title: SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization.
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.
authors.forename: Yi
authors.initials: Y
authors.lastname: Qiao
authors.forename: Aaron R
authors.initials: AR
authors.lastname: Quinlan
authors.forename: Amir A
authors.initials: AA
authors.lastname: Jazaeri
authors.forename: Roeland Gw
authors.initials: RG
authors.lastname: Verhaak
authors.forename: David A
authors.initials: DA
authors.lastname: Wheeler
authors.forename: Gabor T
authors.initials: GT
authors.lastname: Marth
mesh_terms: D000465:Algorithms; D002999:Clone Cells; D019295:Computational Biology / Q000379:methods*; D005787:Gene Frequency; D014644:Genetic Variation; D006801:Humans; D008957:Models, Genetic; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology; D064878:Web Browser