Detection of copy number variants and loss of heterozygosity from impure tumor samples using whole exome sequencing data.

ABSTRACT: Using whole-exome sequencing (WES) for the detection of chromosomal aberrations from tumor samples has become increasingly popular, as it is cost-effective and time efficient. However, factors which present in WES tumor samples, including diversity in exon size, batch effect and tumor impurity, can complicate the identification of somatic mutation in each region of the exon. To address these issues, the authors of the present study have developed a novel method, PECNV, for the detection of genomic copy number variants and loss of heterozygosity in WES datasets. PECNV combines normalized logarithm ratio of read counts (Log Ratio) and B allele frequency (BAF), and then employs expectation maximization (EM) algorithm to estimate parameters involved in the models. A comprehensive assessment of

SUBMITTER: Liu X 

PROVIDER: S-EPMC6126229 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature