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The Scientific World Journal
Volume 2013, Article ID 895496, 9 pages
http://dx.doi.org/10.1155/2013/895496
Research Article

Evaluation of Allele Frequency Estimation Using Pooled Sequencing Data Simulation

1Vanderbilt Ingram Cancer Center, Center for Quantitative Sciences, Nashville, TN, USA
2Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN, USA
3VANTAGE, Vanderbilt University, Nashville, TN, USA

Received 15 November 2012; Accepted 30 December 2012

Academic Editors: L. Han, X. Li, and Z. Su

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 [12 citations]

The following is the list of published articles that have cited the current article.

  • Yan Guo, Shilin Zhao, Pei-Fang Su, Chung-I Li, Fei Ye, Charles R. Flynn, and Yu Shyr, “Statistical strategies for microRNAseq batch effect reduction,” Translational Cancer Research, vol. 3, no. 3, pp. 260–+, 2014. View at Publisher · View at Google Scholar
  • Fei Ye, David C. Samuels, Travis Clark, and Yan Guo, “High-Throughput Sequencing in Mitochondrial DNA Research,” Mitochondrion, 2014. View at Publisher · View at Google Scholar
  • P. Koteja, M. T. Stuglik, J. Radwan, and W. Babik, “Accuracy of allele frequency estimation using pooled RNA-Seq,” Molecular Ecology Resources, vol. 14, no. 2, pp. 381–392, 2014. View at Publisher · View at Google Scholar
  • Yan Guo, Fei Ye, Quanghu Sheng, Travis Clark, and David C. Samuels, “Three-stage quality control strategies for DNA re-sequencing data,” Briefings in Bioinformatics, vol. 15, no. 6, pp. 879–889, 2014. View at Publisher · View at Google Scholar
  • Leng Han, Kasey C. Vickers, David C. Samuels, and Yan Guo, “Alternative applications for distinct RNA sequencing strategies,” Briefings In Bioinformatics, vol. 16, no. 4, pp. 629–639, 2015. View at Publisher · View at Google Scholar
  • Rebecca S. Just, Jodi A. Irwin, and Walther Parson, “Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing,” Forensic Science International: Genetics, 2015. View at Publisher · View at Google Scholar
  • Yan Guo, Shilin Zhao, Margot Bjoring, and Leng Han, “Advanced Datamining Using RNAseq Data,” Big Data Analytics in Bioinformatics and Healthcare, pp. 1–20, 2015. View at Publisher · View at Google Scholar
  • Quanhu Sheng, Kasey Vickers, Shilin Zhao, Jing Wang, David C. Samuels, Olivia Koues, Yu Shyr, and Yan Guo, “Multi-perspective quality control of Illumina RNA sequencing data analysis,” Briefings in Functional Genomics, pp. elw035, 2016. View at Publisher · View at Google Scholar
  • Matteo Chiara, and Giulio Pavesi, “Evaluation of Quality Assessment Protocols for High Throughput Genome Resequencing Data,” Frontiers in Genetics, vol. 8, 2017. View at Publisher · View at Google Scholar
  • Jingwen Wang, Kai Puhakainen, Jari Jalava, Neeta Datta, Rigbe G. Weldatsadik, T. Sakari Jokiranta, Juha Kere, Hong Jiao, Kati Raïsänen, Tiina Skoog, and Jaana Vuopio, “Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus,” Scientific Reports, vol. 7, 2017. View at Publisher · View at Google Scholar
  • Yan Guo, Noralane M. Lindor, Stephen B. Gruber, Daniel D. Buchanan, Leon Raskin, Liping Du, Mark Clendenning, and Christophe Rosty, “Targeted sequencing of established and candidate colorectal cancer genes in the Colon Cancer Family Registry Cohort,” Oncotarget, vol. 8, no. 55, pp. 93450–93463, 2017. View at Publisher · View at Google Scholar
  • Quanhu Sheng, David C. Samuels, Yu Shyr, Yan Guo, and Shilin Zhao, “The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data,” BMC Genomics, vol. 18, 2017. View at Publisher · View at Google Scholar