SpringerProtocols: Abstract: 10. Universal Tag Arrays in Forensic SNP Analysis

10. Universal Tag Arrays in Forensic SNP Analysis

By: Marie Allen², Anna-Maria Divne²

Abstract

Full Text

Download PDF (416K)

Microarray-based single nucleotide polymorphism (SNP) genotyping enables simultaneous and rapid detection of a large number of markers and is thus an attractive method for forensic individual acid identification. This assay relies on a one-color detection system and minisequencing in solution before hybridization to universal tag arrays. The minisequencing reaction is based on incorporation of a fluorescent dideoxynucleotide to a primer containing a tag-sequence flanking the position to be interrogated. This one-color system detects C and T polymorphisms in separate reactions on multiple polymerase chain reaction targets with the fluorophore TAMRA coupled to the respective dideoxynucleotide. After incorporation, tagged primer sequences are hybridized through their complementary sequence on the array, and positive signals are detected by a confocal laser-scanner.

Affiliation(s): (2) Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden

Book Title: Forensic DNA Typing Protocols

Series: Methods in Molecular Biology | Volume: 297 | Pub. Date: Nov-30-2004 | Page Range: 141-153 | DOI: 10.1385/1-59259-867-6:141

Subject: Genetics/Genomics

Key Words: Microarrays - universal tag-arrays - minisequencing - forensic - SNP

References

Download References

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

2.	Prokunina, L., Castillejo-Lopez, C., Oberg, F., Gunnarsson, I., Berg, L., Magnusson, V., et al. (2002) A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans. Nat. Genet. 32, 666–669.

3.	Reynolds, R., & Varlaro, J. (1996) Gender determination of forensic samples using PCR amplification of ZFX/ZFY gene sequences. J. Forensic Sci. 41, 279–286.

4.	Andrews, R. M., Kubacka, I., Chinnery, P. F., Lightowlers, R. N., Turnbull, D. M., and Howell, N. (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 23, 147.

5.	Gerry, N. P., Witowski, N. E., Day, J., Hammer, R. P., Barany, G., and Barany, F. (1999) Universal DNA microarray method for multiplex detection of low abundance point mutations. J. Mol. Biol. 292, 251–262.

6.	Syvanen, A. C. (1999) From gels to chips: “minisequencing” primer extension for analysis of point mutations and single nucleotide polymorphisms. Hum Mutat. 13, 1–10.

7.	Dubiley, S., Kirillov, E., and Mirzabekov, A. (1999). Polymorphism analysis and gene detection by minisequencing on an array of gel-immobilized primers. Nucleic Acids Res. 27, e19.

8.	Fortina, P., Delgrosso, K., Sakazume, T., Santacroce, R., Moutereau, S., Su, H. J., Graves, D., McKenzie, S., and Surrey, S. (2000). Simple two-color array-based approach for mutation detection. Eur. J. Hum. Genet. 8, 884–94.

9.	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.

10.	Landegren, U. (1993). Ligation-based DNA diagnostics. Bioessays 15, 761–5.

11.	Guo, Z., Guilfoyle, R. A., Thiel, A. J., Wang, R., and Smith, L. M. (1994). Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucleic Acids Res. 22, 5456–5465.

12.	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.

13.	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.

14.	Knoth, K., Roberds, S., Poteet, C., and Tamkun, M. (1988). Highly degenerate, inosine-containing primers specifically amplify rare cDNA using the polymerase chain reaction. Nucleic Acids Res. 16, 10,932.

Comments (Loading...)

Post comment/View all comments