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SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization

Year: 2014
Type: article
Abstract: Many tumors are composed of genetically divergent cell subpopulations. We report SubcloneSeeker, a package capable of exhaustive identification of subclone structures and evolutionary histories with bulk somatic variant allele frequency measurements from tumor biopsies. We present a statistical framework to elucidate whether specific sets of mutations are present within the same subclones, and the order in which they occur. We demonstrate how subclone reconstruction provides crucial information about tumorigenesis and relapse mechanisms; guides functional study by variant prioritization, and has the potential as a rational basis for informed therapeutic strategies for the patient. SubcloneSeeker is available at: https://github.com/yiq/SubcloneSeeker.
DOI: 10.1186/preaccept-1691129011290725
Authors: Yi Qiao, Aaron R Quinlan, Amir A Jazaeri, Roeland Verhaak, David A Wheeler, Gabor T Marth
Institutions: Boston College, University of Virginia Health System, University of Virginia Medical Center, The University of Texas MD Anderson Cancer Center, Baylor College of Medicine, University of Utah
Language: English
Subfield: Cancer Research
Open Access status: gold
Estimated APC paid: $5,490
OpenAlex ID: W2124531484
FWCI: 2.959
Cites: 57
Cited by: 61
Related to: 10