Association mapping using pooled DNA

Methods in Molecular Biology

Volumn 376, Issue , 2007, Pages 161-175

  Yang, Hsin Chou ^a   Fann, Cathy S J ^a  

^a NONE

Author keywords

Allele frequency; DNA pooling; Haplotype; Linkage disequilibrium; Microarray; Preferential amplification; SWEFF

Indexed keywords

DNA;

ARTICLE; CHROMOSOME MAP; GENE FREQUENCY; GENOTYPE; HUMAN; METABOLISM; METHODOLOGY; NUCLEIC ACID AMPLIFICATION;

CHROMOSOME MAPPING; DNA; GENE FREQUENCY; GENOTYPE; HUMANS; NUCLEIC ACID AMPLIFICATION TECHNIQUES;

EID: 36549088042     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-389-7:161     Document Type: Article

References (67)

1. Arnheim, N., Strange, C., and Erlich, H. (1.985) Use of pooled DNA samples to detect linkage disequilibrium of polymorphic restriction fragments and human disease: Studies of the HLA class II loci. Proc. Natl. Acad. Sci. USA 82, 6970-6974.
2. Risch, N. and Teng, J. (1998) The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases I. DNA pooling. Genome Res. 8, 1273-1288.
3. Jawaid, A., Bader, J. S., Purcell, S., Cherny, S.S., and Sham, P. (2002) Optimal selection strategies for QTL mapping using pooled DNA samples. Eur. J. Hum. Genet. 10, 125-132.
4. Yang, H. C., Pan, C. C., Lin, C. Y., and Fann, C. S. J. (2006) PDA: pooled DNA analyzer. BMC Bioinformatics 7, 233.
5. Zeng, D. and Lin, D. Y (2005) Estimating haplotype-disease associations with pooled genotype data. Genet. Epidemiol. 28, 70-82.
6. Scott, D. A., Carmi, R., EIbedour, K., Yosefsberg, S., Stone, E. M., and Sheffield, V. C. (1.996) An autosomal recessive nonsyndromic-hearing-loss locus identified by DNA pooling using two inbred Bedouin kindreds. Am. J. Hum. Genet. 59, 385-391.
7. Darvasi, A. and Soller, M. (1994) Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus. Genetics 138, 1365-1373.
8. Visscher, P. M. and Le Hellard, S. (2003) Simple method to analyze SNP-based association studies using DNA pools. Genet. Epidemiol. 24, 291-296.
9. Yang, H. C., Pan, C. C., Lu, R. C. Y., and Fann, C. S. J. (2005) New adjustment factors and sample size calculation in a DNA-pooling experiment with preferential amplification. Genetics 169, 399-410.
10. Bader, J. S. and Sham, P. (2002) Family-based association tests for quantitative traits using pooled DNA. Eur. J. Hum. Genet. 10, 870-878.
11. Lee, W. C. (2005) A DNA pooling strategy for family-based association studies. Cancer Epidem. Biomar. 14, 958-962.
12. Zou, G. and Zhao, H. (2005) Family-based association tests for different family structures using pooled DNA. Ann. Hum, Genet, 69, 429-442.
13. Baro, J. Á., Carieos, C., Corral, N., López, T., and Cañón, J. (2001) Power analysis of QTL detection in half-sib families using selective DNA pooling. Genet. Sel. Evol. 33, 231-247.
14. Barratt, B. J., Payne, F., Ranee, . E., Nutland, S., Todd, J. A., and Clayton, D. G. (2002) Identification of the sources of error in allele frequency estimations from pooled DNA indicates an optimal experimental design. Ann. Hum. Genet. 66, 393-405.
15. Downes, K., Barratt, B. J., Akan, P., et al. (2004) SNP allele frequency estimation in DNA pools and variance components analysis. BioTech 36, 840-845.
16. Zou, G. and Zhao, II. (2004) The impacts of errors in individual genotyping and DNA pooling on association studies. Genet. Epidemiol. 26, 1-10.
17. Quade S. R. E., Elston, R. C., and Goddard, K. A. B. (2005) Estimating haplotype frequencies in pooled DNA samples when there is genotyping error. BMC Genet. 6, 25.
18. Barcellos, L. F., Klitz, W., Field, L. L., et al. (1997) Association mapping of disease loci, by use of a pooled DNA genomic screen. Am. J. Hum. Genet. 61, 734-747.
19. Bansal, A., van den Boom, D., Kammerer, S., et al. (2002) Association testing by DNA pooling: an effective initial screen. Proc. Natl. Acad. Sci. USA 99, 16,871-16,874.
20. Mohlke, K. L., Erdos, M. R., Scott, L. J., et al. (2002) High-throughput screening for evidence of association by using mass spectrometry genotyping on DNA pools. Proc. Natl. Acad. Sci. USA 99, 16,928-16,933.
21. Williams, N. M., Spurlock, G., Norton, N., et al. (2002) Mutation screening and LD mapping in the VCFS deleted region of chromosome 22q11 in schizophrenia using a novel DNA pooling approach. Mol. Psychiatr. 7, 1092-1100.
22. Herbon, N., Werner, M., Braig, C., et al. (2003) High-resolution SNP scan of chromosome 6p21 in pooled samples from patients with complex diseases. Genomics 81, 510-518.
23. Hinds, D. A., Seymour, A. B., Durham, L. K., et al. (2004) Application of pooled genotyping to scan candidate regions for association with HDL cholesterol levels. Hum. Genomics 1, 421-434.
24. Johnson, M. P. and Griffiths, L. R. (2005) A genetic analysis of serotonergic biosynthetic and metabolic enzymes in migraine using a DNA pooling approach. J. Hum. Genet. 50, 607-610.
25. Wolf ord, J. K., Blunt, D., Ballecer, C., and Prochazka, M. (2000) High-throughput SNP detection by using DNA pooling and denaturing high performance liquid chromatography (DHPLC). Hum. Genet. 107, 483-487.
26. Buetow, K. H., Edmonson, M., MacDonald, R., et al. (2001) High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc. Natl. Acad. Sci. USA 98, 581-584.
27. Shubitowski, D. M., Venta, P. J., Douglass, C. L., Zhou, R. X., and Ewart, S. L. (2001) Polymorphism identification within 50 equine gene-specific sequence tagged sites. Anim. Genet. 32, 78-88.
28. Pan, X. and Weissman, S. M. (2002) An approach for global scanning of single nucleotide variations. Proc. Nail. Acad. Sci. USA 99, 9346-9351.
29. Nelson, M. R., Mamellos, G., Kammerer, S., et al. (2004) Large-scale validation of single nucleotide polymorphisms in gene regions. Genome Res. 14, 1664-1668.
30. Yang, H. C., Lin, C. H., Hung, S. L, and Fann, C. S. J. (2006) Polymorphism validation using DNA pools prior to conducting large-scale genetic studies. Ann. Hum. Genet. 70, 350-359.
31. Dubreuil, P., Rebourg, C., Merlino, M., and Charcosset, A. (1999) Evaluation of a DNA pooled-sampling strategy for estimating the RFLP diversity of maize populations. Plant Mol. Biol. Rep. 17, 123-138.
32. Hillel, J., Groenen, M. A. M., Tixier-Boichard, M., et al. (2003) Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. Genet. Sel. Evol. 35,'533-557.
33. Gonda, M. G., Arias, J. A., Shook, G. E., and Kirkatrick, B. W. (2004) Identification of an ovulation rate QTL in cattle on BAT 14 using selective DNA pooling and interval mapping. Anim. Genet. 35, 298-304.
34. Kraft, T., Fridlimd, B., Hjerdin, A., Sail, T., Tuvesson, S., and Hallden, C. (1997) Estimating genetic variation in cultivated and wild beets using pools of individuals. Genome 40, 527-533.
35. Shaw, S. H., Carrasquillo, M. M., Kashuk, C., Puffenberger, E. G., and Chakravarti, A. (1998) Allele frequency distributions in pooled DNA samples: applications to mapping complex disease genes. Genome Res. 8, 111-123.
36. Schnack, H. G., Bakker, S. C., van't Slot, R., et al. (2004) Accurate determination of microsatellite allele frequencies in pooled DNA samples. Eur. J. Hum. Genet. 12, 925-934.
37. Breen, G. Harold, D., Ralston, S., Shaw, D., and St. Clair, D. (2000) Determining SNP allele frequencies in DNA pools. Biotechniques 28, 464-466.
38. Genner, S., Holland, M. J., and Higuchi, R. (2000) High-throughput SNP allelefrequency determination in pooled DNA samples by kinetic PCR. Genome Res. 10, 258-266.
39. Sasaki, T., Tahira, T., Suzuki, A., et al. (2001) Precise estimation of allele frequencies of single-nucleotide polymorphisms by a quantitative SSCP analysis of pooled DNA. Am. J. Hum. Genet. 68, 214-218.
40. Norton, N., Williams, N. M., Williams, H. J., et al. (2002) Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools. Hum. Genet. 110, 471-478.
41. Werner, M., Sych, M., IIerbon, N., Illig, T., König, I. R., and Wjst, M. (2002) Large-scale determination of SNP allele frequencies in DNA pools using MALDI-TOF mass spectrometry. Hum. Mutat. 20, 57-64.
42. Lavebratt, C., Sengul, S., Jansson, M., and Schalling, M. (2004) Pyrosequencing™-based SNP allele frequency estimation in DNA pools. Hum. Mutât. 23, 92-97.
43. Pfeiffer, R. M., Rutter, J. L., Gail, M. H., Struewing, .T., and Gastwirth, J. L. (2002) Efficiency of DNA pooling to estimate joint allele frequencies and measure linkage disequilibrium. Genet. Epidemiol. 11, 94-102.
44. Ito, T., Chiku, S., Inoue, E., et al. (2003) Estimation of haplotype frequencies, link-age disequilibrium measures, and combination of haplotype copies in each pool by use of pooled DNA data. Am. J. Hum. Genet. 11, 384-398.
45. Wang, S., Kidd, K. K., and Zhao, H. (2003) On the use of DNA pooling to estimate haplotype frequency. Genet. Epidemiol. 24, 74-82.
46. Yang, Y., Zhang, J., Hoh, J., et al. (2003) Efficiency of single-nucleotide polymorphism haplotype estimation from pooled DNA. Proc. Natl. Acad. Sci. USA 100, 7225-7230.
47. Le Hellard, S., Ballereau, S. J., Visscher, P. M., et al. (2002) SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Res. 30, e74.
48. Shifman, S., Pisantć-Shalom, A., Yakir, B., and Darvasi, A. (2002) Quantitative technologies for allele frequency estimation of SNPs in DNA pools. Mol. Cell. Probe. 16, 429-434.
49. Sham, P., Bader, J. S., Craig, I., O'Donovan, M., and Owen, M. (2002) DNA pooling: A tool for large-scale association studies. Nat. Rev. Genet. 3, 862-871.
50. Uhl, G. R., Liu, Q. R., Walther, D., Hess, J., and Naiman, D. (2001) Polysubstance abuse-vulnerability genes: genome scans for association, using 1,004 subjects and 1,494 single-nucleotide polymorphisms. Am. J. Hum, Genet. 69, 1290-1300.
51. Lindroos, K., Sigurdsson, S., Johansson, K., Rönnblom, L., and Syvänen, A. C. (2002) Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system. Nucleic Acids Res. 30, e70.
52. Ye, B. C., Zuo, P., Yi, B., and Li, S. (2004) Estimation of relative allele frequencies of single-nucleotide polymorphisms in different populations by microarray hybridization of pooled DNA. Anal. Biochem. 333, 72-78.
53. Hoogendoorn, B., Norton, N., Kirov, G., et al. (2000) Cheap, accurate and rapid allele frequency estimation of single nucleotide polymorphisms by primer extension and DHPLC in DNA pools. Hum. Genet. 107, 488-493.
54. Moskvina, V., Norton, N., Williams, N., Holmans, P., Owen, M., and O'Donovan, M. (2005) Streamlined analysis of pooled genotype data in SNP-based association studies. Genet. Epidemiol, 28, 273-282.
55. Simpson, C. L., Knight, J., Butcher, L. M., et al. (2005) A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays. Nucleic Acids Res. 33, e25.
56. Yang, H. C., Liang, Y. J., Huang, M. C., et al. (2005) A genome-wide study of preferential amplification/hybridization in microarray-based pooled DNA experiments. Nucleic Acids Res. DOI: 10, 1093/nar/gkl 4c.
57. Purcell, S., Cherny, S. S., and Sham, P. C. (2003) Genetic power calculator: design of linkage and association genetic mapping studies of complex traits. Bioinformatics 19, 149-150.
58. Seaman, S. R. and Müller-Myhsok, B. (2005) Rapid simulation of p values for product methods and multiple-testing adjustment in association studies. Am. J. Hum. Genet. 76, 399-408.
59. Salem, R. M., Wessel, J., and Schork, N. J. (2005) A comprehensive literature review of haplotyping software and methods for use with unrelated individuals. Hum, Genomics 2, 39-66.
60. Hoh, J., Matsuda, F., Peng, X., Markovic, D., Lathrop, M. G., and Ott, J. (2003) SNP haplotyping tagging from DNA pools of two individuals. BMC Bioinformatics 4, 14.
61. Matsuzaki, H., Dong, S., Loi, H., et al. (2004) Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat. Methods 1, 109-111.
62. Butcher, L. M., Meaburn, E., Liu, L., et al. (2004) Genotyping pooled DNA on microarrays: a systematic genome screen of thousands of SNPs in large samples to detect QTLs for complex traits. Behav. Genet. 34, 549-555.
63. Meabuni, E., Butcher, L. M., Liu, L., et al. (2005) Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs. BMC Genomics 6, 52.
64. Liu, Q. R., Drgon, T., Walther, D., et al. (2005) Pooled association genome scanning: validation and use to identify addiction vulnerability loci in two samples. Proc. Natl. Acad. Sci. USA 102, 11,864-11,869.
65. Butcher, L. M., Meabuni, E., Knight, J., et al. (2005) SNPs, microaiTays and pooled DNA: identification of four loci associated with mild mental impairment in a sample of 6000 children. Hum. Mol. Genet. 14, 1315-1325.
66. Craig, I., Meaburn, E., Butcher, L., Hill, L., and Plomin, R. (2005) Single-nucleotide polymorphism genotyping in DNA pools. In: Pharmacogenomics: Methods and Protocols, (Innocenti, F., ed.), Humana, Totowa, NJ, pp. 147-164.
67. Liu, W. M., Di, X., Yang, G., et al. (2003) Algorithms for large-scale genotyping microarrays. Bioinformatics 19, 2397-2403.