Clinical sequencing studies routinely involve molecular profiling of patients for mutations and copy number alterations. However, detection of “actionable” aberrations to guide treatment decisions require accurate, tumor purity-, ploidy-, and clonal heterogeneity-adjusted integer copy number calls. In this chapter, we describe the FACETS algorithm, an Allele-Specific Copy Number (ASCN) analysis tool with a broad application to whole-genome, whole-exome, as well as targeted panel sequencing platforms to annotate the genome for the detection of copy number alterations including homozygous/heterozygous deletions, copy-neutral loss-of-heterozygosity (LOH) events, allele-specific gains/amplifications, and cellular fraction profiles. We will describe some methodological details on joint segmentation of total and allele-specific copy number, on the estimation of integer copy number calls adjusting for tumor purity, ploidy, and intratumor heterogeneity, along with comprehensive output and integrated visualization. We also provide a tutorial on the installation, application, and tips to run and interpret FACETS.
CITATION STYLE
Arora, A., Shen, R., & Seshan, V. E. (2022). FACETS: Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing. In Methods in Molecular Biology (Vol. 2493, pp. 89–105). Humana Press Inc. https://doi.org/10.1007/978-1-0716-2293-3_7
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