A study of the efficiency of pooling in haplotype estimation

Bioinformatics

Volumn 26, Issue 20, 2010, Pages 2556-2563

  Kuk, Anthony Y C ^a   Xu, Jinfeng ^a   Yang, Yaning ^b  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENOTYPE; HAPLOTYPE; REGRESSION ANALYSIS; STATISTICAL MODEL;

ALGORITHMS; GENE FREQUENCY; GENOTYPE; HAPLOTYPES; LIKELIHOOD FUNCTIONS; LINKAGE DISEQUILIBRIUM; REGRESSION ANALYSIS;

EID: 77957768673     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq492     Document Type: Article

References (24)

1. Bansal,A. et al. (2002) Association testing by DNA pooling: An effective initial screen. Proc. Natl Acad. Sci. USA, 99, 16871-16874.
2. Barcellos,L.F. et al. (1997) Association mapping of disease loci, by use of a pooled DNA genomic screen. Am. J. Hum. Genet., 61, 734-747.
3. Barratt,B.J. et al. (2002) Identification of the sources of error in allele frequency estimations from pooled DNAindicates an optimal experimental design. Ann. Hum. Genet., 66, 393-405.
4. Fitzmaurice,G.M. et al. (1993) Regression models for discrete longitudinal responses (with discussion). Stat. Sci., 8, 284-309.
5. Homer,N. et al. (2008) Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genet., 4, e1000167.
6. Ito,T. et al. (2003) Estimation of haplotype frequencies, linkage-disequilibrium measures, and combination of haplotype copies in each pool by use of pooled DNA data. Am. J. Hum. Genet., 72, 384-398.
7. Jacobs,K.B. et al. (2009)Anew statistic and its power to infer membership in a genome- wide association study using genotype frequencies. Nat. Genet., 41, 1253-1257.
8. Kirk,K.M. and Cardon,L.R. (2002) The impact of genotyping error on haplotype reconstruction and frequency estimation. Eur. J. Hum. Genet., 10, 616-622.
9. Kirkpatrick,B. et al. (2007) HAPLOPOOL: Improving haplotype frequency estimation through DNA pools and phylogenetic modeling. Bioinformatics, 23, 3048-3055.
10. Kuk,A.Y.C. et al. (2009) Computationally feasible estimation of haplotype frequencies from pooled DNA with and without Hardy-Weinberg equilibrium. Bioinformatics, 25, 379-386.
11. Liang,K.Y. et al. (1992) Multivariate regression analysis for categorical data (with Discussion). J. R. Stat. Soc. B, 54, 3-40.
12. Liao,J.G. and Rosen,O. (2001) Fast and stable algorithms for computing and sampling from the noncentral hypergeometric distribution. Am. Stat., 55, 366-369.
13. McLachlan,G.J. and Krishnan,T. (1997) The EM Algorithm and Extensions. Wiley, New York.
14. Niu,T. (2004) Algorithms for inferring haplotypes. Genet. Epidemiol., 27, 334-347.
15. Norton,N. et al. (2004) DNA pooling as a tool for large-scale association studies in complex traits. Ann. Med., 36, 146-152.
16. Pearson,J.V. et al. (2007) Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies. Am. J. Hum. Genet., 80, 126-139.
17. Quade,S. et al. (2005) Estimating haplotype frequencies in pooled DNA samples when there is genotyping error. BMC Genet., 6, 1471-2156.
18. Sham,P. et al. (2002) DNA pooling: A tool for large-scale association studies. Nat. Rev. Genet., 3, 862-871.
19. Wang,S. et al. (2003) On the use of DNA pooling to estimate haplotype frequencies. Genet. Epidemiol., 24, 74-82.
20. Xu,J. et al. (2008) Testing linkage disequilibrium from pooled DNA: A contingency table perspective. Stat. Med., 27, 5801-5815.
21. Yang,Y. et al. (2003) Efficiency of single-nucleotide polymorphism haplotype estimation from pooled DNA. Proc. Natl Acad. Sci. USA, 100, 7225-7230.
22. Zhang,H. et al. (2008) PoooL: An efficient method for estimating haplotype frequencies from large DNA pools. Bioinformatics, 24, 1942-1948.
23. Zou,G. and Zhao,H. (2003) Haplotype frequency estimation in the presence of genotyping errors. Hum. Hered., 56, 131-138.
24. Zuo,Y. et al. (2006) Two-stage designs in case-control association analysis. Genetics, 173, 1747-1760.