Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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HapAnalyzer: Minimum Haplotype Analysis System for Association Studies

  • Jung, Ho-Youl (Division of Epidemiology and Bioinformatics, National Genome Research Institute, National Institute of Health) ;
  • Park, Jung-Sun (Division of Epidemiology and Bioinformatics, National Genome Research Institute, National Institute of Health) ;
  • Park, Yun-Ju (Division of Epidemiology and Bioinformatics, National Genome Research Institute, National Institute of Health) ;
  • Kim, Young-Jin (Division of Epidemiology and Bioinformatics, National Genome Research Institute, National Institute of Health) ;
  • Kimm, Kuchan (Division of Epidemiology and Bioinformatics, National Genome Research Institute, National Institute of Health) ;
  • Koh, InSong (Division of Epidemiology and Bioinformatics, National Genome Research Institute, National Institute of Health)
  • Published : 2004.06.01
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Abstract

HapAnalyzer is an analysis system that provides minimum analysis methods for the SNP-based association studies. It consists of Hardy-Weinberg equilibrium (HWE) test, linkage disequilibrium (LD) computation, haplotype reconstruction, and SNP (or haplotype)-phenotype association assessment. It is well suited to a case-control association study for the unrelated population.

Keywords

References

  1. Abecasis, G. R. and Cookson, W.O.C. (2000). GOLD-Graphical Overview of Linkage Disequilibrium. Bioinformatics 16, 182-183 https://doi.org/10.1093/bioinformatics/16.2.182
  2. Cleak, A. G. (1990). Inference of haplotypes from PCR amplified samples of diploid populations. Molecular Biology and Evolution 7, 111-122
  3. Clark, A. G. (1990). Inference of haplotypes from PCRamplified samples of diploid populations. Molecular Biology and Evolution 7, 111 -122
  4. Devlin, B. and Risch, N. (1995). A Comparison of Linkage Disequilibrium Measures for Fine-ScaIe Mapping. Genomics 29, 311-322 https://doi.org/10.1006/geno.1995.9003
  5. Gabriel, S. B. et al. (2002). The Structure of Haplotype Blocks in the Human Genome. Science 296, 2225-2229 https://doi.org/10.1126/science.1069424
  6. Jung, H-.Y. et al. (2003). iHapIor: A Hybrid Method for Haplotype Reconstruction, In Proceedings of the Second Annual Conference of the Korean Society for Boinformatics (KSB/2003), 2, 221-228
  7. Barrett, J. (2003). HapIoView. http://www.broad.mit.edu/personal/jcbarret/haplo/incdex.php
  8. Qin, Z. S., Niu, T., and Liu, J. S. (2002). Partition-Ligation-Expectation-Maximization Algorithm for Haplotype Inference with Single- Nucleotide Polymorphisms. American Journal of Human Genetics 71, 1242-1247 https://doi.org/10.1086/344207
  9. Sebastiani, P., Lazarus, R., Weiss, S. T., Kunkel, L. M., Kohane, I. S., and Ramoni, M. F., (2003). Minimal haplotype tagging. Proceedings of the National Academy of Science, 100, 9900-9905 https://doi.org/10.1073/pnas.1633613100
  10. Zhang, K., Deng, M., Chen, T., Waterman, M. S., and Sun, F. (2002). A dynamic programming algorithm for haplotype block partitioning. Proc. Natl. Acad. Sci. USA 99, 7335-7339 https://doi.org/10.1073/pnas.102186799