FACETS: Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing Journal Article
| Authors: | Arora, A.; Shen, R.; Seshan, V. E. |
| Article Title: | FACETS: Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing |
| Abstract: | 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. © 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature. |
| Keywords: | single nucleotide polymorphism; genetics; polymorphism, single nucleotide; neoplasm; neoplasms; allele; alleles; dna sequence; sequence analysis, dna; dna copy number variations; copy number variation; ploidy; high throughput sequencing; high-throughput nucleotide sequencing; humans; human; purity; allele-specific copy number analysis; high-throughput dna sequencing; integer copy number |
| Journal Title: | Methods in Molecular Biology |
| Volume: | 2493 |
| ISSN: | 1064-3745 |
| Publisher: | Humana Press Inc |
| Date Published: | 2022-06-26 |
| Start Page: | 89 |
| End Page: | 105 |
| Language: | English |
| DOI: | 10.1007/978-1-0716-2293-3_7 |
| PUBMED: | 35751811 |
| PROVIDER: | scopus |
| DOI/URL: | |
| Notes: | Book Chapter: 7 in "Varian Calling: Methods and Protocols" (ISBN: 978-1-0716-2292-6) -- Export Date: 1 August 2022 -- Source: Scopus |
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