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Protocols

ParseCNV specifications

Information


Unique identifier OMICS_02566
Name ParseCNV
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Joseph Glessner

Publication for ParseCNV

ParseCNV citations

 (9)
library_books

Copy number variation meta analysis reveals a novel duplication at 9p24 associated with multiple neurodevelopmental disorders

2017
Genome Med
PMCID: 5709845
PMID: 29191242
DOI: 10.1186/s13073-017-0494-1

[…] probes., all qc steps were performed for cases and controls together in each cohort. about 20% of samples in each cohort were excluded during qc filtering., fisher exact test implemented in software parsecnv [] was used to conduct the cnv association analysis on each of the individual cohorts chop scz, chop asd, chop adhd, and depression. it was also used to compare cnv frequency between cases […]

library_books

Partial microduplication in the histone acetyltransferase complex member KANSL1 is associated with congenital heart defects in 22q11.2 microdeletion syndrome patients

2017
Sci Rep
PMCID: 5431949
PMID: 28496102
DOI: 10.1038/s41598-017-01896-w

[…] absolute cnv counts and genomic length, and then proceeded to perform association analysis between chd phenotype and cnvs. to minimize false positives, a combination of penncnv for cnv detection and parsecnv for association study, followed by a validation of the cnvs with a second independent technique was chosen, . results indicated that a microduplication in the first three exons of kat8 […]

library_books

Genomic copy number variation association study in Caucasian patients with nonsyndromic cryptorchidism

2016
BMC Urol
PMCID: 5073740
PMID: 27769252
DOI: 10.1186/s12894-016-0180-4

[…] after sample quality control, gene- and cnv-based association tests were performed using cleaned data from group 1 (493 cases and 1586 controls) and group 2 (307 cases and 1102 controls) using parsecnv software. meta-analysis was performed using gene-based test results as input to identify significant genes, and cnvs in or around significant genes were identified in cnv-based association […]

library_books

A Genome Wide Study of Copy Number Variation Associated with Nasopharyngeal Carcinoma in Malaysian Chinese Identifies CNVs at 11q14.3 and 6p21.3 as Candidate Loci

2016
PLoS One
PMCID: 4701378
PMID: 26730743
DOI: 10.1371/journal.pone.0145774

[…] using plink v.1.07 was carried out to assess the frequency difference between npc cases and healthy controls using gender and age as covariates. gene-based association was carried out using parsecnv v.17 []. gwama v.1.4 [] was used for i2 heterogeneity analysis. g*power v.3.1.9.2 was employed for power analysis for z tests logistic regression, using post-hoc computation of achieved […]

library_books

CNV Analysis Associates AKNAD1 with Type 2 Diabetes in Jordan Subpopulations

2015
Sci Rep
PMCID: 4543987
PMID: 26292654
DOI: 10.1038/srep13391

[…] removed., after qc, we performed pca based on snp genotypes of a set of ld (linkage disequilibrium)-pruned snps using software eigenstrat., we tested cnv association with t2d case control status via parsecnv which uses an unbiased segment-based scoring approach to identify cnv regions (cnvrs) associated with the disease status. briefly, for each snp, cnv frequency between cases and controls […]

library_books

Molecular Characterization of an Intact p53 Pathway Subtype in High Grade Serous Ovarian Cancer

2014
PLoS One
PMCID: 4252108
PMID: 25460179
DOI: 10.1371/journal.pone.0114491

[…] model according to calculations of the log r ratio and b-allele frequency values. the cnv frequency between tumor and normal samples was evaluated for each snp using fisher’s exact test in the parsecnv algorithm . threshold criteria for recurring cnv regions (cnvrs) were as follows: fisher’s exact test p value of <0.0005 and no overlap with structural variations in samples from healthy […]


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ParseCNV institution(s)
Department of Pediatrics, Division of Human Genetics, The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA

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