Feb 4, 2016

sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors

BioRxiv : the Preprint Server for Biology
Wenhan ChenLachlan J M Coin

Abstract

Accurate identification of copy number alterations is an essential step in understanding the events driving tumor progression. While a variety of algorithms have been developed to use high-throughput sequencing data to profile copy number changes, no tool is able to reliably characterize ploidy and genotype absolute copy number from tumor samples which contain less than 40% tumor cells. To increase our power to resolve the copy number profile from low-cellularity tumor samples, we developed a novel approach which pre-phases heterozygote germline SNPs in order to replace the commonly used 'B-allele frequency' with a more powerful 'parental-haplotype frequency'. We apply our tool - sCNAphase - to characterize the copy number and loss-of-heterozygosity profiles of four publicly available breast cancer cell-lines. Comparisons to previous spectral karyotyping and microarray studies revealed that sCNAphase reliably identified overall ploidy as well as the individual copy number mutations from each cell-line. Analysis of artificial cell-line mixtures demonstrated the capacity of this method to determine the level of tumor cellularity, consistently identify sCNAs and characterize ploidy in samples with as little as 10% tumor cells. Thi...Continue Reading

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Mentioned in this Paper

Study
Tumor Cells, Uncertain Whether Benign or Malignant
Neoplastic Cell
Neoplasms
Profile (Lab Procedure)
Sequencing
ScnA protein, Thiobacillus thioparus
Analysis
Malignant Neoplasms
Alleles

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