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.

Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2 / Prandi, D.; Demichelis, F.. - In: CURRENT PROTOCOLS IN BIOINFORMATICS. - ISSN 1934-3396. - 67:1(2019), p. e81. [10.1002/cpbi.81]

Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2

Prandi D.;Demichelis F.
2019-01-01

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.
2019
1
Prandi, D.; Demichelis, F.
Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2 / Prandi, D.; Demichelis, F.. - In: CURRENT PROTOCOLS IN BIOINFORMATICS. - ISSN 1934-3396. - 67:1(2019), p. e81. [10.1002/cpbi.81]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11572/312483
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