Haplotype reconstruction for scnp DNA: A consensus vote approach with extensive sequence data from populations of the migratory locust (Locusta migratoria)

Molecular Ecology

Volumn 17, Issue 8, 2008, Pages 1930-1947

  Huang, Zu Shi ^a,b   Ji, Ya Jie ^a   Zhang, De Xing ^a  

^a INSTITUTE OF ZOOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Ambiguous genotype; Consensus vote; Flanking region of nuclear microsatellite DNA; Locusta migratoria; Statistical haplotype reconstruction

Indexed keywords

DNA; MICROSATELLITE DNA;

ALGORITHM; ANIMAL; ARTICLE; BAYES THEOREM; CHEMISTRY; EVALUATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENETICS; GENOTYPE; HAPLOTYPE; LOCUST; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; STATISTICAL ANALYSIS; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; BASE SEQUENCE; BAYES THEOREM; CLONING, MOLECULAR; DATA INTERPRETATION, STATISTICAL; DNA; GENOTYPE; HAPLOTYPES; LIKELIHOOD FUNCTIONS; LOCUSTA MIGRATORIA; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; SEQUENCE ALIGNMENT; VARIATION (GENETICS);

LOCUSTA MIGRATORIA;

EID: 42049118295     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2008.03730.x     Document Type: Article

References (78)

1. Adkins RM (2004) Comparison of the accuracy of methods of computational haplotype inference using a large empirical dataset. BMC Genetics, 5, 22.
2. Andres AM, Clark AG, Shimmin L et al 2007) Understanding the accuracy of statistical haplotype inference with sequence data of known phase. Genetic Epidemiology, 31, 659 671.
3. Antunes A, Templeton AR, Guyomard R, Alexandrino P (2002) The role of nuclear genes in intraspecific evolutionary inference: genealogy of the transferrin gene in the brown trout. Molecular Biology and Evolution, 19, 1272 1287.
4. Ayers KL, Sabatti C, Lange K (2007) A dictionary model for haplotyping, genotype calling, and association testing. Genetic Epidemiology, 31, 672 683.
5. Bartish IV, Kadereit JW, Comes HP (2006) Late Quaternary history of Hippophae rhamnoides L. (Elaeagnaceae) inferred from chalcone synthase intron (Chsi) sequences and chloroplast DNA variation. Molecular Ecology, 15, 4065 4083.
6. Becker T, Knapp M (2002) Efficiency of haplotype frequency estimation when nuclear family information is included. Human Heredity, 54, 45 53.
7. Brown DG, Harrower IM (2006) Integer programming approaches to haplotype inference by pure parsimony. IEEE-ACM Transactions on Computational Biology and Bioinformatics, 3, 141 154.
8. Brumfield RT, Beerli P, Nickerson DA, Edwards SV (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology and Evolution, 18, 249 256.
9. Clark AG (1990) Inference of haplotypes from PCR-amplified samples of diploid populations. Molecular Biology and Evolution, 7, 111 122.
10. Clark AG, Weiss KM, Nickerson DA et al 1998) Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. American Journal of Human Genetics, 63, 595 612.
11. Clayton D (2001) snphap: a program for estimating frequencies of large haplotypes of single nucleotide polymorphisms. http://www-gene.cimr.cam.ac.uk/ clayton/software/snphap.txt.
12. Cohen JC, Kiss RS, Pertsemlidis A et al 2004) Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science, 305, 869 872.
13. Crandall KA, Templeton AR (1993) Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics, 134, 959 969.
14. Eronen L, Geerts F, Toivonen H (2004) A Markov chain approach to reconstruction of long haplotypes. In : Proceedings of the 9th Pacific Symposium on Biocomputing (eds Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE pp. 104 115. World Scientific, Singapore.
15. Eronen L, Geerts F, Toivonen H (2006) haplorec: efficient and accurate large-scale reconstruction of haplotypes. BMC Bioinformatics, 7, 542.
16. Excoffier L, Laval G, Balding D (2003) Gametic phase estimation over large genomic regions using an adaptive window approach. Human Genomics, 1, 7 19.
17. Excoffier L, Laval G, Schneider S (2005) arlequin version 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47 50.
18. Excoffier L, Slatkin M (1995) Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Molecular Biology and Evolution, 12, 921 927.
19. Fallin D, Schork NJ (2000) Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. American Journal of Human Genetics, 67, 947 959.
20. Greenspan G, Geiger D (2004) Model-based inference of haplotype block variation. Journal of Computational Biology, 11, 493 504.
21. Guo SW, Thompson EA (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics, 48, 361 372.
22. Gusfield D (2001) Inference of haplotypes from samples of diploid populations: complexity and algorithms. Journal of Computational Biology, 8, 305 323.
23. Gusfield D (2002) Haplotyping as perfect phylogeny: conceptual framework and efficient solutions. In : Proceedings of the 6th International Conference on Computational Molecular Biology (eds Myers G, Hannenhalli S, Istrail S, Pevzner P, Waterman M pp. 166 175. ACM Press, New York.
24. Gusfield D (2003) Haplotype inference by pure parsimony. In : Proceedings of the 14th Annual Symposium on Combinatorial Pattern Matching (eds Baeza-Yates R, Chavez E, Crochemore M Lecture Notes in Computer Science, 2676, pp. 144 155. Springer-Verlag, Berlin.
25. Halldorsson BV, Bafna V, Edwards N et al 2004) A survey of computational methods for determining haplotypes. In : Computational Methods for SNPs and Haplotype Inference (eds Istrail S, Waterman M, Clark A Lecture Notes in Computer Science, 2983, pp. 26 47. Springer-Verlag, Berlin.
26. Halperin E, Eskin E (2004) Haplotype reconstruction from genotype data using imperfect phylogeny. Bioinformatics, 20, 1842 1849.
27. Hawley ME, Kidd KK (1995) haplo: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes. Journal of Heredity, 86, 409 411.
28. Hoehe MR, Kopke K, Wendel B et al 2000) Sequence variability and candidate gene analysis in complex disease: association of μ opioid receptor gene variation with substance dependence. Human Molecular Genetics, 9, 2895 2908.
29. Huang YT, Chao KM, Chen T (2005) An approximation algorithm for haplotype inference by maximum parsimony. Journal of Computational Biology, 12, 1261 1274.
30. Hurley JD, Engle LJ, Davis JT, Welsh AM, Landers JE (2005) A simple, bead-based approach for multi-SNP molecular haplotyping. Nucleic Acids Research, 32, e186.
31. International HapMap Consortium (2005) A haplotype map of the human genome. Nature, 437, 1299 1320.
32. Kimmel G, Shamir R (2005) GERBIL: genotype resolution and block identification using likelihood. Proceedings of the National Academy of Sciences, USA, 102, 158 162.
33. Kirk KM, Cardon LR (2002) The impact of genotyping error on haplotype reconstruction and frequency estimation. European Journal of Human Genetics, 10, 616 622.
34. Kruglyak L, Nickerson DA (2001) Variation is the spice of life. Nature Genetics, 27, 234 236.
35. Lancia G, Bafna V, Istrail S, Lippert R, Schwartz R (2001) SNPs problems, complexity, and algorithms. In : Proceedings of the Ninth Annual European Symposium on Algorithms (ed. Meyer auf der Heide F Lecture Notes in Computer Science, 2161, pp. 182 193. Springer-Verlag, Berlin.
36. Lancia G, Pinotti MC, Rizzi R (2004) Haplotyping populations by pure parsimony: complexity of exact and approximation algorithms. Informs Journal on Computing, 16, 348 359.
37. Landwehr N, Mielikainen T, Eronen L, Toivonen H, Mannila H (2007) Constrained hidden Markov models for population-based haplotyping. BMC Bioinformatics, 8, S9.
38. Li SS, Khalid N, Carlson C, Zhao LP (2003) Estimating haplotype frequencies and standard errors for multiple single nucleotide polymorphisms. Biostatistics, 4, 513 522.
39. Li Z, Zhou W, Zhang XS, Chen L (2005) A parsimonious tree-grow method for haplotype inference. Bioinformatics, 21, 3475 3481.
40. Lin S, Chakravarti A, Cutler DJ (2004) Haplotype and missing data inference in nuclear families. Genome Research, 14, 1624 1632.
41. Lin S, Cutler DJ, Zwick ME, Chakravarti A (2002) Haplotype inference in random population samples. American Journal of Human Genetics, 71, 1129 1137.
42. Lippert R, Schwartz R, Lancia G, Istrail S (2002) Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem. Briefings in Bioinformatics, 3, 23 31.
43. Long JC, Williams RC, Urbanek M (1995) An E-M algorithm and testing strategy for multiple-locus haplotypes. American Journal of Human Genetics, 56, 799 810.
44. Marchini J, Cutler D, Patterson N et al 2006) A comparison of phasing algorithms for trios and unrelated individuals. American Journal of Human Genetics, 78, 437 450.
45. Mountain JL, Knight A, Jobin M et al 2002) SNPSTRs: empirically derived, rapidly typed, autosomal haplotypes for inference of population history and mutational processes. Genome Research, 12, 1766 1772.
46. Niu T (2004) Algorithms for inferring haplotypes. Genetic Epidemiology, 27, 334 347.
47. Niu T, Qin ZS, Xu X, Liu JS (2002) Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. American Journal of Human Genetics, 70, 157 169.
48. Olsen KM, Schaal BA (1999) Evidence on the origin of cassava: phylogeography of Manihot esculenta. Proceedings of the National Academy of Sciences, USA, 96, 5586 5591.
49. Orzack SH, Gusfield D, Olson J et al 2003) Analysis and exploration of the use of rule-based algorithms and consensus methods for the inferral of haplotypes. Genetics, 165, 915 928.
50. Patil N, Berno AJ, Hinds DA et al 2001) Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science, 294, 1719 1723.
51. Pritchard JK (2001) Are rare variants responsible for susceptibility to complex diseases? American Journal of Human Genetics, 69, 124 137.
52. Qin ZS, Niu T, Liu JS (2002) Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. American Journal of Human Genetics, 71, 1242 1247.
53. Rohde K, Fuerst R (2001) Haplotyping and estimation of haplotype frequencies for closely linked biallelic multilocus genetic phenotypes including nuclear family information. Human Mutation, 17, 289 295.
54. Ryynanen HJ, Primmer CR (2004) Distribution of genetic variation in the growth hormone 1 gene in Atlantic salmon (Salmo salar) populations from Europe and North America. Molecular Ecology, 13, 3857 3869.
55. Sabbagh A, Darlu P (2005) Inferring haplotypes at the NAT2 locus: the computational approach. BMC Genetics, 6, 30.
56. Salem RM, Wessel J, Schork NJ (2005) A comprehensive literature review of haplotyping software and methods for use with unrelated individuals. Human Genomics, 2, 39 66.
57. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
58. Schaid DJ (2002) Relative efficiency of ambiguous vs. directly measured haplotype frequencies. Genetic Epidemiology, 23, 426 443.
59. Scheet P, Stephens M (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. American Journal of Human Genetics, 78, 629 644.
60. Sharan R, Halldorsson BV, Istrail S (2006) Islands of tractability for parsimony haplotyping. IEEE-ACM Transactions on Computational Biology and Bioinformatics, 3, 303 311.
61. Sotka EE, Wares JP, Barth JA, Grosberg RK, Palumbi SR (2004) Strong genetic clines and geographical variation in gene flow in the rocky intertidal barnacle Balanus glandula. Molecular Ecology, 13, 2143 2156.
62. Stephens M, Donnelly P (2003) A comparison of Bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics, 73, 1162 1169.
63. Stephens M, Scheet P (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. American Journal of Human Genetics, 76, 449 462.
64. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978 989.
65. Taylor MS, Hellberg ME (2006) Comparative phylogeography in a genus of coral reef fishes: biogeographic and genetic concordance in the Caribbean. Molecular Ecology, 15, 695 707.
66. Templeton AR (2004) Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology, 13, 789 809.
67. Thomas A (2003a) Accelerated gene counting for haplotype frequency estimation. Annals of Human Genetics, 67, 608 612.
68. Thomas A (2003b) gchap: fast MLEs for haplotype frequencies by gene counting. Bioinformatics, 19, 2002 2003.
69. Tishkoff SA, Pakstis AJ, Ruano G, Kidd KK (2000) The accuracy of statistical methods for estimation of haplotype frequencies: an example from the CD4 locus. American Journal of Human Genetics, 67, 518 522.
70. Tost J, Brandt O, Boussicault F et al 2002) Molecular haplotyping at high throughput. Nucleic Acids Research, 30, e96.
71. Wang L, Xu Y (2003) Haplotype inference by maximum parsimony. Bioinformatics, 19, 1773 1780.
72. Xing EP, Sohn KA, Jordan MI, Teh YW (2006) Bayesian muti-population haplotype inference via a hierarchical Dirichlet process mixture. In : Proceedings of the 23rd International Conference on Machine Learning (eds Cohen W, Moore A pp. 1049 1056. ACM Press, New York.
73. Xu CF, Lewis K, Cantone KL et al 2002) Effectiveness of computational methods in haplotype prediction. Human Genetics, 110, 148 156.
74. Zhang DX, Hewitt GM (1998) Isolation of animal cellular total DNA. In : Molecular Tools for Screening Biodiversity: Plants and Animals (eds Karp A, Isaac PG, Ingram DS pp. 5 9. Chapman & Hall, London.
75. Zhang DX, Hewitt GM (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Molecular Ecology, 12, 563 584.
76. Zhang Y, Niu T, Liu JS (2006) A coalescence-guided hierarchical Bayesian method for haplotype inference. American Journal of Human Genetics, 79, 313 322.
77. Zhang J, Rowe WL, Struewing JP, Buetow KH (2002) hapscope: a software system for automated and visual analysis of functionally annotated haplotypes. Nucleic Acids Research, 30, 5213 5221.
78. Zhang DX, Yan LN, Ji YJ et al 2003) Isolation, characterization and cross-species amplification of eight microsatellite DNA loci in the migratory locust (Locusta migratoria). Molecular Ecology Notes, 3, 483 486.