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Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome.

Daniall MasoodLuyao RenCu NguyenFrancesco G BrunduLily ZhengYongmei ZhaoErich JaegerYong LiSeong Won ChaAaron HalpernSean TruongMichael VirataChunhua YanQingrong ChenAndy PangReyes AlbertoChunlin XiaoZhaowei YangWanqiu ChenCharles WangFrank CrossSeverine CatreuxLeming ShiJulia A BeaverWenming XiaoDaoud M Meerzaman
Published in: Genome biology (2024)
NGS technologies and current bioinformatics tools can offer reliable results for detection of copy gain, loss, and LOH. However, when working with a hyper-diploid genome, some software tools can call excessive copy gain or loss due to inaccurate assessment of genome ploidy. With performance matrices on various experimental conditions, this study raises awareness within the cancer research community for the selection of sequencing platforms, sample preparation, sequencing coverage, and the choice of CNV detection tools.
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