Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data

BMC Genetics

Volumn 13, Issue , 2012, Pages

  Nettelblad, Carl ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Genotype inference; Haplotyping; Hidden Markov models; Nuclear family data; Phasing

Indexed keywords

MERLIN;

ACCURACY; ARTICLE; GENE STRUCTURE; GENETIC LINE; GENOME ANALYSIS; GENOTYPE; HAPLOTYPE; HUMAN; MATING; PARENT; PEDIGREE; PROGENY;

GENOTYPE; HAPLOTYPES; HUMANS; MARKOV CHAINS; MODELS, STATISTICAL; PARENTS; PEDIGREE; SIBLINGS;

EID: 84867222152     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-13-85     Document Type: Article

References (25)

1. Marchini J, Howie B. Genotype imputation for genome-wide association studies. Nat Rev Genet 2010, 11(7):499-511. 10.1038/nrg2796, 20517342.
2. Lin S, Chakravarti A, Cutler D. Haplotype and missing data inference in nuclear families. Genome Res 2004, 14(8):1624. 10.1101/gr.2204604, 509272, 15256514.
3. Ding X, Zhang Q, Simianer H. Haplotype Reconstruction and Estimation of Haplotype Frequencies from Nuclear Families with One Parent Available and Varying Numbers of Children Using the Exact Likelihood. Human Heredity 2009, 67:174-175. 10.1159/000181155, 19077435.
4. Abecasis G, Cherny S, Cookson W, Cardon L. Merlin - rapid analysis of dense genetic maps using sparse gene flow trees. Nat genet 2001, 30:97-101.
5. Nettelblad C, Holmgren S, Crooks L, Carlborg O. cnF2freq: Efficient Determination of Genotype and Haplotype Probabilities in Outbred Populations Using Markov Models. BICoB '09: Proceedings of the 1st International Conference on Bioinformatics and Computational Biology 2009, 307-319. Springer-Verlag, Berlin, Heidelberg.
6. Nettelblad C. Haplotype inference based on Hidden Markov Models in the QTL-MAS 2010 multi-generational dataset. BMC Proceedings Volume 5 2010(Suppl 3), S10-S10. BioMed Central Ltd.
7. Rabiner LR. A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 1989, 77(2):257-286., http://dx.doi.org/10.1109/5.18626
8. Lander E, Green P, Abrahamson J, Barlow A, Daly M, Lincoln S, Newberg L, , et al. Newburg L MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1987, 1(2):174. 10.1016/0888-7543(87)90010-3, 3692487, Newburg L.
9. Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES. Parametric and nonparametric linkage analysis: a unified multipoint approach. Am j human genet 1996, 58(6):1347-1363., http://view.ncbi.nlm.nih.gov/pubmed/8651312
10. Therneau T, Atkinson E, Sinnwell J, Schaid D, McDonnell S. kinship2: Pedigree functions. R package version 1.3.3. [http://CRAN.R-project.org/package=kinship2], 2011.
11. Haldane JBS. The combination of linkage values, and the calculation of distance between the loci of linked factors. J Genet 1919, 8:299-309.
12. Broman KW, Wu H, Sen S, Churchill GA. R/qtl: QTL mapping in experimental crosses. Bioinformatics 2003, 19(7):889-890. 10.1093/bioinformatics/btg112, 12724300., http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/7/889
13. Howie BN, Donnelly P, Marchini J. A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies. PLoS Genet 2009, 5(6):e1000529. 10.1371/journal.pgen.1000529, 2689936, 19543373., http://dx.doi.org/10.1371
14. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 2010, 34(8):816-834. 10.1002/gepi.20533, 3175618, 21058334., http://dx.doi.org/10.1002/gepi.20533
15. Baum LE, Petrie T, Soules G, Weiss N. A Maximization Technique Occurring in the Statistical Analysis of Probabilistic Functions of Markov Chains. Ann Math Stat 1970, 41:164-171., http://dx.doi.org/10.2307/2239727
16. Dempster A, Laird N, Rubin D. Maximum likelihood from incomplete data via EM algorithm (with discussion). J R Statis Soc 1977, 39:1-38.
17. Seaton G, Hernandez J, Grunchec J, White I, Allen J, De Koning D, Wei W, Berry D, Haley C, Knott S. GridQTL: a grid portal for QTL mapping of compute intensive datasets. Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte 2006, 13-18. MG, Brasil.
18. Walters J, Balu V, Kompalli S, Chaudhary V. Evaluating the use of GPUs in liver image segmentation and HMMER database searches. Parallel & Distributed Processing, 2009. IPDPS 2009. IEEE International Symposium on IEEE 2009, 1-12. Rome, Italy,.
19. Elsen JM, Tesseydre S, Filangi O, Roy P, Demeure O. XVth QTLMAS: simulated dataset. BMC Proc 2012, 6(Suppl 2):S1. 10.1186/1753-6561-6-S2-S1, 3504924, 23173715., http://www.biomedcentral.com/1753-6561/6/S2/S1
20. Zhang K, Zhao H. A comparison of several methods for haplotype frequency estimation and haplotype reconstruction for tightly linked markers from general pedigrees. Genet epidemiol 2006, 30(5):423-437. 10.1002/gepi.20154, 16685719.
21. Li Y, Willer C, Ding J, Scheet P, Abecasis G. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet epidemiol 2010, 34(8):816-834. 10.1002/gepi.20533, 3175618, 21058334.
22. Howie B, Marchini J, Stephens M. Genotype Imputation with Thousands of Genomes. G3: Genes, Genomes, Genet 2011, 1(6):457-470.
23. Huang J, Ellinghaus D, Franke A, Howie B, Li Y. 1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data. Eur J Human Genet 2012, 20(7):801-805., http://dx.doi.org/10.1038/ejhg.2012.3
24. Boost C++ Libraries. , http://www.boost.org
25. The R Project for statistical computing. , http://www.r-project.org