The KIPS Transactions:PartB (정보처리학회논문지B)

Korea Information Processing Society (한국정보처리학회)
권호 표지
DOI QR코드

DOI QR Code

The Correctness Comparison of MCIH Model and WMLF/GI Model for the Individual Haplotyping Reconstruction

일배체형 재조합을 위한 MCIH 모델과 WMLF/GI 모델의 정확도 비교

  • 정인선 (전남대학교 전산학과) ;
  • 강승호 (전남대학교 전산학과) ;
  • 임형석 (전남대학교 전자컴퓨터공학부)
  • Published : 2009.04.30
Download PDF
⟨ Previous Next ⟩

Abstract

Minimum Letter Flips(MLF) and Weighted Minimum Letter Flips(WMLF) can perform the haplotype reconstruction more accurately from SNP fragments when they have many errors and gaps by introducing the related genotype information. And it is known that WMLF is more accurate in haplotype reconstruction than those based on the MLF. In the paper, we analyze two models under the conditions that the different rates of homozygous site in the genotype information and the different confidence levels according to the sequencing quality. We compare the performance of the two models using neural network and genetic algorithm. If the rate of homozygous site is high and sequencing quality is good, the results of experiments indicate that WMLF/GI has higher accuracy of haplotype reconstruction than that of the MCIH especially when the error rate and gap rate of SNP fragments are high.

일배체형 조합 문제를 해결하기 위해 제시된 MLF(Minimum Letter Flips) 모델이나 WMLF(Weighted Minimum Letter Flips) 모델은 유전자형 정보를 도입함으로써 오류와 손실이 많을 때에도 높은 정확도를 얻을 수 있다. 그리고 MLF 모델에 비해 가중치 버전인 WMLF모델의 정확도가 높다는 사실도 밝혀졌다. 본 논문에서는 유전자형 정보상의 동형(homozygous)의 분포 비율과 유전자 서열판독기계의 성능에 따른 신뢰도의 차이를 매개변수로 하여 두 모델을 구체적으로 비교, 분석한다. 두 모델의 성능 비교를 위해 신경망과 유전자 알고리즘을 사용한다. 실험결과 동형의 비율이 크고 판독기계의 성능이 좋으면 특히 손실율과 오류율이 높은 경우에 WMLF/GI 모델의 정확도가 더 우수함을 보인다.

Keywords

References

  1. R. Cilibrasi, L. V. Iersel, S. Kelk, and J. Tromp, 'On the complexity of Several Haplotyping Problem,' 5th Workshop on Algorithms in Bioinformatics(WABI), LNBI 3692, pp. 128-139, 2005
  2. M. J. Daly, J. D. Rioux, S. F. Schaffner, T. J. Hudson, and E. S. Lander, 'High-resolution haplotype structure in the human genome,' Nature Genetics 29, pp.229-232, 2001 https://doi.org/10.1038/ng1001-229
  3. H. J. Greenberg, W. E. Hart, and G. Lancia, 'Opportunities for Combinatorial Optimization in Computational Biology,' INFORMS Journal on Computing Vol.16, No.3, pp.211-231, 2004 https://doi.org/10.1287/ijoc.1040.0073
  4. D. E. Goldberg, Genetic Algorithms in serarch, Optimization and Machine Learning, Addison-Wesley, 1989
  5. S. H. Kang, I. S. Jeong, M. H. Choi, and H. S. Lim, 'Haplotype Assembly from Weighted SNP Fragments and Related Genotype Information,' Frontiers in Algorithmics Workshop(FAW) 2008, LNCS 5059, pp.45-54, 2008 https://doi.org/10.1007/978-3-540-69311-6_8
  6. R. Rizzi, V. Bafna, S. Istrail, and G. Lancia, 'Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem,' 2nd Workshop on Algorithms in Bioinformatics(WABI), LNCS 2452, pp.29-43, 2002 https://doi.org/10.1007/3-540-45784-4_3
  7. J. C. Stephens, et al, 'Haplotype variation and linkage disequilibrium in 313 human genes,' Science, Vol.293, pp. 489-493, 2001 https://doi.org/10.1126/science.1059431
  8. J. D Terwilliger and K. M Weiss, 'Linkage disequilibrium mapping of complex disease: fantasy or reality?,' Current Opinion in Biotechnology, Vol.9, No.6, pp.578-594, 1998 https://doi.org/10.1016/S0958-1669(98)80135-3
  9. Y. Wang, E. Feng, R. Wang, and D. Zhang, 'The haplotype assembly model with genotype information and iterative local-exhaustive search algorithm,' Computational Biology and Chemistry, Vol.31, pp.288-293, 2007 https://doi.org/10.1016/j.compbiolchem.2007.03.012
  10. R. S. Wang, L. Y. Wu, Z. P. Li, and X. S. Zhang, 'Haplotype reconstruction from SNP fragments by minimum error correction,' Bioinformatics, Vol.21, No.10, pp.2456-2462, 2005 https://doi.org/10.1093/bioinformatics/bti352
  11. X. S. Zhang, R. S. Wang, L. Y. Wu, and L. Chen, 'Models and Algorithms for Haplotyping Problem,' Current Bioinformatics, Vol.1, pp.105-114, 2006 https://doi.org/10.2174/157489306775330570
  12. X. S. Zhang, R. S. Wang, L. Y. Wu, and W. Zhang, 'Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype,' Evolutionary Bioinformatics Online, Vol.2, pp.271-280, 2006
  13. Y. Y. Zhao, L. Y. Wu, J. H. Zhang, R. S. Wang, and X. S. Zhang, 'Haplotype assembly from aligned weighted SNP fragments,' Computational Biology and Chemistry, Vol.29, pp.281-287, 2005 https://doi.org/10.1016/j.compbiolchem.2005.05.001
  14. 강승호, 정인선, 최문호, 임형석, '신뢰도를 가진 SNP 단편들과 유전자형으로부터 일배체형 조합', 정보과학회논문지, 제35권 제11호, pp.509-516, 2008