PatternCNV protocols

PatternCNV statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

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Associated diseases

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PatternCNV specifications

Information


Unique identifier OMICS_04189
Name PatternCNV
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Perl, R
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for PatternCNV

PatternCNV in pipeline

2017
PMCID: 5420801
PMID: 28408749
DOI: 10.1038/emm.2017.9

[…] project 6500. nonflagged snps, based on dbsnp138, were filtered out to sort out passenger calls, and possible false-positive calls in the segmental duplicate region were also removed. adtex and patterncnv were used to detect somatic copy-number variations (cnvs) for the six blood/gs paired samples., , the cnv microarray test was performed using the affymetrix cytoscan hd array system […]


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PatternCNV in publications

 (7)
PMCID: 5606870
PMID: 28944238
DOI: 10.1002/mgg3.317

[…] variants and those located in introns, untranslated regions, or intergenic regions were excluded from this study., all copy number variations (cnvs) were called using an updated version of patterncnv, which uses all the samples to learn the pattern and variance of the coverage to better enable cnv calling (wang et al. ). it computes the differences in observed coverage versus […]

PMCID: 5420801
PMID: 28408749
DOI: 10.1038/emm.2017.9

[…] project 6500. nonflagged snps, based on dbsnp138, were filtered out to sort out passenger calls, and possible false-positive calls in the segmental duplicate region were also removed. adtex and patterncnv were used to detect somatic copy-number variations (cnvs) for the six blood/gs paired samples., , the cnv microarray test was performed using the affymetrix cytoscan hd array system […]

PMCID: 5089432
PMID: 27830186
DOI: 10.1212/NXG.0000000000000117

[…] could be made at that time ()., we recently developed a targeted ngs panel including 21 known cms genes and applied it to this patient. because a copy number variation (cnv) analysis algorithm (patterncnv) is incorporated in the bioinformatics evaluation, this panel has a capability of detecting nucleotide changes, small insertion/deletions, and cnvs. the result from this panel confirmed […]

PMCID: 4687867
PMID: 26695660
DOI: 10.1371/journal.pone.0145176

[…] low or modifier impact, and any variant observed in the 1000 genomes project [] or the exome sequencing project []., all somatic copy number variations (cnvs) were called using an updated version of patterncnv [], which uses reference samples to learn the pattern and variance of the wes coverage to better enable somatic cnv calling. the median reads per kilobase per million mapped reads (rpkm) […]

PMCID: 4633051
PMID: 26536348
DOI: 10.1371/journal.pone.0141906

[…] than in whole genome sequencing and is still further complicated by complexity of tumor genomes. recently developed tools to improve the accuracy of assessing cnvs in exome sequencing data, such as patterncnv, may have utility in further identifying ptcl driver variations in the genomes of malignant t cells in this data set []., our study, together with prior findings, expand the total number […]


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PatternCNV institution(s)
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Division of Epidemiology, Department of Health Sciences Research, Division of Hematology, Department of Internal Medicine, Mayo Clinic, Chinahester, MN, USA; Department of Health Sciences Research, Jacksonville, FL, USA

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