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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.
Citations to this Article [15 citations]
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- Christopher A. Miller, Brian S. White, Nathan D. Dees, Malachi Griffith, John S. Welch, Obi L. Griffith, Ravi Vij, Michael H. Tomasson, Timothy A. Graubert, Matthew J. Walter, Matthew J. Ellis, William Schierding, John F. DiPersio, Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, and Li Ding, “SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution,” Plos Computational Biology, vol. 10, no. 8, 2014.
- Hansook Kim Chong, Tao Wang, Hsiao-Mei Lu, Sara Seidler, Hong Lu, Steven Keiles, Elizabeth C. Chao, A. J. Stuenkel, Xiang Li, and Aaron M. Elliott, “The Validation and Clinical Implementation of BRCAplus: A Comprehensive High-Risk Breast Cancer Diagnostic Assay,” Plos One, vol. 9, no. 5, 2014.
- Renjie Tan, Yadong Wang, Sarah E. Kleinstein, Yongzhuang Liu, Xiaolin Zhu, Hongzhe Guo, Qinghua Jiang, Andrew S. Allen, and Mingfu Zhu, “An Evaluation of Copy Number Variation Detection Tools from Whole-Exome Sequencing Data,” Human Mutation, 2014.
- Mi Yeong Hwang, Sanghoon Moon, Lyong Heo, Young Jin Kim, Ji Hee Oh, Yeon Jung Kim, Yun Kyoung Kim, Juyoung Lee, Bok-Ghee Han, and Bong-Jo Kim, “Combinatorial approach to estimate copy number genotype using whole-exome sequencing data,” Genomics, 2014.
- Yan Guo, Shilin Zhao, Brian D. Lehmann, Quanhu Sheng, Timothy M. Shaver, Thomas P. Stricker, Jennifer A. Pietenpol, and Yu Shyr, “Detection of internal exon deletion with exon Del,” Bmc Bioinformatics, vol. 15, 2014.
- Ming-Yih Wu, Kuang-Han Chao, Chin-Der Chen, Li-Jung Chang, Shee-Uan Chen, and Yu-Shih Yang, “Current Status of Comprehensive Chromosome Screening for Elective Single-Embryo Transfer,” Obstetrics and Gynecology International, vol. 2014, pp. 1–6, 2014.
- Xiaoyu Wang, Xiaohong Li, Yichen Cheng, Xin Sun, Xibin Sun, Steve Self, Charles Kooperberg, and James Y. Dai, “Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinoma,” Human Genomics, vol. 9, no. 1, 2015.
- Jae-Yong Nam, Nayoung K. D. Kim, Sang Cheol Kim, Je-Gun Joung, Ruibin Xi, Semin Lee, Peter J. Park, and Woong-Yang Park, “Evaluation of somatic copy number estimation tools for whole-exome sequencing data,” Briefings in Bioinformatics, pp. bbv055, 2015.
- Xiaobei Zhao, Anyou Wang, Vonn Walter, Nirali M. Patel, David A. Eberhard, Michele C. Hayward, Ashley H. Salazar, Heejoon Jo, Matthew G. Soloway, Matthew D. Wilkerson, Joel S. Parker, Xiaoying Yin, Guosheng Zhang, Marni B. Siegel, Gary B. Rosson, H. Shelton Earp, Norman E. Sharpless, Margaret L. Gulley, Karen E. Weck, D. Neil Hayes, and Stergios J. Moschos, “Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of ,” Plos One, vol. 10, no. 6, 2015.
- WeiBo Wang, Wei Wang, Wei Sun, James J. Crowley, and Jin P. Szatkiewicz, “Allele-specific copy-number discovery from whole-genome and whole-exome sequencing,” Nucleic Acids Research, vol. 43, no. 14, pp. e90–e90, 2015.
- Chih-Jian Lih, Han Si, Biswajit Das, Robin D. Harrington, Kneshay N. Harper, David J. Sims, Paul M. McGregor, Corinne E. Camalier, Andrew Y. Kayserian, P. Mickey Williams, Hua-Jun He, Jamie Almeida, Steve Lund, Steve Choquette, and Kenneth D. Cole, “Certified DNA Reference Materials to Compare HER2 Gene Amplification Measurements Using Next-Generation Sequencing Methods,” The Journal of Molecular Diagnostics, 2016.
- Heather Mason-Suares, Latrice Landry, and Matthew S. Lebo, “Detecting Copy Number Variation via Next Generation Technology,” Current Genetic Medicine Reports, vol. 4, no. 3, pp. 74–85, 2016.
- Lennart F. Johansson, Freerk van Dijk, Eddy N. de Boer, Krista K. van Dijk-Bos, Jan D. H. Jongbloed, Annemieke H. van der Hout, Helga Westers, Richard J. Sinke, Morris A. Swertz, Rolf H. Sijmons, and Birgit Sikkema-Raddatz, “CoNVaDING: Single Exon Variation Detection in Targeted NGS Data,” Human Mutation, vol. 37, no. 5, pp. 457–464, 2016.
- Eloisa S. Moreira, Isabela M. W. Silva, Naila Lourenco, Danielle P. Moreira, Cintia M. Ribeiro, Ana Luiza B. Martins, Karina Griesi-Oliveira, Monize Lazar, Silvia S. Costa, Michel S. Naslavsky, Katia M. Rocha, Meire Aguena, Agnes C. Fett-Conte, Mayana Zatz, Carla Rosenberg, Elaine C. Zachi, Debora R. Bertola, Estevao Vadasz, and Maria Rita Passos-Bueno, “Detection of small copy number variations (CNVs) in autism spectrum disorder (ASD) by custom array comparative genomic hybridization (aCGH),” Research In Autism Spectrum Disorders, vol. 23, pp. 145–151, 2016.
- H.-Y. Jo, M.-H. Park, H.-M. Woo, M.H. Han, B.-Y. Kim, B.-O. Choi, K.W. Chung, and S.K. Koo, “Application of whole-exome sequencing for detecting copy number variants in CMT1A/HNPP,” Clinical Genetics, vol. 90, no. 2, pp. 177–181, 2016.