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CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data

Sergii Ivakhno, Tom Royce, Anthony J. Cox, Dirk J. Evers, R. Keira Cheetham, Simon Tavaré
2010 Computer applications in the biosciences : CABIOS  
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

Min Zhao, Qingguo Wang, Quan Wang, Peilin Jia, Zhongming Zhao
2013 BMC Bioinformatics  
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

Tao Meng, Ahmed T. Soliman, Mei-Ling Shyu, Yimin Yang, Shu-Ching Chen, S.S. Iyengar, John S. Yordy, Puneeth Iyengar
2013 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
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

Günter Klambauer, Karin Schwarzbauer, Andreas Mayr, Djork-Arné Clevert, Andreas Mitterecker, Ulrich Bodenhofer, Sepp Hochreiter
2012 Nucleic Acids Research  
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

Guojun Liu, Junying Zhang, Xiguo Yuan, Chao Wei
2020 Frontiers in Genetics  
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]

Varuni Sarwal, Sebastian Niehus, Ram Ayyala, Sei Chang, Angela Lu, Nicholas Darci-Maher, Russell Littman, Emily Wesel, Jacqueline Castellanos, Rahul Chikka, Margaret G. Distler, Eleazar Eskin (+2 others)
2020 bioRxiv   pre-print
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

Joseph Kenneth Kawash
2018
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