PennCNV statistics
Citations per year
Tool usage distribution map
Associated diseases
Popular tool citations
Related tools
Protocols
PennCNV specifications
Information
| 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 |
Download
Versioning
No version available
Documentation
Maintainer
- person_outline Kai Wang
Additional information
Publications for PennCNV
Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.
Modeling genetic inheritance of copy number variations.
PennCNV citations
(197)Metabolic characterization of isocitrate dehydrogenase (IDH) mutant and IDH wildtype gliomaspheres uncovers cell type specific vulnerabilities
[…] 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
[…] 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
[…] liftover tool to map SNPs to the newer reference genome assembly (http://genome.ucsc.edu/cgi-bin/hgLiftOver). 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
[…] . Genotypes were generated using the Affymetrix Power Tools Release 1.20.5 using the Birdseed (v2) calling algorithm (https://www.affymetrix.com/support/developer/powertools/changelog/index.html) 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
[…] 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
[…] 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 […]
PennCNV reviews
Be the first to review PennCNV