Table of Contents Author Guidelines Submit a Manuscript
Table of Contents Alerts

To receive news and publication updates for BioMed Research International, enter your email address in the box below.

BioMed Research International
Volume 2014 (2014), Article ID 319534, 7 pages
http://dx.doi.org/10.1155/2014/319534
Research Article

Improved Variant Calling Accuracy by Merging Replicates in Whole-Exome Sequencing Studies

Yanfeng Zhang,1 Bingshan Li,2 Chun Li,3 Qiuyin Cai,1 Wei Zheng,1 and Jirong Long1

1Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
2Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
3Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA

Received 28 May 2014; Revised 15 July 2014; Accepted 15 July 2014; Published 4 August 2014

Academic Editor: Ernesto Picardi

Copyright © 2014 Yanfeng Zhang 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.

Linked References

  1. J. Shendure and H. Ji, “Next-generation DNA sequencing,” Nature Biotechnology, vol. 26, no. 10, pp. 1135–1145, 2008. View at Publisher · View at Google Scholar · View at Scopus
  2. J. S. Parla, I. Iossifov, I. Grabill, M. S. Spector, M. Kramer, and W. R. McCombie, “A comparative analysis of exome capture,” Genome biology, vol. 12, article R97, 2011. View at Publisher · View at Google Scholar · View at Scopus
  3. M. N. Bainbridge, M. Wang, D. L. Burgess et al., “Whole exome capture in solution with 3 Gbp of data,” Genome Biology, vol. 11, no. 6, article R62, 2010. View at Publisher · View at Google Scholar · View at Scopus
  4. J. K. Teer and J. C. Mullikin, “Exome sequencing: the sweet spot before whole genomes,” Human Molecular Genetics, vol. 19, no. 2, pp. R145–R151, 2010. View at Publisher · View at Google Scholar · View at Scopus
  5. W. Fu, T. D. O'Connor, G. Jun et al., “Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants,” Nature, vol. 493, no. 7431, pp. 216–220, 2013. View at Publisher · View at Google Scholar · View at Scopus
  6. S. B. Ng, E. H. Turner, P. D. Robertson et al., “Targeted capture and massively parallel sequencing of 12 human exomes,” Nature, vol. 461, no. 7261, pp. 272–276, 2009. View at Publisher · View at Google Scholar · View at Scopus
  7. X. Yi, Y. Liang, E. Huerta-Sanchez et al., “Sequencing of 50 human exomes reveals adaptation to high altitude,” Science, vol. 329, no. 5987, pp. 75–78, 2010. View at Publisher · View at Google Scholar · View at Scopus
  8. J. A. Tennessen, A. W. Bigham, T. D. O'Connor et al., “Evolution and functional impact of rare coding variation from deep sequencing of human exomes,” Science, vol. 337, no. 6090, pp. 64–69, 2012. View at Publisher · View at Google Scholar
  9. T. W. Yu, M. H. Chahrour, M. E. Coulter et al., “Using whole-exome sequencing to identify inherited causes of autism,” Neuron, vol. 77, no. 2, pp. 259–273, 2013. View at Publisher · View at Google Scholar · View at Scopus
  10. E. R. Thompson, M. A. Doyle, G. L. Ryland et al., “Exome sequencing identifies rare deleterious mutations in DNA repair genes FANCC and BLM as potential breast cancer susceptibility alleles,” PLoS Genetics, vol. 8, no. 9, Article ID e1002894, 2012. View at Publisher · View at Google Scholar · View at Scopus
  11. S. J. Sanders, M. T. Murtha, A. R. Gupta et al., “De novo mutations revealed by whole-exome sequencing are strongly associated with autism,” Nature, vol. 484, no. 7397, pp. 237–241, 2012. View at Publisher · View at Google Scholar · View at Scopus
  12. M. J. Bamshad, S. B. Ng, A. W. Bigham et al., “Exome sequencing as a tool for Mendelian disease gene discovery,” Nature Reviews Genetics, vol. 12, no. 11, pp. 745–755, 2011. View at Publisher · View at Google Scholar · View at Scopus
  13. A. Kiezun, K. Garimella, R. Do et al., “Exome sequencing and the genetic basis of complex traits,” Nature Genetics, vol. 44, no. 6, pp. 623–630, 2012. View at Publisher · View at Google Scholar · View at Scopus
  14. E. J. Vallender, “Expanding whole exome resequencing into non-human primates,” Genome Biology, vol. 12, article R87, 2011. View at Publisher · View at Google Scholar · View at Scopus
  15. R. D. George, G. McVicker, R. Diederich et al., “Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection,” Genome Research, vol. 21, no. 10, pp. 1686–1694, 2011. View at Publisher · View at Google Scholar · View at Scopus
  16. J. E. McCormack, M. G. Harvey, B. C. Faircloth, N. G. Crawford, T. C. Glenn, and R. T. Brumfield, “A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing,” PLoS ONE, vol. 8, no. 1, Article ID e54848, 2013. View at Publisher · View at Google Scholar · View at Scopus
  17. M. J. Clark, R. Chen, H. Y. K. Lam et al., “Performance comparison of exome DNA sequencing technologies,” Nature Biotechnology, vol. 29, no. 10, pp. 908–916, 2011. View at Publisher · View at Google Scholar · View at Scopus
  18. Y. Guo, J. Long, J. He et al., “Exome sequencing generates high quality data in non-target regions,” BMC Genomics, vol. 13, article 194, 2012. View at Publisher · View at Google Scholar · View at Scopus
  19. Y. T. Gao, X. O. Shu, Q. Dai et al., “Association of menstrual and reproductive factors with breast cancer risk: results from the Shanghai breast cancer study,” International Journal of Cancer, vol. 87, no. 2, pp. 295–300, 2000. View at Google Scholar
  20. W. Zheng, J. Long, Y. Gao et al., “Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1,” Nature Genetics, vol. 41, no. 3, pp. 324–328, 2009. View at Publisher · View at Google Scholar · View at Scopus
  21. H. Li and R. Durbin, “Fast and accurate short read alignment with Burrows-Wheeler transform,” Bioinformatics, vol. 25, no. 14, pp. 1754–1760, 2009. View at Publisher · View at Google Scholar · View at Scopus
  22. H. Li, B. Handsaker, A. Wysoker et al., “The sequence alignment/map format and SAMtools,” Bioinformatics, vol. 25, no. 16, pp. 2078–2079, 2009. View at Publisher · View at Google Scholar · View at Scopus
  23. M. A. DePristo, E. Banks, R. Poplin et al., “A framework for variation discovery and genotyping using next-generation DNA sequencing data,” Nature Genetics, vol. 43, no. 5, pp. 491–498, 2011. View at Google Scholar
  24. 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. View at Publisher · View at Google Scholar · View at Scopus
  25. P. Frommolt, A. T. Abdallah, J. Altmüller et al., “Assessing the enrichment performance in targeted resequencing experiments,” Human Mutation, vol. 33, no. 4, pp. 635–641, 2012. View at Publisher · View at Google Scholar · View at Scopus
  26. S. C. Schuster, W. Miller, A. Ratan et al., “Complete Khoisan and Bantu genomes from southern Africa,” Nature, vol. 463, no. 7283, pp. 943–947, 2010. View at Publisher · View at Google Scholar · View at Scopus
  27. K. J. McKernan, H. E. Peckham, G. L. Costa et al., “Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding,” Genome Research, vol. 19, no. 9, pp. 1527–1541, 2009. View at Publisher · View at Google Scholar · View at Scopus
  28. The 1000 Genomes Project Consortium, “An integrated map of genetic variation from 1,092 human genomes,” Nature, vol. 491, no. 7422, pp. 56–65, 2012. View at Google Scholar
  29. X. Liu, S. Han, Z. Wang et al., “Variant callers for next-generation sequencing data: a comparison study,” PLoS ONE, vol. 8, no. 9, Article ID e75619, 2013. View at Google Scholar
  30. A. Sirmaci, Y. J. K. Edwards, H. Akay, and M. Tekin, “Challenges in whole exome sequencing: an example from hereditary deafness,” PLoS ONE, vol. 7, no. 2, Article ID e32000, 2012. View at Publisher · View at Google Scholar · View at Scopus
  31. M. N. Bainbridge, M. Wang, Y. Wu et al., “Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities,” Genome Biology, vol. 12, no. 7, article R68, 2011. View at Publisher · View at Google Scholar · View at Scopus
  32. J. Freudenberg, P. K. Gregersen, and Y. Freudenberg-Hua, “A simple method for analyzing exome sequencing data shows distinct levels of nonsynonymous variation for human immune and nervous system genes,” PLoS ONE, vol. 7, no. 6, Article ID e38087, 2012. View at Publisher · View at Google Scholar · View at Scopus
  33. A. Roberts, C. Trapnell, J. Donaghey, J. L. Rinn, and L. Pachter, “Improving RNA-Seq expression estimates by correcting for fragment bias,” Genome Biology, vol. 12, no. 3, article R22, 2011. View at Publisher · View at Google Scholar · View at Scopus
  34. A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, and B. Wold, “Mapping and quantifying mammalian transcriptomes by RNA-Seq,” Nature Methods, vol. 5, no. 7, pp. 621–628, 2008. View at Publisher · View at Google Scholar · View at Scopus
  35. J. T. Leek, R. B. Scharpf, H. C. Bravo et al., “Tackling the widespread and critical impact of batch effects in high-throughput data,” Nature Reviews Genetics, vol. 11, no. 10, pp. 733–739, 2010. View at Publisher · View at Google Scholar · View at Scopus