Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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A Program for Efficient Phasing of Three-Generation Trio SNP Genotype Data

  • Accepted : 2011.09.02
  • Published : 2011.09.30
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Abstract

Here, we report a computer program written in Python, which phases SNP genotypes and infers inherited deletions based on the pattern of Mendelian inheritance within a trio pedigree. When tiered trio genotypes that encompass three generations are available, it narrows a recombination event down to a region between two consecutive heterozygous markers. In addition, the phase information that is inferred from the upper trio that is formed by one of the parents and grandparents can be propagated to phase the genotypes of the lower trio that is formed by the parents and an offspring.

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References

  1. Browning, S.R. (2008). Missing data imputation and haplotype phase inference for genome-wide association studies. Hum. Genet. 124, 439-450. https://doi.org/10.1007/s00439-008-0568-7
  2. Conrad, D.F., Andrews, T.D., Carter, N.P., Hurles, M.E., and Pritchard, J.K. (2006). A high-resolution survey of deletion polymorphism in the human genome. Nat. Genetics. 38, 75-81. https://doi.org/10.1038/ng1697
  3. Freeman, J.L., Perry, G.H., Feuk, L., Redon, R., McCarroll, S.A., Altshuler, D.M., Aburatani, H., Jones, K.W., Tyler-Smith, C., Hurles, M.E., Carter, N.P., Scherer, S.W., and Lee, C. (2006). Copy number variation: new insights in genome diversity. Genome Res. 16, 949-961. https://doi.org/10.1101/gr.3677206
  4. Gabriel, S.B., Schaffner, S.F., Nguyen, H., Moore, J.M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., Liu-Cordero, S.N., Rotimi, C., Adeyemo, A., Cooper, R., Ward, R., Lander, E.S., Daly, M.J., and Altshuler, D. (2002). The structure of haplotype blocks in the human genome. Science 296, 2225-2229. https://doi.org/10.1126/science.1069424
  5. Howie, B.N., Donnelly, P., and Marchini, J. (2009). A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 5, e1000529. https://doi.org/10.1371/journal.pgen.1000529
  6. Iliadis, A., Watkinson, J., Anastassiou, D., and Wang, X. (2010). A haplotype inference algorithm for trios based on deterministic sampling. BMC Genet. 11, 78.
  7. Kong, A., Thorleifsson, G., Gudbjartsson, F., Masson, G., Sigurdsson, A., Jonasdottir, A., Walters, B., Jonasdottir, A., Gylfason, A., Kristinsson, K., Gudjonsson, S., Frigge, L., Helgason, A., Thorsteinsdottir, U., and Stefansson, K. (2010). Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467, 1099-1103. https://doi.org/10.1038/nature09525
  8. Marchini, J., Cutler, D., Patterson, N., Stephens, M., Eskin, E., Halperin, E., Lin, S., Qin, Z.S., Munro, H.M., Abecasis, G.R., Donnelly, P., and International HapMap Consortium. (2006). A comparison of phasing algorithms for trios and unrelated individuals. Am. J. Hum. Genet. 78, 437-450. https://doi.org/10.1086/500808
  9. Park, M., Kim, D.J., Kim, K.J., Hong, C.B., Kim, Y.J., Cheong, H.S., Shin, H.D., Lee, E.J., Kim, H.N., Chung, H.W., Kim, E.K., Lee, J.Y., and Kim, H.L. (2009). Gene associations of common deletion polymorphisms in families with Avellino corneal dystrophy. Biochem. Biophys. Res. Comm. 387, 688-693. https://doi.org/10.1016/j.bbrc.2009.07.084
  10. Stephens, M., and Donnelly, P. (2003). A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am. J. Hum. Genet. 73, 1162-1169. https://doi.org/10.1086/379378