Ploidy‐ and Purity‐Adjusted Allele‐Specific DNA Analysis Using CLONETv2. Issue 1 (21st June 2019)

• Record Type: Journal Article
• Authors: Prandi, Davide; Demichelis, Francesca
• Editors: Baxevanis, Andreas D.; Petsko, Gregory A.; Stein, Lincoln D.; Stormo, Gary D.
• Is Part Of: Current protocols in bioinformatics. Volume 67:Issue 1(2019)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2019-06-21
• Subjects: allele‐specific analysis -- cancer genomics -- clonality -- ploidy -- purity; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/cpbi.81
• Languages: English
• ISSNs: 1934-3396

Abstract

Abstract: High‐throughput DNA sequencing technology provides base‐level and statistically rich information about the genomic content of a sample. In the contexts of cancer research and precision oncology, thousands of genomes from paired tumor and matched normal samples are profiled and processed to determine somatic copy‐number changes and single‐nucleotide variations. Higher‐order informative analyses, in the form of allele‐specific copy‐number assessments or subclonality quantification, require reliable estimates of tumor DNA ploidy and tumor cellularity. CLONETv2 provides a complete set of functions to process matched normal and tumor pairs using patient‐specific genotype data, is independent of low‐level tools (e.g., aligner, segmentation algorithm, mutation caller) and offers high‐level functions to compute allele‐specific copy number from segmented data and to identify subclonal population in the input sample. CLONETv2 is applicable to whole‐genome, whole‐exome and targeted sequencing data generated either from tissue or from liquid biopsy samples. © 2019 The Authors.