Haplotyping methods for pedigrees

Human Heredity

Volumn 67, Issue 4, 2009, Pages 248-266

  Gao, Guimin ^a   Allison, David B ^a   Hoeschele, Ina ^b  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^b VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

Family data; Haplotype inference; Pedigree

Indexed keywords

ALGORITHM; ARTICLE; BAYES THEOREM; CHROMOSOME ANALYSIS; COMPUTER PROGRAM; FAMILY STUDY; GENE LINKAGE DISEQUILIBRIUM; GENE SEQUENCE; HAPLOTYPE; HUMAN; MARKER GENE; NUCLEAR FAMILY; PEDIGREE; PEDIGREE ANALYSIS; POPULATION GENETIC PARAMETERS; SAMPLER; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; BAYES THEOREM; CHROMOSOME MAPPING; COMPUTER SIMULATION; HAPLOTYPES; HUMANS; LIKELIHOOD FUNCTIONS; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 58549115758     PISSN: 00015652     EISSN: 14230062     Source Type: Journal    
DOI: 10.1159/000194978     Document Type: Article

References (80)

1. Marchini J, Cutler D, Patterson N, Stephens M, Eskin E, Halperin E, Lin S, Qin ZS, Munro HM, Abecasis GR, Donnelly PA: Comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet 2006; 78: 437-450.
2. Sobel E, Lange K, O'Connell JR, Weeks DE: Haplotyping algorithm; in Speed T, Waterman MS (eds): IMA volumes in mathematics and its applications. Genetic mapping and DNA sequencing. New York, Springer-Verlag, 1996, Vol 81, pp 89-110.
3. Akey J, Jin L, Xong M: Haplotypes vs. single marker linkage disequilibrium tests: What do we gain? Eur J Hum Genet 2001; 9: 291- 300.
4. Hugot JP, Chamaillard M, Zuoali H, Lesage S, Cezard JP, Belaiche J, Almer S, Tysk C, O'Morain CA, Gassull M, Binder V, Finkel Y, Cortot A, Modigliani R, Laurent-Puig P, Gower-Rousseau C, Macry J, Colombel JF, Sahbatou M, Thomas G: Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature 2001; 411: 599-603.
5. Lin S, Chakravarti A, Cutler DJ: Haplotype and missing data inference in nuclear familes. Genome Res 2004; 14: 1624-1632.
6. Haines JL: Chromlook: an interactive program for error detection and mapping in reference linkage data. Genomics 1992;14: 517- 519.
7. Schaid DJ, McDonnell SK, Wang L, Cunningham JM, Thibodeau SN: Caution on pedigree haplotype inference with software that assumes linkage equilibrium. Am J Hum Genet 2002; 71: 992-995.
8. Abecasis GR, Cherny SS, Cookson WO, Cardon LR: Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 2002; 30: 97-101.
9. Burdick JT, Chen WM, Abecasis GR, Cheung VG: In silico method for inferring genotypes in pedigrees. Nat Genet 2006; 38: 1002-1004.
10. Niu T: Algorithms for inferring haplotypes. Genet Epidemiol 2004; 27: 334-347.
11. Salem RM, Wessel J, Schork NJ: A comprehensive literature review of haplotyping software and methods for use with unrelated individuals. Hum Genomics 2005; 2: 39-66.
12. Clerget-Darpoux F, Elston RC: Are linkage analysis and the collection of family data dead? Prospects for family studies in the age of genome-wide association. Hum Hered 2007; 64: 91-96.
13. Lin S, Speed TP: An algorithm for haplotype analysis. J Comput Biol 1997; 4: 535-546.
14. Gao G, Hoeschele I, Sorensen P, Du FX: Conditional probability methods for haplotyping in pedigrees. Genetics 2004; 167: 2055-2065.
15. Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES: Parametric and nonparametric linkage analysis: a unified multipoint approach. Am J Hum Genet 1996; 58: 1347-1363.
16. Gudbjartsson DF, Jonasson K, Frigge ML, Kong A: Allegro, a new computer program for multipoint linkage analysis. Nat Genet 2000; 25: 12-13.
17. Gudbjartsson DF, Thorvaldsson T, Kong A, Gunnarsson G, Ingolfsdottir A: Allegro version 2. Nat Genet 2005; 37: 1015-1016.
18. Sobel E, Lange K: Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker sharing statistics. Am J Hum Genet 1996; 58: 1323-1337.
19. Thomas A, Gutin A, Abkevich V, Bansal A:Multilocus linkage analysis by blocked Gibbssampling. Stat Comput 2000; 10: 259-269.
20. Lin S, Skrivanek Z, Irwin M: Haplotypingusing SIMPLE: caution on ignoring interference. Genet Epidemiol 2003; 25: 384-387.
21. Gao G, Hoeschele I: A rapid conditional enumeration haplotyping method in pedigrees. Genet Sel Evol 2008; 40: 25-36.
22. Abecasis GR, Wigginton JE: Handling marker- marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 2005; 77: 754-767.
23. Rohde K, Fuerst R: Haplotyping and estimation of haplotype frequencies for closely linked biallelic multilocus genetic phenotypes including nuclear family information. Hum Mutation 2001; 17: 289-295.
24. Ding X, Zhang Q, Flury C, Simianer H: Haplotype reconstruction and estimation of haplotype frequencies from nuclear families with only one parent available. Hum Hered 2006; 62: 12-19.25 Lindholm E, Zhang J, Hodge SE Greenberg DA: The reliability of haplotyping inference in nuclear families: Misassignment rates for SNPs and microsatellites. Hum Hered 2004; 57: 117-127.
25. Gao G, Hoeschele I: Approximating identity- by-descent matrices using multiple haplotype configurations on pedigrees. Genetics 2005; 171: 365-376.
26. Haldane JBS: The combination of linkage values and the calculation of distances between the loci of linked factors. J Genet 1919; 8: 299-309.
27. Lander ES, Green P: Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci USA 1987; 84: 2363-2367. Fishelson M, Dovgolevsky N, Geiger D: Maximum likelihood haplotyping for general pedigrees. Hum Hered 2005; 59: 41-60.
28. Thompson EA: Statistical inference from genetic data on pedigrees. NSF-CBMS Regional Conference Series in Probability and Statistics, Vol 6. Beachwood, OH: Institute of Mathematical Statistics, 2000.
29. Rabiner LR: A tutorial on hidden Markov models and selected applications in speech recognition. Proc IEEE 1989; 77: 257-286.
30. Baum LE: An inequality and associated maximization technique in statistical estimation for probabilistic functions on Markov processes; in Shisha O (ed): Inequalities- III; Proceedings of the Third Symposium on Inequalities. University of California Los Angeles, 1969, Academic Press, New York, 1972, pp 1-8.
31. Fujita M, McGeer PC, Yang JC: Multi-terminal binary decision diagrams: An efficient data structure for matrix representation. Formal methods in system design 1997; 10: 149-169.
32. Ingolfsdottir A, Gudbjartsson D: Genetic linkage analysis algorithms and their implementation; in Priami C et al (ed): Transact on Computat Systems Biol III, LNBI 3737. Berlin/ Heidelberg, Springer-Verlag, 2005, pp 123-144.
33. Lafferty J, Vardy A: Ordered Binary decision diagrams and minimal trellises. IEEE Trans Computers 1999; 48: 971-986. Hermanns H, Meyer-Kayser J, Siegle M: Multi terminal binary decision diagrams to represent and analyse continuous time Markov chains. In 3 rd Int. Workshop on the Numerical Solution of Markov Chains. Prensas Univesitaris de Zaragoza, 1999, pp 188-207.
34. O'Connell JR: Zero-recombinant haplotyping: applications to fine mapping using SNPs. Genet Epidemiol 2000; 19(suppl 1): S64-S70.
35. Zhang K, Sun F, Zhao H: HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. Bioinformatics 2005; 21: 90-103.
36. Elston RC, Stewart J: A general model for the genetic analysis of pedigree data. Hum Hered 1971; 21: 523-542.
37. Ott J: Analysis of human genetic linkage. Baltimore and London. The Johns Hopkins University Press, 1999.
38. Cannings C, Thompson E, Skolnick M: Probability functions on complex pedigrees. Adv Appl Prob 1978; 10: 26-61.
39. Lange K, Elston RC: Extensions to pedigree analysis. I. Likelihood calculations for simple and complex pedigrees. Hum Hered 1975; 25: 95-105.
40. Lange K, Boehnke M: Extensions to pedigree analysis. V. Optimal calculation of Mendelian likelihoods. Hum Hered 1983; 33: 291- 301.
41. Ploughman LM, Boehnke M: Estimating the power of a proposed linkage study for a complex genetic trait. Am J Hum Genet 1989; 44: 543-551.
42. Janss LLG, Van Arendonk JAM, Van der Werf JHJ: Computing approximate monogenic model likelihoods in large pedigrees with loops. Genet Sel Evol 1995; 27: 567-579.
43. Wang T, Fernando RL, Stricker C, Elston RC: An approximation to the likelihood for a pedigree with loops. Theor Appl Genet 1996; 93: 1299-1309.
44. Fernandez SA, Fernando RL, Guldbrandtsen B, Totir LR, Carriquiry AL: Sampling genotypes in large pedigrees with loops. Genet Sel Evol 2001; 33: 337-367.
45. Lauritzen SL, Spiegelhalter DL: Local computations with probabilities on graphical structures and their application to expert systems. J R Stat Soc B 1988; 50: 157-224.
46. Lauritzen SL, Sheehan NA: Graphical models for genetic analyses. Stat Sci 2003; 18: 489- 514.
47. Heath SC: Genetic linkage analysis using Markov chain Monte Carlo techniques; in Green PJ, Hjort NL, Richardson S (ed): Highly Structured Stochastic System. London/ New York/Oxford, Oxford University Press, 2003, pp 363-381.
48. Fernandez SA, Fernando RL: Determining peeling order using sparse matrix algorithms. J Dairy Sci 2002; 85: 1623-1629.
49. Pearl J: Probabilistic Reasoning in Intelligent Systems. San Francisco, Morgan Kaufmann, 1988.
50. Lauritzen SL: Graphical Models. Oxford University Press, 1996.
51. Dechter R: Bucket elimination: a unifying framework for probabilistic inference; in M I (ed): Learning in Graphical Models. Kluwer Academic Press, 1998, pp 75-104.
52. Murphy KP: A brief introduction to graphical models and Bayesian networks. Http://www.cs.ubc.ca/murphyk/Bayes/bayes-tutorial. pdf. 2001.
53. O'Connell JR, Weeks DE: An optimal algorithm for automatic genotype elimination. Am J Hum Genet 1999; 65: 1733-1740.
54. Lange K, Goradia TM: An algorithm for automatic genotype elimination. Am J Hum Genet 1987; 40: 250-256.
55. O'Connell JR, Weeks DE: The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance. Nat Genet 1995; 11: 402-408.
56. Jensen CS, Kjaerulff U, Kong A: Blocking Gibbs sampling in very large probabilistic expert systems. Int J Hum Comp Stud 1995; 42: 647-666.
57. Irwin M, Cox N, Kong A: Sequential imputation for multilocus linkage analysis. Proc Natl Acad Sci USA 1994; 91: 11684-11688.
58. Skrivanek Z, Lin S, Irwin M: Linkage analysis with sequential imputation. Genet Epidemiol 2003; 25: 25-35.
59. Heath SC: Markov chain Monte Carlo segregation and linkage analysis for oligogenic models. Am J Hum Genet 1997; 61: 8748- 760.
60. Thompson EA, Heath SC: Estimation of conditional multilocus gene identity among relatives; in Seillier-Moiseiwitsch F (ed): Statistics in Molecular Biology and Genetics: Selected Proceedings of a 1997 Joint AMSIMS- SIAM Summer Conference on Statistics in Molecular Biology, IMS Lecture Note- Monograph Series Volume 33, Hayward, CA: Institute of Mathematical Statistics, 1999, pp 95-113.
61. Heath SC, Thompson EA: MCMC samplers for multilocus analyses on complex pedigrees. Am J Hum Genet 1997; 61:A278.
62. Broman KW, Weber JL: Characterization of human crossover interference. Am J Hum Genet 2000; 66: 1911-1926.
63. Lin S, Cheng R, Wright FA: Genetic crossover interference in the human genome. Ann Hum Genet 2001; 65: 79-93.
64. Wijsman E: A deductive method of haplotype analysis in pedigrees. Am J Hum Genet 1987; 41: 356-373.
65. Tapadar P, Ghosh S, Majumder PP: Haplotyping in pedigrees via a genetic algorithm. Hum Hered 2000; 50: 43-56.
66. Qian D, Beckmann L: Minimum-recombinant haplotyping in pedigrees. Am J Hum Genet 2002; 70: 1434-1445.
67. Li J, Jiang T: Computing the minimum recombinant haplotype configuration from incomplete genotype data on a pedigree by integer linear programming. J Comp Biol 2005; 12: 719-739. [http://www.cs.ucr.edu/ ̃jili/haplotyping. html]
68. Baruch E, Weller JI, Cohen M, Ron M, Seroussi E: Efficient inference of haplotypes from genotypes on a large animal pedigree. Genetics 2006; 172: 1757-1765. 72 Dempster A, Laird N, Rubin D: Maximum likelihood from incomplete data via the E-M algorithm. J R Stat Soc Ser B 1977; 39: 1-38.
69. Qin ZS, Niu T, Liu JS: Partition-ligation-expectation- maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet 2002; 71: 1242-1247. Gao /Allison /Hoeschel266 Hum Hered 2009;67:248-266 e 74 Liu PY, Lu Y, Deng HW: Accurate haplotype inference for multiple linked single-nucleotide polymorphisms using sibship data. Genetics 2006; 174: 499-509.
70. Excoffier L, Slatkin M: Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 1995; 12: 921-927.
71. Hawley ME, Kidd KK: HAPLO: a program using the EM algorithm to estimate frequencies of multi-site haplotypes. J Hered 1995; 86: 409-411.
72. Niu T, Qin ZS, Xu X, Liu JS: Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet 2002; 70: 157-169.
73. Stephens M, Smith NJ, Donnelly P: A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001; 68: 978-989.
74. Stephens M, Scheet P: Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet 2005; 76: 449-462.
75. Halperin E, Eskin E: Haplotype reconstruction from genotype data using imperfect phylogeny. Bioinformatics 2004; 20: 1842- 1849.
76. International HapMap Consortium: A haplotype map of the human genome. Nature 2005; 437: 1299-1320.
77. Sobel E, Papp JC, Lang K: Detection and integration of genotyping errors in statistical genetics. Am J Hum Genet 2002; 70: 496- 508.
78. Douglas JA Skol AD, Boehnke M: Probability of detection of genotyping errors and mutations as inheritance inconsistencies in nuclear- family data. Am J Hum Genet 2002; 70: 487-495.
79. Weiss LA, Pan L, Abeny M, Ober C: The sexspecific genetic architecture of quantitative traits in humans. Nat Genet 2006; 38: 218-222.
80. Zhang Y, Niu T, Liu JS: A coalescence-guided hierarchical Bayesian method for haplotype inference. Am J Hum Genet 2006; 79: 313-22.