Abstract
Copy number variants (CNVs) and copy neutral loss of heterozygosity (CN-LOH) represent important types of genomic abnormalities in cancer. Genomic DNA microarray serves as the current gold standard method for detecting genome-wide CNVs and CN-LOH. However, as next-generation sequencing (NGS) is widely used to detect gene variants in clinical testing, the ability of NGS to detect CNVs and CN-LOH has also been demonstrated. This chapter describes a protocol for detecting genome-wide large somatic CNVs and CN-LOH using a single nucleotide polymorphism (SNP) sequencing backbone. When combined with a targeted gene mutation panel, this strategy allows for simultaneous detection of somatic gene mutations and genome-wide CNVs and CN-LOH.
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Acknowledgments
We would like to thank Oliver Tam for assisting the design of SNP sequencing backbone.
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Shen, W., Szankasi, P., Durtschi, J., Kelley, T.W., Xu, X. (2019). Genome-Wide Copy Number Variation Detection Using NGS: Data Analysis and Interpretation. In: Murray, S. (eds) Tumor Profiling. Methods in Molecular Biology, vol 1908. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9004-7_8
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DOI: https://doi.org/10.1007/978-1-4939-9004-7_8
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