Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies.

ABSTRACT:

Background

Genomic aberrations can be used to determine cancer diagnosis and prognosis. Clinically relevant novel aberrations can be discovered using high-throughput assays such as Single Nucleotide Polymorphism (SNP) arrays and next-generation sequencing, which typically provide aggregate signals of many cells at once. However, heterogeneity of tumor subclones dramatically complicates the task of detecting aberrations.

Results

The aggregate signal of a population of subclones can be described as a linear system of equations. We employed a measure of allelic imbalance and total amount of DNA to characterize each locus by the copy number status (gain, loss or neither) of the strongest subclonal component. We designed simulated data to compare our measure to existing approache

SUBMITTER: Parisi F 

PROVIDER: S-EPMC3114747 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature