Skip to main content

SNP Typing in Forensic Genetics

A Review

  • Protocol
Forensic DNA Typing Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 297))

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 119.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 159.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. 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.

    Article  PubMed  CAS  Google Scholar 

  2. 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.

    Article  PubMed  CAS  Google Scholar 

  3. 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.

    Article  PubMed  CAS  Google Scholar 

  4. The Y Chromosome Consortium. (2002) A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res. 12, 339–348.

    Article  Google Scholar 

  5. Gill, P. (2001) An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int. J. Legal Med. 114, 204–210.

    Article  PubMed  CAS  Google Scholar 

  6. 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.

    Article  PubMed  CAS  Google Scholar 

  7. 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.

    Article  PubMed  CAS  Google Scholar 

  8. 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.

    Google Scholar 

  9. 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.

    Google Scholar 

  10. 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.

    Google Scholar 

  11. 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.

    Article  PubMed  CAS  Google Scholar 

  12. Clegg, R. M. (1992) Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol. 221, 353–388.

    Article  Google Scholar 

  13. 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.

    Article  PubMed  CAS  Google Scholar 

  14. 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.

    Article  PubMed  CAS  Google Scholar 

  15. 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.

    PubMed  CAS  Google Scholar 

  16. Livak, K.J. (1999) allelic discrimination using fluorogenic probes and the 5' nuclease assay. Genet. Anal. Biomol. Engin. 14, 143–149.

    Article  CAS  Google Scholar 

  17. 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.

    PubMed  CAS  Google Scholar 

  18. 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.

    Article  PubMed  CAS  Google Scholar 

  19. Tyagi, S., and Kramer, F. R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303–308.

    Article  PubMed  CAS  Google Scholar 

  20. 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.

    Article  PubMed  CAS  Google Scholar 

  21. Tyagi, S., Bratu, D. P., and Kramer, F. R. (1998) Multicolour molecular beacons for allele discrimination. Nat. Biotechnol. 16, 49–53.

    Article  PubMed  CAS  Google Scholar 

  22. Tyagi, S., Marras, S. A. E., and Kramer, F. R. (2000) Wavelength-shifting molecular beacons. Nat. Biotechnol. 18, 1191–1196.

    Article  PubMed  CAS  Google Scholar 

  23. 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.

    Article  PubMed  CAS  Google Scholar 

  24. 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.

    Article  PubMed  CAS  Google Scholar 

  25. 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.

    Article  PubMed  CAS  Google Scholar 

  26. 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.

    Article  PubMed  CAS  Google Scholar 

  27. 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.

    Article  PubMed  CAS  Google Scholar 

  28. 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.

    Article  PubMed  CAS  Google Scholar 

  29. Ronaghi, M., Uhlen, M., and Nyrén, P., (1998) A sequencing method based on real-time pyrophosphate. Science 281, 363–365.

    Article  PubMed  CAS  Google Scholar 

  30. 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.

    Article  PubMed  CAS  Google Scholar 

  31. Sokolov, B. P. (1990) Primer extension technique for the detection of single nucleotide in genomic DNA. Nucleic Acids Res. 18, 3671.

    Article  PubMed  CAS  Google Scholar 

  32. 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.

    Article  PubMed  CAS  Google Scholar 

  33. 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.

    Article  PubMed  CAS  Google Scholar 

  34. 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.

    Article  PubMed  CAS  Google Scholar 

  35. 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.

    PubMed  CAS  Google Scholar 

  36. 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.

    PubMed  CAS  Google Scholar 

  37. 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.

    Article  PubMed  CAS  Google Scholar 

  38. 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.

    Article  PubMed  CAS  Google Scholar 

  39. Haff, L. A., and Smirnov, I. P. (1997) Multiplex genotyping of PCR products with MassTag-labeled primers. Nucleic Acids Res. 25, 3749–3750.

    Article  PubMed  CAS  Google Scholar 

  40. Ross, P., Hall, L., Smirnov, I., and Haff, L. (1998) High level multiplex genotyping by MALDI-TOF mass spectrometry. Nat. Biotechnol. 16, 1347–1351.

    Article  PubMed  CAS  Google Scholar 

  41. 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.

    Article  PubMed  CAS  Google Scholar 

  42. Shumaker, J. M., Metspalu, A., and Caskey, C. T. (1996) Mutation detection by solid phase primer extension. Hum Mutat. 7, 346–354.

    Article  PubMed  CAS  Google Scholar 

  43. 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.

    PubMed  CAS  Google Scholar 

  44. 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.

    Article  PubMed  CAS  Google Scholar 

  45. 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.

    Article  PubMed  CAS  Google Scholar 

  46. 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.

    Article  PubMed  CAS  Google Scholar 

  47. Chen, X., Levine, L., and Kwok, P. Y. (1999) Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res. 9, 492–498.

    PubMed  CAS  Google Scholar 

  48. 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.

    Article  PubMed  CAS  Google Scholar 

  49. 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.

    Article  PubMed  CAS  Google Scholar 

  50. 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.

    PubMed  CAS  Google Scholar 

  51. Germer, S., and Higuchi, R. (1999) Single-tube genotyping without oligonucleotide probes. Genome Res. 9, 72–78.

    PubMed  CAS  Google Scholar 

  52. 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.

    Article  PubMed  CAS  Google Scholar 

  53. Landergren, U., Kaiser, R., Sanders, J., and Hood, L. (1988) A ligase-mediated gene detection technique. Science 241, 1077–1080.

    Article  Google Scholar 

  54. Barany, F. (1991) The ligase chain reaction in a PCR world. PCR Methods Appl. 1, 5–16.

    PubMed  CAS  Google Scholar 

  55. 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.

    Article  PubMed  CAS  Google Scholar 

  56. Eggerding, F. A. (1995) A one-step Coupled Amplification and Oligonucleotide Ligation procedure for multiplex genetic typing. PCR Methods Appl. 4, 337–345.

    PubMed  CAS  Google Scholar 

  57. Chen, X., Livak, K. J., and Kwok, P. Y. (1998) A homogeneous, ligase-mediated DNA diagnostic test. Genome Res. 8, 549–556.

    PubMed  CAS  Google Scholar 

  58. 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.

    Article  PubMed  CAS  Google Scholar 

  59. 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.

    Article  PubMed  CAS  Google Scholar 

  60. 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.

    Article  PubMed  CAS  Google Scholar 

  61. 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.

    Article  PubMed  CAS  Google Scholar 

  62. 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.

    Article  PubMed  CAS  Google Scholar 

  63. 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.

    PubMed  CAS  Google Scholar 

  64. 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.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Humana Press Inc., Totowa, NJ

About this protocol

Cite this protocol

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

Download citation

  • DOI: https://doi.org/10.1385/1-59259-867-6:107

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-264-3

  • Online ISBN: 978-1-59259-867-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics