Abstract
Intra-tumor heterogeneity reflects cancer genome evolution and provides key information for diagnosis and treatment. When bulk tumor tissues are profiled for somatic copy number alterations (sCNA) and point mutations, it may be difficult to estimate their cellular fractions when a mutation falls within a sCNA. We present the Clonal Heterogeneity Analysis Tool, which estimates cellular fractions for both sCNAs and mutations, and uses their distributions to inform macroscopic clonal architecture. In a set of approximately 700 breast tumors, more than half appear to contain multiple recognizable aneuploid tumor clones, and many show subtype-specific differences in clonality for known cancer genes.
Keywords
BiologyHuman geneticsComputational biologyDNA sequencingSNP arrayGeneticsSNPDNAEvolutionary biologyComputational genomicsPersonal genomicsGenomicsGenomeSingle-nucleotide polymorphismGeneGenotype
MeSH Terms
Breast NeoplasmsCell LineageFemaleGene FrequencyGenetic HeterogeneityHumansLoss of HeterozygosityModelsGeneticPolymorphismSingle NucleotideSequence AnalysisDNASoftware
Affiliated Institutions
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Publication Info
- Year
- 2014
- Type
- article
- Volume
- 15
- Issue
- 9
- Pages
- 473-473
- Citations
- 84
- Access
- Closed
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Cite This
Bo Li,
Jun Z. Li
(2014).
A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data.
Genome biology
, 15
(9)
, 473-473.
https://doi.org/10.1186/s13059-014-0473-4
Identifiers
- DOI
- 10.1186/s13059-014-0473-4
- PMID
- 25253082
- PMCID
- PMC4203890