PennCNV statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PennCNV

Tool usage distribution map

This map represents all the scientific publications referring to PennCNV per scientific context
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Associated diseases

This word cloud represents PennCNV usage per disease context

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PennCNV specifications


Unique identifier OMICS_00729
Name PennCNV
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Affymetrix
Operating system Unix/Linux
Programming languages C, Perl
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Kai Wang

Additional information

Publications for PennCNV

PennCNV citations


Metabolic characterization of isocitrate dehydrogenase (IDH) mutant and IDH wildtype gliomaspheres uncovers cell type specific vulnerabilities

PMCID: 5905129
PMID: 29692895
DOI: 10.1186/s40170-018-0177-4
call_split See protocol

[…] to Affymetrix CytoScanHD arrays. We first processed the raw intensity CEL files using the R package affy2sv [] to generate B-allele frequency (BAF) and log R ratio (LRR) values. Secondly, we used the PennCNV software (parameters: exome HMM model with gcmodel adjustment, filtered by 10 SNPs minimum 10 and with region length longer than 50 k) [], the R package GenoCN (parameters: cnv-only snpInfo$PF […]


A method for determining haploid and triploid genotypes and their association with vascular phenotypes in Williams syndrome and 7q11.23 duplication syndrome

BMC Med Genet
PMCID: 5883342
PMID: 29614955
DOI: 10.1186/s12881-018-0563-3

[…] ence variation of the remaining (in WS) or duplicated (in Dup7) alleles within 7q11.23 causes variability in gene functioning, which may, in turn, impact symptom severity. Available software, such as PennCNV, has been used to identify CNVs using commonly-acquired SNP-chip data. However, using this same chip data to also determine the underlying non-diploid genotypes of CNV regions has not been don […]


Genome wide Association Study (GWAS) of Germline Copy Number Variations (CNVs) Reveal Genetic Risks of Prostate Cancer in Chinese population

PMCID: 5868157
PMID: 29581771
DOI: 10.7150/jca.22802

[…] liftover tool to map SNPs to the newer reference genome assembly ( By choosing proper population frequency of B allele (PFB) and GCmodel files, we then used PennCNV to identify CNVs and generate a quality control summary for each sample . […]


Diffuse gliomas classified by 1p/19q co deletion, TERT promoter and IDH mutation status are associated with specific genetic risk loci

Acta Neuropathol
PMCID: 5904227
PMID: 29460007
DOI: 10.1007/s00401-018-1825-z

[…] . Genotypes were generated using the Affymetrix Power Tools Release 1.20.5 using the Birdseed (v2) calling algorithm ( and PennCNV []. After quality control (Supplementary Figs. 1, 2, Supplementary Table 1) there were 521 TCGA glioma cases and 2648 controls (Table ). Glioma tumour molecular data (IDH mutation, 1p/19q co-d […]


A Two Stage Whole Genome Gene Expression Association Study of Young Onset Hypertension in Han Chinese Population of Taiwan

Sci Rep
PMCID: 5789005
PMID: 29379041
DOI: 10.1038/s41598-018-19520-w

[…] on. Statistical significance was claimed under a significance threshold of p-value < 0.05.Furthermore, the intensity data of 497,849 SNPs were used to call the CNV regions. CNVs were identified using PennCNV and QuantiSNP, respectively, which identifies CNVs by integrating intensity data from neighboring probes using a hidden Markov model (HMM). Gene-based CNVs association analysis was used to tes […]


Widespread modulation of gene expression by copy number variation in skeletal muscle

Sci Rep
PMCID: 5780461
PMID: 29362391
DOI: 10.1038/s41598-018-19782-4

[…] tected based on comparative genomic hybridization [CGH]. On the other hand, CNVs can also be computationally inferred from SNP-arrays,. A frequently used algorithm to infer CNVs from SNP-chip data is PennCNV, which shows good consistency with the CGH gold standard,. In addition, recent developments have also enabled the detection of CNVs from next-generation sequencing data. However, the extent to […]

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PennCNV institution(s)
Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA; Center for Applied Genomics and Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA; Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA; Department of Mathematics, Georgetown University, Washington DC, USA
PennCNV funding source(s)
Supported by NARSAD Distinguished Investigator Award; University Research Foundation grant, McCabe Pilot Award from the University of Pennsylvania; National Institute of Health (grant R01HG004517), an Institute Development Award to the Center for Applied Genomics from the Children’s Hospital of Philadelphia.

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