Abstract
Single nucleotide polymorphisms (SNPs) are emerging as new markers of interest to the forensic community because of their abundance in the human genome, their low mutation rate, the opportunity they present of analyzing smaller fragments of deoxyribonucleic acid (DNA) than with short tandem repeats-important in degraded DNA samples-and the possibility of automating the analysis with high-throughput technologies. Many new technologies for genotyping SNPs have been developed in the past few years. We describe the principles of the allelic discrimination reactions and the technologies used for each of them. The aim of this chapter is to help in the understanding of the methodologies used in SNP genotyping and in the selection of the most appropriate techniques for forensic purposes.
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References
Sachidanandam, R., Weissman, D., Schmidt, S. C., Kakol, J. M., Stein, L. D., Marth, G., et al. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933.
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., et al. (2001) The sequence of the human genome. Science 291, 1304–1351.
Zhao, Z., Fu, Y.X., Hewett-Emmett, D., and Boerwinkle, E. (2003) Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution. Gene 312, 207–213.
The Y Chromosome Consortium. (2002) A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res. 12, 339–348.
Gill, P. (2001) An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int. J. Legal Med. 114, 204–210.
Chakraborty, R., Stivers, D. N., Su, B., Zhong, Y., and Budowle, B. (1999) The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems. Electrophoresis 20, 1682–1696.
Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., et al. (2002) The structure of haplotype blocks in the human genome. Science 296, 2225–2229.
Brion, M., Blanco-Verea, A., Lareu, M., Carracedo, A. (in press) 29 Y-chromosome SNP analysis in European populations, in Progress in Forensic Genetics, 10 (Doutremepuich, C., and Morling, N., eds), Elsevier, Amsterdam.
Phillips, C., Lareu, M., Salas, A., Carracedo, A. (in press) Non binary Single Nucleotide Polymorphism markers, in Progress in Forensic Genetics, 10 (Doutremepuich, C., and Morling, N., eds), Elsevier, Amsterdam.
Phillips, C., Lareu, M., Salas, A., Fondevila, M., Berniel, G., Carracedo, A., et al (in press) Population specific single nucleotide polymorphism, in Progress in Forensic Genetics, 10 (Doutremepuich, C., and Morling, N., eds), Elsevier, Amsterdam.
Wallace, R. B., Shaffer, J., Murphy, R. F., Bonner, J., Hirose, T., and Itakura, K. (1979) Hybridization of synthetic oligodeoxyribonucleotides to phi 174 DNA: the effect of single base pair mismatch. Nucleic Acids Res. 6, 3543–3557.
Clegg, R. M. (1992) Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol. 221, 353–388.
Lareu, M., Puente, J., Sobrino, B., Quintans, B., Brion, M., and Carracedo, A. (2001) The use of the LightCycler for the detection of Y chromosome SNPs. Forensic Sci. Int. 118, 163–168.
Holland, P. M., Abramson, R. D., Watson, R., and Gelfand, D. H. (1991) Detection of specific polymerase chain reaction product by utilizing the 5'-3' exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. USA 88, 7276–7280.
Livak, K. J., Flood, S. J., Marmaro, J., Giusti, W., and Deetz, K. (1995) Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl. 4, 357–362.
Livak, K.J. (1999) allelic discrimination using fluorogenic probes and the 5' nuclease assay. Genet. Anal. Biomol. Engin. 14, 143–149.
Lee, L. G., Livak, K. J., Mullah, B., Graham, R. J., Vinayak, R. S., and Woudenberg, T. M. (1999) Seven-color, homogeneous detection of six PCR products. BioTechniques 27, 342–349.
Latif, S., Bauer-Sardina, I., Ranade, K., Livak, K. J., and Kwok, P. Y. (2001) Fluorescence polarization in homogeneous nucleic acid analysis II: 5'-nuclease assay. Genome Res. 11, 436–440.
Tyagi, S., and Kramer, F. R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303–308.
Kostrikis, L. G., Tyagi, S., Mhlanga, M. M., Ho, D. D., and Kramer, F. R. (1998) Spectral genotyping of human alleles. Science 279, 1228–1229.
Tyagi, S., Bratu, D. P., and Kramer, F. R. (1998) Multicolour molecular beacons for allele discrimination. Nat. Biotechnol. 16, 49–53.
Tyagi, S., Marras, S. A. E., and Kramer, F. R. (2000) Wavelength-shifting molecular beacons. Nat. Biotechnol. 18, 1191–1196.
Conner, B. J., Reyes, A. A., Morin, C., Itakura, K., Teplitz, R. L., and Wallace, R. B. (1983) Detection of sickle cell beta S-globin allele by hybridization with synthetic oligonucleotides. Proc Natl Acad Sci USA 80, 278–282.
Wang, D. G., Fan, J. B., Siao, C. J., Berno, A., Young, P., Sapolsky, R., et al. (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077–1082.
Mei, R., Galipeau, P. C., Prass, C., Berno, A., Ghandour, G., Patil, N., et al. (2000) Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res. 10, 1126–1137.
Fodor, S. P., Read, J. L., Pirrung, M. C., Stryer, L., Lu, A. T., and Solas, D. (1991) Light-directed, spatially addressable parallel chemical synthesis. Science 251, 767–773.
Pease, A. C., Solas, D., Sullivan, E. J., Cronin, M. T., Holmes, C. P., and Fodor, S. P. (1994) Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci USA 91, 5022–5026.
Ronaghi, M., Karamohamed, S., Pettersson, B., Uhlen, M., and Nyren, P. (1996) Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem. 242, 84–89.
Ronaghi, M., Uhlen, M., and Nyrén, P., (1998) A sequencing method based on real-time pyrophosphate. Science 281, 363–365.
Syvanen, A. C., Aalto-Setala, K., Harju, L., Kontula, K., and Soderlund, H. (1990) A primer-guided nucleotide incorporation assay in the genotyping of apolipoprotein E. Genomics 8, 684–692.
Sokolov, B. P. (1990) Primer extension technique for the detection of single nucleotide in genomic DNA. Nucleic Acids Res. 18, 3671.
Kuppuswamy, M. N., Hoffmann, J. W., Kasper, C. K., Spitzer, S. G., Groce, S. L., and Bajaj, S. P. (1991) Single nucleotide primer extension to detect genetic diseases: experimental application to hemophilia B (factor IX) and cystic fibrosis genes. Proc. Natl. Acad. Sci. USA 88, 1143–1147.
Sanchez, J., Børsting, C., Hallenberg, C., Buchard, A., Hernandez, A., and Morling, N. (2003) Multiplex PCR and minisequencing of SNPs-a model with 35 Y chromosome SNPs. Forensic Sci. Int. 137, 74–84.
Quintans, B., Alvarez-Iglesias, V., Salas, A., Phillips, C., Lareu, M., and Carracedo, A. (2004) Typing of mitochondrial coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing. Forensic Sci. Int. 140, 251.
Haff, L. A., and Smirnov, I. P. (1997) Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry. Genome Res. 7, 378–388.
Braun, A., Little, D. P., and Koster, H. (1997) Detecting CFTR gene mutations by using primer oligo base extension and mass spectrometry. Clin. Chem. 43, 1151–1158.
Fei, Z., Ono, T., and Smith, L. M. (1998) MALDI-TOF mass spectrometric typing of single nucleotide polymorphisms with mass-tagged ddNTPs. Nucleic Acids Res. 26, 2827–2828.
Sauer, S., Lechner, D., Berlin, K., Lehrach, H., Escary, J. L., Fox, N., et al. (2000) A novel procedure for efficient genotyping of single nucleotide polymorphisms. Nucleic Acids Res. 28, E13.
Haff, L. A., and Smirnov, I. P. (1997) Multiplex genotyping of PCR products with MassTag-labeled primers. Nucleic Acids Res. 25, 3749–3750.
Ross, P., Hall, L., Smirnov, I., and Haff, L. (1998) High level multiplex genotyping by MALDI-TOF mass spectrometry. Nat. Biotechnol. 16, 1347–1351.
Kim, S., Shi, S., Bonome, T., Ulz, M. E., Edwards, J. R., Fodstad, H., et al. (2003) Multiplex genotyping of the human beta2-adrenergic receptor gene using solidphase capturable dideoxynucleotides and mass spectrometry. Anal. Biochem. 316, 251–258.
Shumaker, J. M., Metspalu, A., and Caskey, C. T. (1996) Mutation detection by solid phase primer extension. Hum Mutat. 7, 346–354.
Pastinen, T., Kurg, A., Metspalu, A., Peltonen, L., and Syvanen, A. C. (1997) Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res. 7, 606–614.
Fan, J. B., Chen, X., Halushka, M. K., Berno, A., Huang, X., Ryder, T., et al. (2000) Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res. 10, 853–860.
Hirschhorn, J. N., Sklar, P., Lindblad-Toh, K., Lim, Y. M., Ruiz-Gutierrez, M., Bolk, S., et al. (2000) SBE-TAGS: an array-based method for efficient singlenucleotide polymorphism genotyping. Proc. Natl. Acad. Sci. USA 97, 12,164–12,169.
Pastinen, T., Raitio, M., Lindroos, K., Tainola, P., Peltonen, L., and Syvänen, A. C. (2000) A system for specific, high-throughput genotyping by allele-specific primer extension on micorarrays. Genome Res. 10, 1031–1042.
Chen, X., Levine, L., and Kwok, P. Y. (1999) Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res. 9, 492–498.
Pastinen, T., Raitio, M., Lindroos, K., Tainola, P., Peltonen, L., and Syvanen, A. C. (2000) A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res. 10, 1031–1042.
Newton, C. R., Graham, A., Heptinstall, L. E., Powell, S. J., Summers, C., Kalsheker, N., et al. (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 17, 2503–2516.
Okayama, H., Curiel, D. T., Brantly, M. L., Holmes, M. D., and Crystal, R. G. (1989) Rapid, nonradioactive detection of mutations in the human genome by allele-specific amplification. J. Lab. Clin. Med. 114, 105–113.
Germer, S., and Higuchi, R. (1999) Single-tube genotyping without oligonucleotide probes. Genome Res. 9, 72–78.
Myakishev, M. V., Khripin, Y., Hu, S., and Hamer, D. H. (2001) High-throughput SNP genotyping by allele-specific PCR with universal energy-transfer-labeled primers. Genome Res. 11, 163–169.
Landergren, U., Kaiser, R., Sanders, J., and Hood, L. (1988) A ligase-mediated gene detection technique. Science 241, 1077–1080.
Barany, F. (1991) The ligase chain reaction in a PCR world. PCR Methods Appl. 1, 5–16.
Grossman, P. D., Bloch, W., Brinson, E., Chang, C. C., Eggerding, F. A., Fung, S., et al. (1994) High-density multiplex detection of nucleic acid sequences: oli gonucleotide ligation assay and sequence-coded separation. Nucleic Acids Res. 22, 4527–4534.
Eggerding, F. A. (1995) A one-step Coupled Amplification and Oligonucleotide Ligation procedure for multiplex genetic typing. PCR Methods Appl. 4, 337–345.
Chen, X., Livak, K. J., and Kwok, P. Y. (1998) A homogeneous, ligase-mediated DNA diagnostic test. Genome Res. 8, 549–556.
Lyamichev, V., Mast, A. L., Hall, J. G., Prudent, J. R., Kaiser, M. W., Takova, T., et al. (1999) Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol. 17, 292–296.
Kaiser, M. W., Lyamicheva, N., Ma, W., Miller, C., Neri, B., Fors, L., et al. (1999) A comparison of eubacterial and archaeal structure-specific 5'-exonucleases. J. Biol. Chem. 274, 21387–21394.
Ryan, D., Nuccie, B., and Arvan, D. (1999) Non-PCR-dependent detection of the factor V Leiden mutation from genomic DNA using a homogeneous Invader microtiter plate assay. Mol. Diagn. 4, 135–144.
Hall, J. G., Eis, P. S., Law, S. M., Reynaldo, L. P., Prudent, J. R., Marshall, D. J., et al. (2000) Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. Proc. Natl. Acad. Sci. USA 97, 8272–8277.
Mein, C. A., Barratt, B. J., Dunn, M. G., Siegmund, T., Smith, A. N., Esposito, L., et al. (2000) Evaluation of single nucleotide polymorphism typing with Invader on PCR amplicons and its automation. Genome Res. 10, 330–343.
Hsu, T. M., Law, S. M., Duan, S., Neri, B. P., and Kwok, P. Y. (2001) Genotyping single-nucleotide polymorphisms by the invader assay with dual-color fluorescence polarization detection. Clin. Chem. 47, 1373–1377.
Griffin, T. J., Hall, J. G., Prudent, J. R., and Smith, L. M. (1999) Direct genetic analysis by matrix-assisted laser desorption/ionization mass spectrometry. Proc. Natl. Acad. Sci. USA 96, 6301–6306.
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Sobrino, B., Carracedo, A. (2005). SNP Typing in Forensic Genetics. In: Carracedo, A. (eds) Forensic DNA Typing Protocols. Methods in Molecular Biology, vol 297. Humana Press. https://doi.org/10.1385/1-59259-867-6:107
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DOI: https://doi.org/10.1385/1-59259-867-6:107
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