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BioMed Research International
Volume 2013 (2013), Article ID 915636, 7 pages
Comparative Study of Exome Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as Control
1Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37027, USA
2Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37037, USA
3Department of Biochemistry, Vanderbilt University, Nashville, TN 37027, USA
Received 3 September 2013; Accepted 24 September 2013
Academic Editor: Zhongming Zhao
Copyright © 2013 Yan Guo et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- S. B. Ng, K. J. Buckingham, C. Lee et al., “Exome sequencing identifies the cause of a mendelian disorder,” Nature Genetics, vol. 42, no. 1, pp. 30–35, 2010.
- J. T. Glessner, K. Wang, G. Cai et al., “Autism genome-wide copy number variation reveals ubiquitin and neuronal genes,” Nature, vol. 459, no. 7246, pp. 569–572, 2009.
- T. L. Yang, Y. Guo, H. Shen et al., “Copy number variation on chromosome 10q26.3 for obesity identified by a genome-wide study,” The Journal of Clinical Endocrinology & Metabolism, vol. 98, no. 1, pp. E191–E195, 2013.
- A. Bergamaschi, Y. H. Kim, P. Wang et al., “Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer,” Genes Chromosomes and Cancer, vol. 45, no. 11, pp. 1033–1040, 2006.
- M. Moroni, S. Veronese, S. Benvenuti et al., “Gene copy number for epidermal growth factor receptor (EGFR) and clinical response to antiEGFR treatment in colorectal cancer: a cohort study,” The Lancet Oncology, vol. 6, no. 5, pp. 279–286, 2005.
- F. Cappuzzo, C. Ligorio, L. Toschi et al., “EGFR and HER2 gene copy number and response to first-line chemotherapy in patients with advanced non-small cell lung cancer (NSCLC),” Journal of Thoracic Oncology, vol. 2, no. 5, pp. 423–429, 2007.
- A. Vasson, C. Leroux, L. Orhant et al., “Custom oligonucleotide array-based CGH: a reliable diagnostic tool for detection of exonic copy-number changes in multiple targeted genes,” European Journal of Human Genetics, vol. 21, no. 9, pp. 977–987, 2013.
- H. Lybæk, L. A. Meza-Zepeda, S. H. Kresse, T. Høysæter, V. M. Steen, and G. Houge, “Array-CGH fine mapping of minor and cryptic HR-CGH detected genomic imbalances in 80 out of 590 patients with abnormal development,” European Journal of Human Genetics, vol. 16, no. 11, pp. 1318–1328, 2008.
- J. Schoumans, K. Nielsen, I. Jeppesen et al., “A comparison of different metaphase CGH methods for the detection of cryptic chromosome aberrations of defined size,” European Journal of Human Genetics, vol. 12, no. 6, pp. 447–454, 2004.
- K. Hashimoto, N. Mori, T. Tamesa et al., “Analysis of DNA copy number aberrations in hepatitis C virus-associated hepatocellular carcinomas by conventional CGH and array CGH,” Modern Pathology, vol. 17, no. 6, pp. 617–622, 2004.
- A. Abyzov, A. E. Urban, M. Snyder, and M. Gerstein, “CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing,” Genome Research, vol. 21, no. 6, pp. 974–984, 2011.
- V. Boeva, T. Popova, K. Bleakley et al., “Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data,” Bioinformatics, vol. 28, no. 3, pp. 423–425, 2012.
- D. Y. Chiang, G. Getz, D. B. Jaffe et al., “High-resolution mapping of copy-number alterations with massively parallel sequencing,” Nature Methods, vol. 6, no. 1, pp. 99–103, 2009.
- A. Magi, M. Benelli, S. Yoon, F. Roviello, and F. Torricelli, “Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm,” Nucleic Acids Research, vol. 39, no. 10, article e65, 2011.
- P. Medvedev, M. Fiume, M. Dzamba, T. Smith, and M. Brudno, “Detecting copy number variation with mated short reads,” Genome Research, vol. 20, no. 11, pp. 1613–1622, 2010.
- C. A. Miller, O. Hampton, C. Coarfa, and A. Milosavljevic, “ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads,” PLoS ONE, vol. 6, no. 1, Article ID e16327, 2011.
- S. M. Waszak, Y. Hasin, T. Zichner et al., “Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity,” PLoS Computational Biology, vol. 6, no. 11, Article ID e1000988, 2010.
- J. F. Sathirapongsasuti, H. Lee, B. A. J. Horst et al., “Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV,” Bioinformatics, vol. 27, no. 19, pp. 2648–2654, 2011.
- N. Krumm, P. H. Sudmant, A. Ko et al., “Copy number variation detection and genotyping from exome sequence data,” Genome Research, vol. 22, no. 8, pp. 1525–1532, 2012.
- G. Klambauer, K. Schwarzbauer, A. Mayr et al., “cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate,” Nucleic Acids Research, vol. 40, no. 9, article e69, 2012.
- M. I. Love, A. Myišičková, R. Sun, V. Kalscheuer, M. Vingron, and S. A. Haas, “Modeling read counts for CNV detection in exome sequencing data,” Statistical Applications in Genetics and Molecular Biology, vol. 10, no. 1, article 52, 2011.
- V. Plagnol, J. Curtis, M. Epstein et al., “A robust model for read count data in exome sequencing experiments and implications for copy number variant calling,” Bioinformatics, vol. 28, no. 21, pp. 2747–2754, 2012.
- A. Gusnanto, H. M. Wood, Y. Pawitan, P. Rabbitts, and S. Berri, “Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data,” Bioinformatics, vol. 28, no. 1, pp. 40–47, 2012.
- J. Li, R. Lupat, K. C. Amarasinghe et al., “CONTRA: copy number analysis for targeted resequencing,” Bioinformatics, vol. 28, no. 10, pp. 1307–1313, 2012.
- H. Li and R. Durbin, “Fast and accurate short read alignment with Burrows-Wheeler transform,” Bioinformatics, vol. 25, no. 14, pp. 1754–1760, 2009.
- H. Li, B. Handsaker, A. Wysoker et al., “The sequence alignment/Map format and SAMtools,” Bioinformatics, vol. 25, no. 16, pp. 2078–2079, 2009.
- A. McKenna, M. Hanna, E. Banks et al., “The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data,” Genome Research, vol. 20, no. 9, pp. 1297–1303, 2010.
- P. J. A. Cock, C. J. Fields, N. Goto, M. L. Heuer, and P. M. Rice, “The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants,” Nucleic Acids Research, vol. 38, no. 6, pp. 1767–1771, 2009.