PennCNV protocols

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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



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  • person_outline Kai Wang <>

Additional information

Publications for PennCNV

PennCNV in pipelines

PMCID: 5824808
PMID: 29476056
DOI: 10.1038/s41467-017-02621-x

[…] not pass the quality control (0/1 column in supplementary data ) and were excluded from further analysis. logr values were corrected for gc content bias using the genomic wave correction tool of the penncnv software suite., the bioinformatics procedures and statistical tools to analyze the data are described in more detail in the supplementary methods (supplementary figs. –, supplementary tables  […]

PMCID: 5267451
PMID: 28122487
DOI: 10.1186/s12711-017-0286-5

[…] pipeline used for sv detection and validation, which has the advantage that sv were called with lower false positive rates, but false negatives undoubtedly do occur., the comparison between our penncnv calls and large sv (larger than 5 kb) suggested a low overlapping rate (only 12 to 15%). this low percentage is mainly due to the different spectrums of detection: rp and sr methods […]

PMCID: 5468233
PMID: 28607403
DOI: 10.1038/s41598-017-03496-0

[…] all four clones at an equal ratio of 25%) did not pass quality control (call rate <0.98) and was discarded. logr values were further normalised using the genomic wave correction tool from the penncnv software suite and the cn profiles of the 15 remaining samples were computed using ascat. the shannon diversity indices were calculated using the clonal frequencies of each mixture […]

PMCID: 5628936
PMID: 28945760
DOI: 10.1371/journal.pgen.1007001

[…] for each tumor and matched control from whole genome sequencing data. in a small number of cases data was obtained directly from affymetrix snp6.0 arrays () and rescaled and transformed using penncnv []. ascat 2.2 was then used to generate segmented copy number profiles and estimate the purity and ploidy of the sample using a penalty of 50 and gamma value of 1 [,]. note that given […]

PMCID: 5073740
PMID: 27769252
DOI: 10.1186/s12894-016-0180-4

[…]  k intersection of snps between platforms used in the 2 case–control groups, cnv detection, sample quality control (qc), and association tests were performed separately in groups 1 and 2. we used the penncnv software package [–] to make cnv calls based on signal intensity data from genotyping arrays including log r ratio (lrr) and b allele frequency (baf) for each snp. adjacent cnv calls were then […]

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PennCNV in publications

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

[…] 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 […]

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

[…] explain clinical variability, we test for genotype-phenotype associations., blood samples for 25 individuals with ws and 13 individuals with dup7 were genotyped with illumina-humanomni5m snp-chips. penncnv and in-house code were used to make genotype calls for each snp in the 7q11.23 locus. we tested for association between the presence of aortic arteriopathy and genotypes of the remaining […]

PMCID: 5888565
DOI: 10.1093/schbul/sby018.978

[…] patients recruited at the centre for addiction and mental health (camh) (toronto, canada) was run on the affymetrix snp array 6. 0. cnvs were called using two algorithms (canary software and penncnv) for deletions >200 kb and duplications >500 kb. cnvs called by both algorithms were included in further analysis. all cnvs were individually assessed to determine overlap with known, […]

PMCID: 5840339
PMID: 29511269
DOI: 10.1038/s41598-018-22427-1

[…] type of variation in our data, we take sample from an adenocarcinoma (adca) patient (g2202) and compared the cnv profile of the primary tumor, adjacent normal cr culture and tumor cr culture using penncnv, an integrated markov model for copy number variation analysis from whole-genome snp genotyping data at a high kilobase-resolution for each chromosome,. as expected, a normal cr culture […]

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

[…] 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 ., during snp genotyping, samples were removed if they (i) had an overall genotyping rate of <95%; or (ii) […]

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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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