OncoSNP statistics

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OncoSNP specifications

Information


Unique identifier OMICS_00728
Name OncoSNP
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Christopher Yau <>

Publication for OncoSNP

OncoSNP in publications

 (16)
PMCID: 5603517
PMID: 28924153
DOI: 10.1038/s41467-017-00408-8

[…] samples, using illumina humanhap550 or 610 snp arrays including 442 samples with matched blood dna samples (supplementary data¬†). tumor-based copy number segments were first calculated by ascat and oncosnp, and then curated manually. tumor samples were excluded if the copy number results were suggestive of noise or if no amplification/deletion events were detected. following thorough quality […]

PMCID: 4867884
PMID: 27226674
DOI: 10.1080/01621459.2014.998762

[…] obtain site-wise posterior probabilities of state occupation. shows an example copy number analysis of chromosome 1 of a colorectal cancer cell line sw837 from an snp microarray dataset using the oncosnp software from yau et al. (). the chromosome exhibits a number of copy number alterations leading to changes in the pattern of the log r ratio and b allele frequency along the chromosome. […]

PMCID: 5058651
PMID: 27144525
DOI: 10.18632/oncotarget.9093

[…] annovar [] using ncbi refseq database., sample pairs (n = 5) with snp array data, log2 ratios were calculated by comparing the tumor sample signals with pooled normal samples from illumina. then oncosnp r package [] was used to perform segmentation analysis on generating loh and cnv segments. the segmentation results were further manually reviewed to identify missing focal copy number […]

PMCID: 5095014
PMID: 27167335
DOI: 10.18632/oncotarget.9015

[…] allele-specific pcr chemistry (kbiosciences ltd, hoddesdon uk [])., tumor cin status was determined from existing illumina human610-quad beadchip data on matched tumor and normal dna using oncosnp as described previously []. briefly, copy-number for individual autosomes was estimated by calculating the mode of absolute dna copy-numbers across snps, and the total autosome number […]

PMCID: 4822033
PMID: 27045317
DOI: 10.1038/ncomms11111

[…] performed using the cpdb (http://cpdb.molgen.mpg.de/)., where dna was available, we analysed pre- and post-treatment tumour samples using illumina core exome 24 arrays using standard methods. the oncosnp v2.1 program (https://sites.google.com/site/oncosnp/user-guide) was used in unpaired mode. we used the default top ranked ploidy estimate. a copy number change was called if a region showed […]


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OncoSNP institution(s)
Department of Statistics, University of Oxford, South Parks Road, Oxford, UK

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