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Single-Nucleotide Polymorphism Genotyping in DNA Pools

  • Protocol
Pharmacogenomics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 311))

Abstract

To undertake partial, or complete, genome screens by association-based methodology for quantitative trait loci, multiple individuals have to be screened for large numbers of genetic markers. Consequently, much recent interest has focused on methods enabling accurate allele quantification in pooled deoxyribonucleic acid (DNA) samples. Microsatellites were the favored markers in initial studies, but the extraordinary wealth of data concerning single-nucleotide polymorphisms (SNPs) has turned attention to the quantification of SNP alleles in pools. All such approaches require accurate estimation of DNA concentrations, followed by the preparation of replicate pools, their validation, and application of procedures for determining allele frequencies. This chapter describes the important steps in preparing pools and surveys a variety of techniques that have been proposed for SNP detection. Finally, we describe the application of a generic approach using pooled DNA for detection of allele frequency differences between case and control populations based on primer extension protocols and outline a strategy for estimating SNP allele frequencies employing microarrays.

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References

  1. Plomin, R., DeFries, J., Craig, I., and McGuffin, P. (2003) Behavioral genetics, in Behavioral Genetics in the Postgenomic Era (Plomin, R., DeFries, J., Craig, I. and McGuffin, P., eds.), APA Books, Washington, pp. 3–15.

    Chapter  Google Scholar 

  2. Risch, N. and Merikangas, K. (1996) The future of genetic studies of complex human diseases. Science 273, 1516–1517.

    Article  PubMed  CAS  Google Scholar 

  3. Kruglyak, L. (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet. 22, 139–144.

    Article  PubMed  CAS  Google Scholar 

  4. Tabor, H. K., Risch, N. J. and Myers, R. M. (2002) Candidate gene approaches for studying complex traits: practical considerations. Nat. Rev. Genet. 3, 1–7.

    Article  Google Scholar 

  5. 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.

    Article  PubMed  CAS  Google Scholar 

  6. Craig, I. W., and McClay, J. (2002) The role of molecular genetics in the postgenomic era, in Behavioral Genetics in the Post-genomics Era (Plomin, R., DeFries, J., Craig, I. and McGuffin, P., eds.), APA Books, Washington, pp. 19–40.

    Google Scholar 

  7. Yang, Y., Zhang, J., Hoh, J., Matsuda, F., Xu, P., Lathrop, M., and Ott, J. (2003) Efficiency of single-nucleotide polymorphism haplotype estimation from pooled DNA. Proc. Natl. Acad. Sci. USA 100, 7225–7230.

    Article  PubMed  CAS  Google Scholar 

  8. Norton, N., Williams, N. M., O’Donovan, M. C., and Owen, M. J. (2004) DNA pooling as a tool for large scale association studies in complex traits. Ann. Med. 36, 146–152.

    Article  PubMed  CAS  Google Scholar 

  9. 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, 74.

    Article  Google Scholar 

  10. Breen, G., Harold, D., Ralston, S., Shaw, D. and St. Clair, D. (2000) Determining SNP allele frequencies in DNA pools. Biotechniques 28, 464–470.

    PubMed  CAS  Google Scholar 

  11. Syvanen, A. C. (2001) Accessing genetic variation; genotyping single nucleotide polymorphisms. Nat. Rev. Genet. 2, 930–942.

    Article  PubMed  CAS  Google Scholar 

  12. Curran, S., Hill, L., O’Grady, G., et al. (2002) Validation of single nucleotide polymorphism (SNP) quantification in pooled DNA samples using SNaPIT™ technology, a glycosylase-mediated polymorphism detection method. Biotechniques 22, 253–262.

    CAS  Google Scholar 

  13. Butcher, L. M., Meaburn, E., Dale, P. S., Schalkwyk, L., Craig, I. W., and Plomin, R. (2004) Association analysis of mild mental impairment using DNA pooling to screen 432 brain expressed single nucleotide polymorphisms. Mol. Psychiatry 10, 384–392.

    Article  Google Scholar 

  14. McClay, J., Sugden, K., Koch, H. G., Higuchi, S., and Craig, I.W. (2002) High-throughput single-nucleotide polymorphism genotyping by fluorescent competitive allele-specific polymerase chain reaction (SNiPTag). Anal. Biochem. 301, 200–206.

    Article  PubMed  CAS  Google Scholar 

  15. Kirov, G., Stephens, M., Williams, N., O’Donovan, M., and Owen, M. (2000) Automated genotyping of single-nucleotide polymorphisms by extension of fluorescently labelled primers: analysis of individual and pooled DNA samples. Balkan, J. Med. Genet. 3, 23–28.

    CAS  Google Scholar 

  16. Zhou, G-H., Kamahori, M., Okano, K., Chuan, G., Harada, K., and Kambara, H. (2001) Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER). Nucleic. Acids. Res. 29, E93.

    Article  PubMed  CAS  Google Scholar 

  17. Gruber, J. D., Colligan, P. B., and Wolford, J. K. (2002) Estimation of single nucleotide polymorphism allele frequency in DNA pools by using pyrosequencing. Hum. Genet. 110, 395–401.

    Article  PubMed  CAS  Google Scholar 

  18. Wasson, J., Skolnick, G., Love-Gregory, L., and Permutt, M. A. (2002) Assessing allele frequencies of single nucleotide polymorphisms in DNA pools by pyrosequencing technology. Biotechniques 32, 1144–1146.

    PubMed  CAS  Google Scholar 

  19. Nordfors, L., Jansson, M., Sandberg, G., et al. (2000) Large-scale genotyping of single nucleotide polymorphisms by Pyrosequencing™ and validation against the 5′ nuclease (Taqman® assay. Hum. Mutat. 19, 395–401.

    Article  Google Scholar 

  20. Lavebratt, C., Sengul, S., Jansson, M., and Schalling, M. (2004) Pyrosequencingbased SNP allele frequency estimation in DNA pools. Hum. Mutat. 23, 92–97.

    Article  PubMed  CAS  Google Scholar 

  21. Germer, S., Holland, M. J., and Higuchi, R. (2000) High-throughput SNP allele frequency determination in pooled DNA samples by kinetic PCR. Genome. Res. 10, 258–266.

    Article  PubMed  CAS  Google Scholar 

  22. Chen, J., Germer, S., Higuchi, R., Berkowitz, G., Godbold, J., and Wetmur, J.G. (2002) Kinetic polymerase chain reaction on pooled DNA: a high-throughput, high-efficiency alternative in genetic epidemiological studies. Cancer Epidemiol. Biomarkers. Prev. 11, 131–136.

    PubMed  CAS  Google Scholar 

  23. Fan, J. B., Chen, X., Halushka, M. K., et al. (2000) Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome. Res. 10, 853–860.

    Article  PubMed  CAS  Google Scholar 

  24. Uhl, G., Liu, Q-R., Walther, W., 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.

    Article  PubMed  CAS  Google Scholar 

  25. Blazej, R. G., Paegel, B. M., and Mathies, R. A. (2003). Polymorphism ratio sequencing: a new approach for single nucleotide polymorphism discovery and genotyping. Genome. Res. 13, 287–293.

    Article  PubMed  CAS  Google Scholar 

  26. Wolford, 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.

    Article  PubMed  CAS  Google Scholar 

  27. Hoogendoorn, B., Norton, N., Kirov, G., et al. (2000b) Cheap, accurate and rapid allele frequency estimation of single nucleotide polymorphisms by primer extension and DHPLC in DNA pools. Hum. Genet. 107, 488–493.

    Article  PubMed  CAS  Google Scholar 

  28. Xiao, M., Latif, S. M., and Kwok, P. Y. (2003) Kinetic FP-TDI assay for SNP allele frequency determination. Biotechniques. 34, 190–197.

    PubMed  CAS  Google Scholar 

  29. Bansal, A., van den Boom, D., Kammerer, S., et al. (2002). Association testing by DNA poling: an effective initial screen. Proc. Natl. Acad. Sci. USA 99, 16,871–16,874.

    Article  PubMed  CAS  Google Scholar 

  30. Werner, M., Sych, M., Herbon, N., Illig, T., König, I. R., and Wjst, M. (2002) Large-scale determination of SNP allele frequencies in DNA pools using MALDI-TOF mass spectroscopy. Hum. Mutat. 20, 57–64.

    Article  PubMed  CAS  Google Scholar 

  31. Ross, P., Hall, L. and Haff, L. A. (2000) Quantitative approach to single-nucleotide polymorphism analysis using MALDI-TOF mass spectrometry. Biotechniques. 29, 620–626, 628–629.

    PubMed  CAS  Google Scholar 

  32. Zhang, S., Van Pelt, C. K., Huang, X., and Schultz, G. A. (2002) Detection of single nucleotide polymorphisms using electrospray ionization mass spectrometry: validation of a one-well assay and quantitative pooling studies. J. Mass. Spectrom. 37, 1039–1050.

    Article  PubMed  CAS  Google Scholar 

  33. 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.

    Article  PubMed  CAS  Google Scholar 

  34. 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. Beh. Genet. 34, 549–555.

    Article  Google Scholar 

  35. Freeman, B., Smith, N., Curtis, C., Huckett, L., Mill, J., and Craig, I. W. (2003) DNA from buccal swabs recruited by mail: evaluation of storage effects on long-term stability and suitability for multiplex polymerase chain reaction genotyping. Beh. Genet. 33, 67–72.

    Article  CAS  Google Scholar 

  36. Hill, L., Craig, I. W., Asherson, P., et al. (1999). DNA pooling and dense marker maps: a systematic search for genes for cognitive ability. Neuroreport. 10, 843–848.

    Article  PubMed  CAS  Google Scholar 

  37. Simpson, C., Knight, J., Butcher, L., et al. (2005) Accurate allele frequency estimation from pooled DNA genotyped on microarrays. N.A.R. In press.

    Google Scholar 

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Authors and Affiliations

  1. SGDP Centre, Institute of Psychiatry, London, UK

    Ian Craig, Emma Meaburn, Lee Butcher, Linzy Hill & Robert Plomin

Authors
  1. Ian Craig
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  2. Emma Meaburn
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  3. Lee Butcher
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  4. Linzy Hill
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  5. Robert Plomin
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Editor information

Editors and Affiliations

  1. Committee on Clinical Pharmacology and Pharmacogenomics, Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL

    Federico Innocenti MD, PhD

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© 2005 Humana Press Inc., Totowa, NJ

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Craig, I., Meaburn, E., Butcher, L., Hill, L., Plomin, R. (2005). Single-Nucleotide Polymorphism Genotyping in DNA Pools. In: Innocenti, F. (eds) Pharmacogenomics. Methods in Molecular Biology™, vol 311. Humana Press. https://doi.org/10.1385/1-59259-957-5:147

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  • DOI: https://doi.org/10.1385/1-59259-957-5:147

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-440-1

  • Online ISBN: 978-1-59259-957-8

  • eBook Packages: Springer Protocols

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