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BioMed Research International
Volume 2013 (2013), Article ID 813912, 7 pages
http://dx.doi.org/10.1155/2013/813912
Research Article

Simpute: An Efficient Solution for Dense Genotypic Data

Yen-Jen Lin,1 Chun-Tien Chang,1 Chuan Yi Tang,1,2 and Wen-Ping Hsieh3

1Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
2Department of Computer Science and Information Engineering, Providence University, Taichung, Taiwan
3Institute of Statistics, National Tsing Hua University, Hsinchu, Taiwan

Received 27 November 2012; Accepted 4 January 2013

Academic Editor: Hao-Teng Chang

Copyright © 2013 Yen-Jen Lin 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. I. Bell, “Single nucleotide polymorphisms and disease gene mapping,” Arthritis Research, vol. 4, supplement 3, pp. S273–S278, 2002. View at Publisher · View at Google Scholar
  2. R. Sachidanandam, D. Weissman, S. C. Schmidt et al., “A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms,” Nature, vol. 409, no. 6822, pp. 928–933, 2001. View at Publisher · View at Google Scholar · View at Scopus
  3. L. Kruglyak and D. A. Nickerson, “Variation is the spice of life,” Nature Genetics, vol. 27, no. 3, pp. 234–236, 2001. View at Publisher · View at Google Scholar · View at Scopus
  4. H. Y. Jung, Y. J. Park, Y. J. Kim, J. S. Park, K. Kimm, and I. Koh, “New methods for imputation of missing genotype using linkage disequilibrium and haplotype information,” Information Sciences, vol. 177, no. 3, pp. 804–814, 2007. View at Publisher · View at Google Scholar · View at Scopus
  5. J. Marchini, B. Howie, S. Myers, G. McVean, and P. Donnelly, “A new multipoint method for genome-wide association studies by imputation of genotypes,” Nature Genetics, vol. 39, no. 7, pp. 906–913, 2007. View at Publisher · View at Google Scholar · View at Scopus
  6. Y. Li, C. J. Willer, J. Ding, P. Scheet, and G. R. Abecasis, “MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes,” Genetic Epidemiology, vol. 34, no. 8, pp. 816–834, 2010. View at Publisher · View at Google Scholar · View at Scopus
  7. D. Y. Lin, Y. Hu, and B. E. Huang, “Simple and efficient analysis of disease association with missing genotype data,” American Journal of Human Genetics, vol. 82, no. 2, pp. 444–452, 2008. View at Publisher · View at Google Scholar · View at Scopus
  8. P. Scheet and M. Stephens, “A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase,” American Journal of Human Genetics, vol. 78, no. 4, pp. 629–644, 2006. View at Publisher · View at Google Scholar · View at Scopus
  9. B. L. Browning and S. R. Browning, “A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals,” American Journal of Human Genetics, vol. 84, no. 2, pp. 210–223, 2008. View at Publisher · View at Google Scholar · View at Scopus
  10. M. N. Chiano and D. G. Clayton, “Fine genetic mapping using haplotype analysis and the missing data problem,” Annals of Human Genetics, vol. 62, no. 1, pp. 55–60, 1998. View at Publisher · View at Google Scholar · View at Scopus
  11. Z. S. Qin, T. Niu, and J. S. Liu, “Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms,” American Journal of Human Genetics, vol. 71, no. 5, pp. 1242–1247, 2002. View at Publisher · View at Google Scholar · View at Scopus
  12. Y. V. Sun and S. L. R. Kardia, “Imputing missing genotypic data of single-nucleotide polymorphisms using neural networks,” European Journal of Human Genetics, vol. 16, no. 4, pp. 487–495, 2008. View at Publisher · View at Google Scholar · View at Scopus
  13. B. Devlin and N. Risch, “A comparison of linkage disequilibrium measures for fine-scale mapping,” Genomics, vol. 29, no. 2, pp. 311–322, 1995. View at Publisher · View at Google Scholar · View at Scopus
  14. J. K. Pritchard and M. Przeworski, “Linkage disequilibrium in humans: models and data,” American Journal of Human Genetics, vol. 69, no. 1, pp. 1–14, 2001. View at Publisher · View at Google Scholar · View at Scopus
  15. R. C. Lewontin, “Interaction of selection and linkage. I. General considerations; heterotic models,” Genetics, vol. 49, no. 1, pp. 49–67, 1964.
  16. K. A. Frazer, D. G. Ballinger, D. R. Cox et al., “A second generation human haplotype map of over 3.1 million SNPs,” Nature, vol. 449, no. 7164, pp. 851–861, 2007. View at Publisher · View at Google Scholar · View at Scopus
  17. M. J. Huentelman, D. W. Craig, A. D. Shieh et al., “SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data,” BMC Genomics, vol. 6, article 149, 2005. View at Publisher · View at Google Scholar · View at Scopus