Genotype error detection using hidden Markov models of haplotype diversity

Journal of Computational Biology

Volumn 15, Issue 9, 2008, Pages 1155-1171

  Kennedy, Justin ^a   Mǎndoiu, Ion ^a   Paşaniuc, Bogdan ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Algorithms; Detection; Genotype error; Haplotype; Hidden Markov model; Likelihood ratio test

Indexed keywords

ALGORITHM; ARTICLE; DIAGNOSTIC ACCURACY; DIAGNOSTIC ERROR; DISEASE ASSOCIATION; GENETIC LINKAGE; GENETIC VARIABILITY; GENOTYPE; GENOTYPE ERROR DETECTION; HAPLOTYPE; HIDDEN MARKOV MODEL; HUMAN; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROBABILITY; SIMULATION; STATISTICAL MODEL;

ALGORITHMS; COMPUTER SIMULATION; GENETIC VARIATION; GENOTYPE; HAPLOTYPES; HUMANS; LIKELIHOOD FUNCTIONS; LINKAGE (GENETICS); MARKOV CHAINS; MODELS, GENETIC;

EID: 55249123420     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2007.0133     Document Type: Article

References (40)

1. Abecasis, G., Cherny, S., and Cardon, L. 2001. The impact of genotyping error on family-based analysis of quantitative traits. Eur. J. Hum. Genet. 9, 130-134.
2. Abecasis, G., Cherny, S., Cookson, W., et al. 2002. Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat. Genet. 30, 97-101.
3. Ahn, K., Haynes, C., Kim, W., et al. 2007. The effects of SNP genotyping errors on the power of the Cochran-Armitage linear trend test for case/control association studies. Ann. Hum. Genet. 71, 249-261.
4. Baum, L., Petrie, T., Soules, G., et al. 1970. A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann. Math. Statist. 41, 164-171.
5. Becker, T., and Knapp, M. 2004. Maximum-likelihood estimation of haplotype frequencies in nuclear families. Genet. Epidemiol. 27, 21-32.
6. Becker, T., Valentonyte, R., Croucher, P., et al. 2006. Identification of probable genotyping errors by consideration of haplotypes. Eur. J. Hum. Genet. 14, 450-458.
7. Cheng, K. 2007. Analysis of case-only studies accounting for genotyping error. Ann. Hum. Genet. 71, 238-248.
8. Cherny, S., Abecasis, G., Cookson, W., et al. 2001. The effect of genotype and pedigree error on linkage analysis: analysis of three asthma genome scans. Genet. Epidemiol. 21, S117-S122.
9. Cutler, D., Zwick, M., Carrasquillo, M., et al. 2001. High-throughput variation detection and genotyping using microarrays. Genome Res. 11, 1913-1925.
10. Di, X., Matsuzaki, H., Webster, T., et al. 2005. Dynamic model based algorithms for screening and genotyping over 100k SNPs on oligonucleotide microarrays. Bioinformatics 21, 1958-1963.
11. Douglas, J., Boehnke, M., and Lange, K. 2000. A multipoint method for detecting genotyping errors and mutations in sibling-pair linkage data. AJHG 66, 1287-1297.
12. Douglas, J., Skol, A., and Boehnke,M. 2002. Probability of detection of genotyping errors and mutations as inheritance inconsistencies in nuclear-family data. AJHG 70, 487-495.
13. Gordon, D., Finch, S., Nothnagel, M., et al. 2002. Power and sample size calculations for case-control genetic association tests when errors are present: application to single nucleotide polymorphisms. Hum. Hered. 54, 22-33.
14. Gordon, D., Heath, S., and Ott, J. 1999. True pedigree errors more frequent than apparent errors for single nucleotide poloymorphisms. Hum. Hered. 49, 65-70.
15. Gusev, A., Paşaniuc, B., and Mändoiu, I. 2008. Highly scalable genotype phasing by entropy minimization. IEEE/ACM Trans. Comput. Biol. Bioinform. 5, 252-261, 2008.
16. Hao, K., and Wang, X. 2004. Incorporating individual error rate into association test of unmatched case-control design. Hum. Hered. 58, 154-163.
17. 1-ε". Acta Math. 182, 105-142.
18. Hosking, L., Lumsden, S., Lewis, K., et al. 2004. Detection of genotyping errors by Hardy-Weinberg equilibrium testing. Eur. J. Hum. Genet. 12, 395-399.
19. Kimmel, G., and Shamir, R. 2005. A block-free hidden Markov model for genotypes and its application to disease association. J. Comput. Biol. 12, 1243-1260.
20. Knapp, M., and Becker, T. 2004. Impact of genotyping errors on type I error rate of the haplotype-sharing transmission/disequilibrium test (HS-TDT). Am. J. Hum. Genet. 74, 589-591.
21. Leal, S. 2005. Detection of genotyping errors and pseudo-SNPs via deviations from Hardy-Weinberg equilibrium. Genet. Epidemiol. 29, 204-214.
22. Liang, L., Zöllner, S., and Abecasis, G. 2007. GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics 23, 1565-1567.
23. Liu, W., Yang, T., Zhao, W., et al. 2007. Accounting for genotyping errors in tagging SNP selection. Am. J. Hum. Genet. 71, 467-479.
24. Lyngsø, R., and Pedersen, C. 2002. The consensus string problem and the complexity of comparing hidden Markov models. J. Comput. Syst. Sci. 65, 545-569.
25. Marchini, J., Spencer, C., Teo, Y., et al. 2007. A Bayesian hierarchical mixture model for genotype calling in a multi-cohort study. In preparation.
26. Mitchell, A., Cutler, D., and Chakravarti, A. 2003. Undetected genotyping errors cause apparent overtransmission of common alleles in the transmission/disequilibrium test. Am. J. Hum. Genet. 72, 598-610.
27. Mukhopadhyaya, N., Buxbauma, S., and Weeks, D. 2004. Comparative study of multipoint methods for genotype error detection. Hum. Hered. 58, 175-189.
28. NCI-NHGRI Working Group on Replication in Association Studies. 2007. Replicating genotype-phenotype associations. Nature 447, 655-660.
29. Nicolae, D., Wu., X., Miyake, K., et al. 2006. Gel: a novel genotype calling algorithm using empirical likelihood. Bioinformatics 22, 1942-1947.
30. Pompanon, F., Bonin, A., Bellemain, E., et al. 2005. Genotyping errors: causes, consequences and solutions. Nat. Rev. Genet. 6, 847-859.
31. Rabbee, N., and Speed, T. 2005. A genotype calling algorithm for affymetrix SNP arrays. Bioinformatics 22, 7-12.
32. Rastas, P., Koivisto, M., Mannila, H., et al. 2007. Phasing genotypes using a hidden Markov model. In: Mãndoiu, I.I., and Zelikovsky, A., eds. Bioinformatics Algorithms: Techniques and Applications. Wiley, New York.
33. Scheet, P., and Stephens, M. 2006. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am. J. Human Genet. 78, 629-644.
34. Schwartz, R. 2004. Algorithms for association study design using a generalized model of haplotype conservation. Proc. CSB 90-97.
35. Sobel, E., and Lange, K. 1996. Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker-sharing statistics. Am. J. Hum. Genet. 58, 1323-1337.
36. Sobel, E., Papp, J., and Lange, K. 2002. Detection and integration of genotyping errors in statistical genetics. Am. J. Hum. Genet. 70, 496-508.
37. Viterbi, A. 1967. Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans. Inform. Theory 13, 260-269.
38. Xiao, Y., Segal, M., Yang, J., et al. 2007. A multi-array multi-SNP genotyping algorithm for affymetrix SNP microarrays. Bioinformatics 23, 1459-1467.
39. Zaitlen, N., Kang, H., Feolo, M., et al. 2005. Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP. Genome Res. 15, 1595-1600.
40. Zheng, G., and Tian, X. 2005. The impact of diagnostic error on testing genetic association in case-control studies. Stat. Med. 24, 869-882.