The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization
Open accessAbstract
Summary: We present a tool for control-free copy number alteration (CNA) detection using deep-sequencing data, particularly useful for cancer studies. The tool deals with two frequent problems in the analysis of cancer deep-sequencing data: absence of control sample and possible polyploidy of cancer cells. FREEC (control-FREE Copy number caller) automatically normalizes and segments copy number profiles (CNPs) and calls CNAs. If ploidy is known, FREEC assigns absolute copy number to each predicted CNA. To normalize raw CNPs, the user can provide a control dataset if available; otherwise GC content is used. We demonstrate that for Illumina single-end, mate-pair or paired-end sequencing, GC-contentr normalization provides smooth profiles that can be further segmented and analyzed in order to predict CNAs. Availability: Source code and sample data are available at http://bioinfo-out.curie.fr/projects/freec/. Contact: freec@curie.fr Supplementary information: Supplementary data are available at Bioinformatics online.
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Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
A comprehensive catalogue of somatic mutations from a human cancer genome
Pleasance, E. D., Cheetham, R. K., Stephens, P. J., McBride, D. J., Humphray, S. J., Greenman, C. D., Varela, I., Lin, M.-L., Ordóñez, G. R., Bignell, G. R., et al. (2010) · Nature · doi:10.1038/nature08658 · Cited by 1,696
Personalized copy number and segmental duplication maps using next-generation sequencing
Alkan, C., Kidd, J. M., Marques-Bonet, T., Aksay, G., Antonacci, F., Hormozdiari, F., Kitzman, J. O., Baker, C., Malig, M., Mutlu, O., et al. (2009) · Nature Genetics · doi:10.1038/ng.437 · Cited by 748
CNV-seq, a new method to detect copy number variation using high-throughput sequencing
Xie, C., & Tammi, M. T. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-80 · Cited by 582
Cited by
CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing
Talevich, E., Shain, A. H., Botton, T., & Bastian, B. C. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004873 · Cited by 2,094
Summarizing and correcting the GC content bias in high-throughput sequencing
Benjamini, Y., & Speed, T. P. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks001 · Cited by 913
GC-Content Normalization for RNA-Seq Data
Risso, D., Schwartz, K., Sherlock, G., & Dudoit, S. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-480 · Cited by 867
Klambauer, G., Schwarzbauer, K., Mayr, A., Clevert, D.-A., Mitterecker, A., Bodenhofer, U., & Hochreiter, S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks003 · Cited by 455
Suda, K., Nakaoka, H., Yoshihara, K., Ishiguro, T., Tamura, R., Mori, Y., Yamawaki, K., Adachi, S., Takahashi, T., Kase, H., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.07.037 · Cited by 414
Metadata
- Authors
- Boeva, V., Zinovyev, A., Bleakley, K., Vert, J.-P., Janoueix-Lerosey, I., Delattre, O., & Barillot, E.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-11-15
- Volume
- 27
- Issue
- 2
- Pages
- 268-269
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2097331151
- Cited by
- 268
- References
- 4
- FWCI
- 6.87
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Boeva, V., Zinovyev, A., Bleakley, K., Vert, J.-P., Janoueix-Lerosey, I., Delattre, O., & Barillot, E. (2011). Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics. https://doi.org/10.1093/bioinformatics/btq635
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