Identification of linked regions using high-density SNP genotype data in linkage analysis

Bioinformatics

Volumn 24, Issue 1, 2008, Pages 86-93

  Lin, Guohui ^a   Wang, Zhanyong ^b   Wang, Lusheng ^b   Lau, Yu Lung ^c   Yang, Wanling ^c  

^a UNIVERSITY OF ALBERTA   (Canada)

^b CITY UNIVERSITY OF HONG KONG   (Hong Kong)

^c UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; COMPUTER PROGRAM; DIAGNOSTIC ERROR; GENE STRUCTURE; GENETIC ALGORITHM; GENETIC ANALYSIS; GENOTYPE; HUMAN; INHERITANCE; LINKAGE ANALYSIS; MATHEMATICAL MODEL; NUCLEAR FAMILY; PENETRANCE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; DATABASES, GENETIC; DNA MUTATIONAL ANALYSIS; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENETIC SCREENING; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM;

EID: 37549056571     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm552     Document Type: Article

References (22)

1. Abecasis,G. et al. (2002) Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat. Genet., 30, 97-101.
2. Broman,K.W. and Weber,J. (2000) Characterization of human crossover interference. Am. J. Hum. Genet., 66, 1911-1926.
3. Chung,R. and Gusfield,D. (2003) Perfect phylogeny haplotyper: Haplotype inferral using a tree model. Bioinformatics, 19, 780-781.
4. Doi,K. et al. (2003) Minimum recombinant haplotype configuration on tree pedigrees. In Proceedings of the WABI'03. pp. 339-353.
5. Elston,R.C. and Stewart,J. (1971) A general model for the analysis of pedigree data. Hum. Hered., 21, 523-542.
6. Gudbjartsson,D.F. et al. (2000) Allegro, a new computer program for multipoint linkage analysis. Nat. Genet., 25, 12-13.
7. Gusfield,D. (2001) Inference of haplotypes from samples of diploid populations: Complexity and algorithms. J. Comput. Biol., 8, 305-323.
8. Halperin,E. and Eskin,E. (2004) Haplotype reconstruction from genotype data using imperfect phylogeny. Bioinformatics, 20, 1842-1849.
9. Hodge,S. et al. (1999) Loss of information due to ambiguous haplotyping of snps. Nat. Genet., 21, 360-361.
10. Kruglyak,L. et al. (1995) Parametric and nonparametric linkage analysis: A unified multipoint approach. Am. J. Hum. Genet., 58 1347-1363.
11. Lander.E. and Green,P. (1987) Construction of multilocus genetic linkage maps in human. Proc. Natl Acad. Sci. USA, 84, 2363-2367.
12. Lathrop,G. M. et al. (1984) Strategies for multilocus linkage analysis in humans. Proc. Natl Acad. Sci. USA, 81, 3443-3446.
13. Leykin,I. et al. (2005) Comparative linkage analysis and visualization of high-density oligonucleotide snp array data. BMC Genet., 6, 7.
14. Li,J. and Jiang,T. (2003) Efficient inference of haplotypes from genotypes on a pedigree. J. Bioinform. Comput. Bio., 1, 41-69.
15. Ott,J. (1999) Aspects or statistical inference. In Analysis of Human Genetic Linkage. 3rd edn. Johns Hopkins University Press, Baltimore.
16. Qian,D. and Beckmann,L. (2002) Minimum recombinant haplotyping in pedigrees. Am. J. Hum. Genet., 70, 1434-1445.
17. Sellick,G. et al. (2004) Genomewide linkage searches for mendelian disease loci can be efficiently conducted using high-density snp genotyping arrays. Nucleic Acids Res., 32, e164.
18. Stephens,M. and Scheet,P. (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am. J. Hum. Genet., 76, 449-462.
19. Wijsman,E. M. (1987) A deductive method of haplotype analysis in pedigrees. Am. J. Hum. Genet., 41, 356-373.
20. Wirtenberger,M. et al. (2005) SNP microarray analysis for genome-wide detection of crossover regions. Hum. Genet., 117 389-397.
21. Zhang,K. et al. (2005) Haplore: A program for haplotype reconstruction in general pedigrees without recombination. Bioinformatics, 21, 90-103.
22. Zhao,H. et al. (1995) Statistical analysis of crossover interference using the chi-square model. Genetics, 139, 1045-1056.