Abstract
The history of genetic markers accurately partitions the progression of molecular genetics into three phases: the RFLP (restriction fragment length polymorphism), microsatellite and SNP (single nucleotide polymorphism) eras. This chapter focuses predominately on the current workhorse, the SNP, though briefly covers the former two and overviews current online databases and portals that act as central repositories as well as hubs to further detailed information. Central gene or disease-based searches are considered and then followed through systematically.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Frank, R., Hargreaves, R. (2003) Clinical biomarkers in drug discovery and development. Nat Rev Drug Discov 2, 566–580.
Roberts, R. J. (2005) How restriction enzymes became the workhorses of molecular biology. Proc Natl Acad Sci USA 102, 5905–5908; Danna, K., Nathans, D. (1971) Proc Natl Acad Sci USA 68, 2913–2917; Smith, H. O., Wilcox, K. W. (1970) J Mol Biol 51, 379–391.
Lander, E. S., Linton, L. M., Birren, B., et al. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860–921.
Ellegren, H. (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5, 435–445.
Waterston, R. H., Lindblad-Toh, K., Birney, E., et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562.
Gibbs, R. A., Weinstock, G. M., Metzker, M. L., et al. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493–521.
Litt, M., Luty, J. A. (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44, 397–401.
Weissenbach, J., Gyapay, G., Dib, C., et al. (1992) A second-generation linkage map of the human genome. Nature 359, 794–801.
Davies, J. L., Kawaguchi, Y., Bennett, S. T., et al. (1994) A genome-wide search for human type 1 diabetes susceptibility genes. Nature 371, 130–136.
Ogura, Y., Bonen, D. K., Inohara, N., et al (2001) A frameshift mutation in NOD2 associated with susceptibility to Crohn’s disease. Nature 411, 603–606.
Kelkar, Y. D., Tyekucheva, S., Chiaromonte, F., Makova, K. D. (2008) The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Res 18, 30–38.
Molla, M., Delcher, A., Sunyaev, S., et al. (2009) Triplet repeat length bias and variation in the human transcriptome. Proc Natl Acad Sci USA 106, 17095–17100.
Day, I. N. (2010) dbSNP in the detail and copy number complexities. Hum Mutat 31, 2–4.
Hawkins, R. D., Hon, G. C., Ren, B. (2010) Next-generation genomics: an integrative approach. Nat Rev Genet 11, 476–486.
Duret, L. (2009) Mutation patterns in the human genome: more variable than expected. PLoS Biol 7, e1000028.
Walser, J. C., Furano, A. V. (2010) The mutational spectrum of non-CpG DNA varies with CpG content. Genome Res20, 875–882.
Roberts, R. J., Vincze, T., Posfai, J., Macelis, D. (2010) REBASE – a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 38, D234–236.
Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27, 573–580.
Sherry, S. T., Ward, M. H., Kholodov, M., et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29, 308–311.
Altshuler, D., Brooks, L. D., Chakravarti, A., et al. (2005) A haplotype map of the human genome. Nature 437, 1299–1320.
Zeggini, E., Rayner, W., Morris, A. P., et al. (2005) An evaluation of HapMap sample size and tagging SNP performance in large-scale empirical and simulated data sets. Nat Genet 37, 1320–1322.
The Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661–678.
McCarthy, M. I., Abecasis, G. R., Cardon, L. R., et al. (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9, 356–369.
Hindorff, L. A., Sethupathy, P., Junkins, H. A., et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106, 9362–9367.
Barrett, J. C., Fry, B., Maller, J., Daly, M. J. (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263–265.
de Bakker, P. I., Yelensky, R., Pe’er, I., et al. (2005) Efficiency and power in genetic association studies. Nat Genet 37, 1217–1223.
Voight, B. F., Kudaravalli, S., Wen, X., Pritchard, J. K. (2006) A map of recent positive selection in the human genome. PLoS Biol 4, e72.
Pickrell, J. K., Coop, G., Novembre, J., et al. (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome Res 19, 826–837.
Coop, G., Pickrell, J. K., Novembre, J., et al. (2009) The role of geography in human adaptation. PLoS Genet 5, e1000500.
Via, M., Gignoux, C., Burchard, E. G. (2010) The 1000 Genomes Project: new opportunities for research and social challenges. Genome Med 2, 3.
Redon, R., Ishikawa, S., Fitch, K. R., et al. (2006) Global variation in copy number in the human genome. Nature 444, 444–454.
Conrad, D. F., Pinto, D., Redon, R., et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature 464, 704–712.
Iafrate, A. J., Feuk, L., Rivera, M. N., et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36, 949–951.
The International Cancer Genome Consortium (2010) International network of cancer genome projects. Nature 464, 993–998.
Golub, T. (2010) Counterpoint: Data first. Nature 464, 679.
Stratton, M. R., Campbell, P. J., Futreal, P. A. (2009) The cancer genome. Nature 458, 719–724.
Spencer, C. C., Deloukas, P., Hunt, S., et al. (2006) The influence of recombination on human genetic diversity. PLoS Genet 2, e148.
Musumeci, L., Arthur, J. W., Cheung, F. S., et al. (2010) Single nucleotide differences (SNDs) in the dbSNP database may lead to errors in genotyping and haplotyping studies. Hum Mutat 31, 67–73.
Gabriel, S. B., Schaffner, S. F., Nguyen, H., et al. (2002) The structure of haplotype blocks in the human genome. Science 296, 2225–2229.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Bell, C.G. (2011). Accessing and Selecting Genetic Markers from Available Resources. In: Yu, B., Hinchcliffe, M. (eds) In Silico Tools for Gene Discovery. Methods in Molecular Biology, vol 760. Humana Press. https://doi.org/10.1007/978-1-61779-176-5_1
Download citation
DOI: https://doi.org/10.1007/978-1-61779-176-5_1
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-175-8
Online ISBN: 978-1-61779-176-5
eBook Packages: Springer Protocols