Journal
ONCOLOGY LETTERS
Volume 16, Issue 4, Pages 4713-4720Publisher
SPANDIDOS PUBL LTD
DOI: 10.3892/ol.2018.9150
Keywords
copy number variant; expectation maximization algorithm; exome sequencing; loss of heterozygosity
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Funding
- National Natural Science Foundation of China [61571414, 61471331, 31100955]
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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 PECNV of PECNV was performed by analyzing simulated datasets contaminated with different normal cell proportion and eight real primary triple-negative breast cancer samples. PECNV demonstrated superior results compared with ExomeCNV and EXCAVATOR for the detection of genomic aberrations in WES data.
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