Abstract
Single nucleotide polymorphisms (SNPs) are ideal markers for identifying genes associated with complex diseases for two main reasons. Firstly, SNPs are densely located on the human genome at about one SNP per approximately 500–1,000 base pairs. Secondly, a large number of commercial platforms are available for semiautomated or fully automated SNP genotyping. These SNP genotyping platforms serve different purposes since they differ in SNP selection, reaction chemistry, signal detection, throughput, cost, and assay flexibility. This chapter aims to give an overview of some of these platforms by explaining the technologies behind each platform and identifying the best application scenarios for each platform through cross-comparison. The readers may delve into more technical details in the following chapters.
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References
Glazier, A. M., Nadeau, J. H. and Aitman, T. J. (2002) Finding genes that underlie complex traits. Science 298, 2345–2349.
Becker, K. G., Barnes, K. C., Bright, T. J. and Wang, S. A. (2004) The genetic association database. Nat. Genet. 36, 431–432.
Ding, C. (2007) 'Other' applications of single nucleotide polymorphisms. Trends Biotechnol. 25, 279–283.
Hardenbol, P., Baner, J., Jain, M., Nilsson, M., Namsaraev, E. A., Karlin-Neumann, G. A., Fakhrai-Rad, H., Ronaghi, M., Willis, T. D., Landegren, U. and Davis, R. W. (2003) Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol. 21, 673–678.
Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y., Scherer, S. W. and Lee, C. (2004) Detection of large-scale variation in the human genome. Nat. Genet. 36, 949–951.
Jongmans, M. C., Admiraal, R. J., van der Donk, K. P., Vissers, L. E., Baas, A. F., Kapusta, L., van Hagen, J. M., Donnai, D., de Ravel, T. J., Veltman, J. A., Geurts van Kessel, A., De Vries, B. B., Brunner, H. G., Hoefsloot, L. H. and van Ravenswaaij, C. M. (2006) CHARGE syndrome: the phenotypic spectrum of mutations in the CHD7 gene. J. Med. Genet. 43, 306–314.
Singleton, A. B., Farrer, M., Johnson, J., Singleton, A., Hague, S., Kachergus, J., Hulihan, M., Peuralinna, T., Dutra, A., Nussbaum, R., Lincoln, S., Crawley, A., Hanson, M., Maraganore, D., Adler, C., Cookson, M. R., Muenter, M., Baptista, M., Miller, D., Blancato, J., Hardy, J. and Gwinn-Hardy, K. (2003) alpha-Synuclein locus triplication causes Parkinson's disease. Science 302, 841.
Redon, R., Ishikawa, S., Fitch, K. R., Feuk, L., Perry, G. H., Andrews, T. D., Fiegler, H., Shapero, M. H., Carson, A. R., Chen, W., Cho, E. K., Dallaire, S., Freeman, J. L., Gonzalez, J. R., Gratacos, M., Huang, J., Kalaitzopoulos, D., Komura, D., MacDonald, J. R., Marshall, C. R., Mei, R., Montgomery, L., Nishimura, K., Okamura, K., Shen, F., Somerville, M. J., Tchinda, J., Valsesia, A., Woodwark, C., Yang, F., Zhang, J., Zerjal, T., Armengol, L., Conrad, D. F., Estivill, X., Tyler-Smith, C., Carter, N. P., Aburatani, H., Lee, C., Jones, K. W., Scherer, S. W. and Hurles, M. E. (2006) Global variation in copy number in the human genome. Nature 444, 444–454.
Bae, J. S., Cheong, H. S., Kim, J. O., Lee, S. O., Kim, E. M., Lee, H. W., Kim, S., Kim, J. W., Cui, T., Inoue I., and Shin, H. D. (2008) Identification of SNP markers for common CNV regions and association analysis of risk of subarachnoid aneurysmal hemorrhage in Japanese population. Biochem. Biophys. Res. Commun. 373, 593–596.
Blauw, H. M., Veldink, J. H., van Es, M. A., van Vught, P. W., Saris, C. G., van der Zwaag, B., Franke, L., Burbach, J. P., Wokke, J. H., Ophoff, R. A. and van den Berg, L. H. (2008) Copy-number variation in sporadic amyotrophic lateral sclerosis: a genome-wide screen. Lancet Neurol. 7, 319–326.
Gunnarsson, R., Staaf, J., Jansson, M., Ottesen, A. M., Goransson, H., Liljedahl, U., Ralfkiaer, U., Mansouri, M., Buhl, A. M., Smedby, K. E., Hjalgrim, H., Syvanen, A. C., Borg, A., Isaksson, A., Jurlander, J., Juliusson, G. and Rosenquist, R. (2008) Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia – a comparative study of four differently designed, high resolution microarray platforms. Genes Chromosomes Cancer 47, 697–711.
Acknowledgements
C.D. is supported by the Stanley Ho Centre for Emerging Infectious Diseases and the Li Ka Shing Institute of Health Sciences.
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© 2009 Humana Press, a part of Springer Science+Business Media, LLC 2003
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Ding, C., Jin, S. (2009). High-Throughput Methods for SNP Genotyping. In: Komar, A. (eds) Single Nucleotide Polymorphisms. Methods in Molecular Biology™, vol 578. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-411-1_16
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DOI: https://doi.org/10.1007/978-1-60327-411-1_16
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