Estimating population haplotype frequencies from pooled DNA samples using PHASE algorithm

Genetics Research

Volumn 90, Issue 6, 2008, Pages 509-524

  Pirinen, Matti ^a   Kulathinal, Sangita ^a,b   Gasbarra, Dario ^a   Sillanpää, Mikko J ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b Indic Society for Education and Development India   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ACCURACY; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; GENE MUTATION; GENETIC ALGORITHM; GENETIC RECOMBINATION; GENOTYPE; HAPLOTYPE; HAPLOTYPE MAP; INTERMETHOD COMPARISON; MAXIMUM LIKELIHOOD METHOD; POPULATION GENETICS; RELIABILITY; SIMULATION; ALGORITHM; ALLELE; BIOLOGICAL MODEL; COMPARATIVE STUDY; DIPLOIDY; EVALUATION; GENE FREQUENCY; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MONTE CARLO METHOD; NUCLEIC ACID DATABASE; PROBABILITY; STATISTICAL MODEL;

ALGORITHMS; ALLELES; DATABASES, NUCLEIC ACID; DIPLOIDY; DNA; GENE FREQUENCY; GENETICS, POPULATION; GENOTYPE; HAPLOTYPES; HUMANS; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD;

EID: 63449137622     PISSN: 00166723     EISSN: 14695073     Source Type: Journal    
DOI: 10.1017/S0016672308009877     Document Type: Article

References (42)

1. Abecasis, G. R., Cherny, S. S., Cookson, W. O. & Cardon, L. R. (2002). Merlin - rapid analysis of dense genetic maps using sparse gene flow trees. Nature Genetics 30, 97-101.
2. Albers, C. A., Heskes, T. & Kappen, H. J. (2007). Haplotype inference in general pedigrees using the cluster variation method. Genetics 177, 1101-1116.
3. Butcher, L. M., Meaburn, E., Liu, L., Fernandez, C., Hill, L., Al-Chalabi, A., Plomin, R., Schalkwyk, L. & Craig, I. W. (2004). Genotyping pooled DNA on microarrays: A systematic genome screen of thousands of SNPs in large samples to detect QTLs for complex traits. Behavior Genetics 34, 549-555.
4. Clark, A. G. (1990). Inference of haplotypes from PCR-amplified samples of diploid populations. Molecular Biology and Evolution 7, 111-122.
5. Douglas, J. A., Boehnke, M., Gillanders, E., Trent, J. M. & Gruber, S. B. (2001). Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibirium studies. Nature Genetics 28, 361-364.
6. Fishelson, M., Dovgolevsky, N. & Geiger, D. (2005). Maximum likelihood haplotyping for general pedigrees. Human Heredity 59, 41-60.
7. Gasbarra, D. & Sillanpää, M. J. (2006). Constructing parental linkage phase and genetic map over distances <1 cM using pooled haploid DNA. Genetics 172, 1325-1335.
8. Gasbarra, D., Sillanpää M. J. & Arjas, E. (2005). Backward simulation of ancestors of sampled individuals. Theoretical Population Biology 67, 75-83.
9. International HapMap Consortium (2003). The international HapMap project. Nature 426, 789-796.
10. International HapMap Consortium (2005). A haplotype map of the human genome. Nature 437, 1299-1320.
11. International HapMap Consortium (2007). A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861.
12. Ito, T., Chiku, S., Inoue, E., Tomita, M., Morisaki, T., Morisaki, H. & Kamatani, N. (2003). Estimation of haplotype frequencies, linkage-disequilibrium measures, and combination of haplotype copies in each pool by use of pooled DNA data. American Journal of Human Genetics 72, 384-398.
13. Johnson, T. (2005). Multipoint linkage disequilibrium mapping using multilocus allele frequency data. Annals of Human Genetics 69 474-497.
14. Johnson, T. (2007). Bayesian method for gene detection and mapping using case and control design and DNA pooling. Biostatistics 8, 546-565.
15. Kirkpatrick, B., Armendariz, C. S., Karp, R. M. & Halperin, E. (2007). HaploPool: Improving haplotype frequency estimation through DNA pools and phylogenetic modeling. Bioinformatics 23, 3048-3055.
16. Lee, W. C. (2005). A DNA pooling strategy for family-based association studies. Cancer Epidemiology Biomarkers and Prevention 14, 958-962.
17. Li, N. & Stephens, M. (2003). Modeling linkage disequilibrium, and identifying recombination hotspots using SNP data. Genetics 165 2213-2233.
18. Long, J. C., Williams, R. C. & Urbanek, M. (1995). An E-M algorithm and testing strategy for multiple-locus haplotypes. American Journal of Human Genetics 56, 799-810.
19. Marchini, J., Cutler, D., Patterson, N., Stephens, M., Eskin, E., Halperin, E., Lin, S., Qin, Z. S., Munro, H. M., Abecasis, G. R., Donnelly, P. & International HapMap Consortium (2006). A comparison of phasing algorithms for trios and unrelated individuals. American Journal of Human Genetics 78, 437-450.
20. Niu, T. (2004). Algorithms for inferring haplotypes. Genetic Epidemiology 27, 334-347.
21. Niu, T., Qin, Z. S., Xu, X. & Liu, J. S. (2002). Bayesian haplotype inference for multiple linked single-nucleotide polymorphism. American Journal of Human Genetics 70, 157-169.
22. Norton, N., Williams, N. M., Williams, H. J., Spurlock, G., Kirov, G., Morris, D. W., Hoogendoorn, B., Owen, M. J. & O'Donovan, M. C. (2002). Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools. Human Genetics 110, 471-478.
23. Pfeiffer, R. M., Rutter, J. L., Gail, M. H., Struewing, J. & Gastwirth, J. L. (2002). Efficiency of DNA pooling to estimate joint allele frequencies and measure linkage disequilibrium. Genetic Epidemiology 22, 94-102.
24. Qian, D. & Beckmann, L. (2002). Minimum-recombinant haplotyping in pedigrees. American Journal of Human Genetics 70, 1434-1445.
25. Quade, S. R. E., Elston, R. C. & Goddard, K. A. B. (2005). Estimating haplotype frequencies in pooled DNA samples when there is genotyping error. BMC Genetics 6, 25.
26. Risch, N. & Teng, J. (1998). The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human disease I. DNA pooling. Genome Research 8, 1273-1288.
27. Robert, C. P. & Casella, G. (1999). Monte Carlo Statistical Methods New York: Springer.
28. Sham, P., Bader, J. S., Craig, I., O'Donovan, M. & Owen, M. (2002). DNA pooling: A tool for large-scale association studies. Nature Reviews Genetics 3, 862-871.
29. Sobel, E. & Lange, K. (1996). Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker-sharing statistics. American Journal of Human Genetics 58, 1323-1337.
30. 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.
31. 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.
32. Stephens, M., Smith, N. J. & Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics 68, 978-989.
33. Tamiya, G., Shinya, M., Imanishi, T., Ikuta, T., Makino, S., Okamoto, K., Furugaki, K., Matsumoto, T., Mano, S., Ando, S., Nozaki, Y., Yukawa, W., Nakashige, R., Yamaguchi, D., Ishibashi, H., Yonekura, M., Nakami, Y., Takayama, S., Endo, T., Saruwatari, T., Yagura, M., Yoshikawa, Y., Fujimoto, K., Oka, A., Chiku, S., Linsen, S. E., Giphart, M. J., Kulski, J. K., Fukazawa, T., Hashimoto, H., Kimura, M., Hoshina, Y., Suzuki, Y., Hotta, T., Mochida, J., Minezaki, T., Komai, K., Shiozawa, S., Taniguchi, A., Yamanaka, H., Kamatani, N., Gojobori, T., Bahram, S. & Inoko, H. (2005). Whole genome association study of rheumatoid arthritis using 27 039 microsatellites. Human Molecular Genetics 14, 2305-2321.
34. Uimari, P. & Sillanpää, M. J. (2001). Bayesian oligogenic analysis of quantitative and qualitative traits in general pedigrees. Genetic Epidemiology 21, 224-242.
35. Wang, J., Koehler, K. J. & Dekkers, J. C. M. (2007). Interval mapping of quantitative trait loci with selective DNA pooling data. Genetics Selection Evolution 39, 685-709.
36. Wang, S., Kidd, K. & Zhao, H. (2003). On the use of DNA pooling to estimate haplotype frequencies. Genetic Epidemiology 24, 74-82.
37. Wijsman, E. (1987). A deductive method of haplotype analysis in pedigrees. American Journal of Human Genetics 41, 356-373.
38. Yang, H. C., Pan, C. C., Lin, C. Y. & Fann, C. S. J. (2006). PDA: Pooled DNA analyzer. BMC Bioinformatics 7, 233.
39. Yang, Y., Zhang, J., Hoh, J., Matsuda, F., Xu, P., Lathrop, M. & Ott, J. (2003). Efficiency of single-nucleotide polymorphism haplotype estimation from pooled DNA. Proceedings of the National Academy of Sciences, USA 100, 7225-7230.
40. Zhang, K., Zhu, J., Shendure, J., Porreca, G. J., Aach, J. D., Mitra, R. D. & Church, G. M. (2006a). Long-range polony haplotyping of individual human chromosome molecules. Nature Genetics 38, 382-387.
41. Zhang, Y., Niu, T. & Liu, J. S. (2006b). A coalescence-guided hierarchical Bayesian method for haplotype inference. American Journal of Human Genetics 79, 313-322.
42. Zou, G. H. & Zhao, H. Y. (2005). Family-based association tests for different family structures using pooled DNA. Annals of Human Genetics 69, 429-442.