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DNA copy specifications

Information


Unique identifier OMICS_27640
Name DNA copy
Alternative name circular binary segmentation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Fortran, R
Computer skills Advanced
Maintained No

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Publication for DNA copy

DNA copy citations

 (291)
library_books

Integrative analysis and machine learning on cancer genomics data using the Cancer Systems Biology Database (CancerSysDB)

2018
BMC Bioinformatics
PMCID: 5921751
PMID: 29699486
DOI: 10.1186/s12859-018-2157-7

[…] t the Broad Institute. Data on somatic copy number alterations were based on the SNP 6.0 microarray platform (Affymetrix Inc., CA, USA) given as genomic segments of equal copy number derived from the Circular Binary Segmentation (CBS) algorithm []. For gene expression analysis, raw RNA-Seq read counts were re-processed and compared between tumor tissues and tissue-derived normal samples using vers […]

library_books

Aggressive natural killer cell leukemia mutational landscape and drug profiling highlight JAK STAT signaling as therapeutic target

2018
Nat Commun
PMCID: 5908809
PMID: 29674644
DOI: 10.1038/s41467-018-03987-2

[…] region. We then filtered out the regions with sequencing coverage lower than 25×. Finally, the log2 copy number ratios for each sample were divided by the reference and calculated and segmented using Circular Binary Segmentation. The copy number data for all human genes in the Ensembl database v67 were calculated by assigning a gene the value of the copy number variant data segment with which it o […]

library_books

Xome Blender: A novel cancer genome simulator

2018
PLoS One
PMCID: 5886411
PMID: 29621252
DOI: 10.1371/journal.pone.0194472

[…] for the amount of input data (unique bases mapped), the relative copy number change is inferred as the log2 of the ratio of tumor depth to normal depth for each contiguous region. Then, it applies a circular binary segmentation (CBS) algorithm (Seshan and Olshen 2010) to delineate segments by copy number and identify significant change-points and finally, merges adjacent segments of similar copy […]

library_books

Genomic profiling of dedifferentiated liposarcoma compared to matched well differentiated liposarcoma reveals higher genomic complexity and a common origin

2018
PMCID: 5880260
PMID: 29610390
DOI: 10.1101/mcs.a002386

[…] For all patients, somatic copy-number calls from whole-exome data using matched normals were obtained by first deriving segments using circular binary segmentation (CBS) () and then deriving log2 ratio scores with an in-house tool, exomeCN, which is a modified version of HMMcopy () tuned for our data. For assessing amplifications and […]

library_books

Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility

2018
Nat Commun
PMCID: 5823854
PMID: 29472540
DOI: 10.1038/s41467-018-03082-6

[…] onsidered variants with a total read depth > 5 and considered both read depth and variant read fraction in defining a homozygous variant nucleotide (Supplementary Table ).Following these assignments, DNA copy (v1.44.0, default parameters) was used to identify blocks of the genome containing at least ten variant calls where at least 90% of the calls share a zygosity of homozygous variant. Calls in […]

library_books

Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution

2018
Nat Commun
PMCID: 5750210
PMID: 29296022
DOI: 10.1038/s41467-017-02424-0

[…] rray/CELfiles.shtml). CNAs for each probe were computed as log2-ratios between the probe signal intensities of each sample and the reference skin sample and then those ratios were segmented using the circular binary segmentation algorithm implemented in the R package DNAcopy. […]

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DNA copy institution(s)
Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, Laurel Hollow, NY, USA
DNA copy funding source(s)
Supported by a grant from the NCI (CA73848), grants from the National Institutes of Health and NCI (CA078544; CA45508); The Long Island Breast Cancer Action Coalition; Lillian Goldman and the Breast Cancer Research Foundation; Marks Family Foundation; and The Miracle Foundation.

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