Acknowledgement
Supported by : 한국연구재단
References
- 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
- 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)
- 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.
- 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
- 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
- The International HapMap Consortium, "A haplotype map of the human genome", Nature, Vol. 437, pp. 1299- 1320, 2005. https://doi.org/10.1038/nature04226
- 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
- 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
- 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
- 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
- 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
- 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)
- 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
- 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
- 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
- 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)
- A. G. Clark, "Haplotypes from PCR-amplified samples of diploid populations", Mol. Biol. Evol., Vol. 7, pp. 111-122, 1990.
- 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
- 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.
- 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
- 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
- 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
- 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.
- 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
- 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
- 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
- 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
- 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
- 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.
- 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
- 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
- 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.
- 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