1-16.
https://search.emarefa.net/detail/BIM-498959
American Medical Association (AMA)
Subramanian, Ayshwarya& Shackney, Stanley& Schwartz, Russell. Inference of Tumor Phylogenies from Genomic Assays on Heterogeneous Samples. Journal of Biomedicine and Biotechnology. 2012. Vol. 2012, no. 2012, pp.1-16.
https://search.emarefa.net/detail/BIM-498959
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-498959