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CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data
2010
Computer applications in the biosciences : CABIOS
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Results: We present a novel approach, called CNAseg, to identify CNAs from second-generation sequencing data. ...
An extensive simulation scheme was developed to recreate different scenarios of copy number changes and depth of coverage by altering a real dataset with spiked-in CNAs. ...
ACKNOWLEDGEMENT We acknowledge the assistance of Dr Phil Stephens of The Wellcome Trust Sanger Institute, UK, in providing the raw COLO-829 Affymetix SNP 6.0 array data. ...
doi:10.1093/bioinformatics/btq587
pmid:20966003
fatcat:lhfcgxucrfb35cmogajhlpkl2q
Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives
2013
BMC Bioinformatics
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Copy number variation (CNV) is a prevalent form of critical genetic variation that leads to an abnormal number of copies of large genomic regions in a cell. ...
sequence data can be analyzed by next-generation sequencing (NGS). ...
This article has been published as part of BMC Bioinformatics Volume 14 Supplement 11, 2013: Selected articles from The Second Workshop on Data Mining of Next-Generation Sequencing in conjunction with ...
doi:10.1186/1471-2105-14-s11-s1
pmid:24564169
pmcid:PMC3846878
fatcat:i2y25xfa4jhqfmyxl5ol2y4zza
Wavelet Analysis in Current Cancer Genome Research: A Survey
2013
IEEE/ACM Transactions on Computational Biology & Bioinformatics
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With the rapid development of next generation sequencing technology, the amount of biological sequence data of the cancer genome increases exponentially, which calls for efficient and effective algorithms ...
In this paper, we provide a survey of how wavelet analysis has been applied to cancer bioinformatics questions. ...
The authors of [88] proposed a CNAseg algorithm to identify the copy number alteration from the second-generation sequencing data. ...
doi:10.1109/tcbb.2013.134
pmid:24407303
fatcat:asuizt6suzaodogz3p3lype554
cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate
2012
Nucleic Acids Research
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Allelespecific copy numbers are of interest because they allow for determining whether an allele is fully functional, which is important, for example, for the identification of mutations leading to cancer ...
CONCLUSION We have introduced cn.MOPS-a novel method and pipeline for the detection of copy number variations in NGS data. cn.MOPS incorporates a probabilistic model that decomposes read variations across ...
FUNDING Funding for open access charge: Funds from the Institute of Bioinformatics, Johannes Kepler University Linz. Conflict of interest statement. None declared. ...
doi:10.1093/nar/gks003
pmid:22302147
pmcid:PMC3351174
fatcat:2tac6xgbxrc7zgz357oswelc5y
RKDOSCNV: A Local Kernel Density-Based Approach to the Detection of Copy Number Variations by Using Next-Generation Sequencing Data
2020
Frontiers in Genetics
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In summary, RKDOSCNV is a simple and effective method for the detection of CNVs from whole genome sequencing (WGS) data, especially for samples with low tumor purity. ...
Copy number variations (CNVs) are significant causes of many human cancers and genetic diseases. ...
AUTHOR CONTRIBUTIONS GL participated in the design of the algorithms and experiments. JZ and XY participated in the design of the entire framework of CNV detection and directed the whole work. ...
doi:10.3389/fgene.2020.569227
pmid:33329705
pmcid:PMC7673372
fatcat:usj76terr5dlpkgx4ckhmwqbkq
A comprehensive benchmarking of WGS-based structural variant callers
[article]
2020
bioRxiv
pre-print
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Dissecting SVs from whole genome sequencing (WGS) data presents a substantial number of challenges and a plethora of SV-detection methods have been developed. ...
Additionally, we have determined the SV callers best suited for low and ultra-low pass sequencing data. ...
CNAseg--a novel framework for identification of copy number changes in cancer from second-generation sequencing data. -PubMed -NCBI. https://www.ncbi.nlm.nih.gov/pubmed/20966003 . 61. Sindi, S. ...
doi:10.1101/2020.04.16.045120
fatcat:vvj2cj4pzzeyxgiixt43sgi5oi
Computational methods of variant calling and their applications
2018
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GROM-RD analyzes multiple biases in read coverage to improve copy number variation (CNV) detection in NGS data. ...
Increasing reliance on next generation sequencing (NGS) data necessitates efficient and accurate means of genome analysis. ...
We developed GROM-RD, an algorithm for identifying copy number variation in next generation sequencing data. ...
doi:10.7282/t31z47mj
fatcat:5i62xdwrrrhgpaancoupvc7wia