Communications of the Korean Institute of Information Scientists and Engineers (정보과학회지)

Korean Institute of Information Scientists and Engineers (한국정보과학회)
권호 표지

개인 유전체 하플로타입 결정을 위한 계산학적 연구

  • Published : 2014.03.14
Download PDF
⟨ Previous Next ⟩

Abstract

Keywords

Acknowledgement

Supported by : 한국연구재단

References

  1. D. C. Koboldt, K. M. Steinberg, D. E. Larson, R. K. Wilson, E. R. Mardis. "The next-generation sequencing revolution and its impact on genomics", Cell, Vol. 155, No. 1, pp. 27-38, 2013. https://doi.org/10.1016/j.cell.2013.09.006
  2. K.-B. Hwang, J.-G. Joung, J.-W. Nam, B.-H. Kim, J.-K. Rhee, B.-T. Zhang, "Machine learning techniques for the analysis of biological data", Communications of the Korea Information Science Society, Vol. 25, No. 3, pp. 35-45, 2007. (in Korean)
  3. D. S. Horner, G. Pavesi, T. Castrignano, P. D. De Meo, S. Liuni, M. Sammeth, E. Picardi, G. Pesole, "Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing", Brief. Bioinform. Vol. 11, No. 2, pp. 181-197, 2013.
  4. S. T. Sherry, W. H. Ward, M. Kholodov, J. Baker, L. Phan, E. M. Smigielski, K. Sirotkin. "dbSNP: the NCBI database of genetic variation", Nucleic Acids Res., Vol. 29, No. 1, pp. 308-311, 2001. https://doi.org/10.1093/nar/29.1.308
  5. R. E. Laing, P. Hess, Y. Shen, J. Wang, S. X. Hu, "The role and impact of SNPs in pharmacogenomics and personalized medicine", Curr. Drug Metab. Vol. 12, No. 5, pp. 460-486, 2011. https://doi.org/10.2174/138920011795495268
  6. The International HapMap Consortium, "A haplotype map of the human genome", Nature, Vol. 437, pp. 1299- 1320, 2005. https://doi.org/10.1038/nature04226
  7. The 1000 Genomes Project Consortium, "A map of human genome variation from population scale sequencing", Nature, Vol. 467, No. 7319, pp. 1061-1073, 2010. https://doi.org/10.1038/nature09534
  8. The 1000 Genomes Project Consortium, "An integrated map of genetic variation from 1,092 human genomes", Nature, Vol. 491, pp. 56-65, 2012. https://doi.org/10.1038/nature11632
  9. Welcome Trust Case Control Consortium. "Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls", Nature, Vol. 447, pp. 661-682, 2007. https://doi.org/10.1038/nature05911
  10. C. S. Ku, E. Y. Loy, Y. Pawitan, K. S. Chia, "The pursuit of genome-wide association studies: where are we now?", J. Hum. Genet., Vol. 55, No. 4, pp.195-206, 2010. https://doi.org/10.1038/jhg.2010.19
  11. J. H. Moore, F. W. Asselbergs, S. M. Williams. "Bioinformatics challenges for genome-wide association studies", Bioinformatics, Vol. 26, No. 4, pp. 445-455, 2010. https://doi.org/10.1093/bioinformatics/btp713
  12. J.-K. Rhee, J.-W. Ha, S.-H. Bae, S.-J. Kim, M. S. Lee, K.-J. Park, B.-T. Zhang, "Identifying compound risk factors of disease by evolutionary learning of SNP combinatorial features", Journal of the Korean Institute of Information Scientists and Engineers: Computing Practices and Letters, Vol. 15, No. 12, pp. 928-932, 2009. (in Korean)
  13. D. C. Crawford, D. A. Nickerson, "Definition and clinical importance of haplotypes", Annu. Rev. Med., Vol. 56, pp. 303-320, 2005. https://doi.org/10.1146/annurev.med.56.082103.104540
  14. S. R. Browning, and B. L. Browing, "Haplotype Phasing: Existing Methods and New Developments", Nat. Rev. Genet., Vol. 12, pp.703-714, 2011. https://doi.org/10.1038/nrg3054
  15. H. C. Fan, J. Wang, A. Potanina, S. R. Quake, "Wholegenome molecular haplotyping of single cells", Nat. Biotechnol. Vol. 29, No. 1, pp. 51-57, 2011. https://doi.org/10.1038/nbt.1739
  16. H. Li, J.-K. Rhee, B.-T. Zhang, K.-B. Hwang, S.-Y. Shin, "A survey on computational methods for haplotype phasing", Journal of the Korea Information Science Society: Software and Applications, Vol. 40, No. 11, pp. 663-674, 2013. (in Korean)
  17. A. G. Clark, "Haplotypes from PCR-amplified samples of diploid populations", Mol. Biol. Evol., Vol. 7, pp. 111-122, 1990.
  18. L. Excoffier, H.E. L. Lischer, "Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows", Mol. Ecol. Resour., Vol. 10, pp. 564-567, 2010. https://doi.org/10.1111/j.1755-0998.2010.02847.x
  19. M. Stephens, N. J. Smith, P. Donnelly, "A new statistical method for haplotype reconstruction from population data", Am. J. Hum. Genet., Vol. 68, pp. 678-689, 2001.
  20. S. R. Browning, B. L. Browning, "Rapid and accurate haplotype phasing and missing data inference for whole genome association studies using localized haplotype clustering", Am. J. Hum. Genet. Vol. 81, pp. 1084-1097, 2007. https://doi.org/10.1086/521987
  21. B. N. Howie, P. Donnelly, J. Marchini, "A flexible and accurate genotype imputation method for the next generation of genome-wide association studies", PLoS Genet., Vol. 5, No. 6, pp. e1000529, 2009. https://doi.org/10.1371/journal.pgen.1000529
  22. P. Scheet, M. Stephens, M, "A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase", Am. J. Hum. Genet., Vol. 78, pp. 629-644, 2006. https://doi.org/10.1086/502802
  23. Y. Li, C. J. Willer, J. Ding, P. Scheet, G. R. Abecasis, "MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes", Genet. Epidemiol. Vol. 34, No. 8, pp. 816-834, 2010.
  24. S. levy, G. Sutton, P. C. Ng, L. Feuk, A. L. Halpern, B. P. Walenz, N. Axelrod, J. Huang, E. F. Kirkness, G. Denisov, Y. Lin, J. R. macDonald, A. W. C. Pang, M. Shago, T. B. Stockwell, A. Tsiamouri, V. Bafna, V. Bansal, S. A. kravitz, D. A. Busam, K. Y. Beeson, T. C. Mcintosh, K. A. Remington, J. F. Abril, J. Gill, J. Borman, Y.-H. Rogers, M. E. Frazier, S. W. Scherer, R. L. Strausberg, J. C. Venter, "The diploid genome sequence of an individual human", PLoS Biology, Vol. 5, No. 10, pp.e254, 2007. https://doi.org/10.1371/journal.pbio.0050254
  25. V. Bansal, A. L. Halpern, N. Axelrod, V. Bafna, "An MCMC algorithm for haplotype assembly from wholegenome sequence data", Genome Res., Vol. 18, No. 8, pp.1336-1346, 2008. https://doi.org/10.1101/gr.077065.108
  26. V. Bansal, V. Bafna, "HapCut: an efficient and accurate algorithm for haplotype assembly problem", Bioinformatics, Vol. 24, pp. i153-i159, 2008. https://doi.org/10.1093/bioinformatics/btn298
  27. D. He, A. Choi, K. Pipatsrisawat, A. Darwiche, E. Eskin, "Optimal algorithms for halpotype assembly from whole-genome sequence data", Bioinformatics, Vol. 26, pp.i183-i190, 2010. https://doi.org/10.1093/bioinformatics/btq215
  28. Z. Z. Chen, F. Deng, L. Wang, "Exact algorithms for haplotype assembly from whole-genome sequence data", Bioinformatics, Vol. 29, No. 16, pp. 1938-1945, 2013 https://doi.org/10.1093/bioinformatics/btt349
  29. J. O. Kitzman, A. P. Mackenzi, A. Adey, J. B. Hiatt, R. P. Patwardhan, P. H. Sudmant, S. B. Ng, C. Alkan, R. Qiu, E. E. Eichler, J. Shendure, "Haplotype-resolved genome sequencing of a Gujarati Indian individual", Nat. Biotechnol., Vol. 29, No. 1, pp.59-63, 2010.
  30. E. K. Suk, G. K. McEwen, J. Duitama, K. Nowick, S. Schulz, S. Palczewski, S. Schreiber, D. T. Holloway, S. McLaughlin, H. Peckham, C. Lee, T. Huebsch, M. R. Hoehe, "A comprehensively molecular haplotyperesolved genome of a European individual", Genome Res., Vol. 21, No. 10, pp.1672-1685, 2011. https://doi.org/10.1101/gr.125047.111
  31. J. Duitama, G. K. McEwen, T. Huebsch, S. Palczewski, S. Schulz, K. Verstrepen, E. K. Suk, M. R. Hoehe, "Fosmid-based whole genome haplotyping of a Hap- Map trio child: evaluation of single individual haplotyping techniques", Nucleic Acids Res., Vol .40, No. 5, pp.2041-2053, 2012. https://doi.org/10.1093/nar/gkr1042
  32. J. Duitama, T. Huebsch, G. McEven, E. K. Suk, M. R. Hcehe, "RefHap: a reliable and fast algorithm for single individual haplotyping", Proceedings of the First ACM international Comference on Bioinformatics and Computational Biology (BCB), pp.160-169, 2010.
  33. W. Y. Yang, F. Hormozdiari, Z. Wang, D. He, B. Pasaniuc, E. Eskin, "Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data", Bioinformatics. Vol. 29, No. 18, pp. 2245-2252, 2013. https://doi.org/10.1093/bioinformatics/btt386