Comparecallssm An Automated Allele Concordance Analysis System

Myriad Genetics (Salt Lake City, Utah) has developed an automated allele concordance analysis system known as CompareCallsSM that can aid in rapid review of single-source STR profiles (Ryan et al. 2004). DNA Advisory Board Standard 17.1.1 (see Appendix IV) states that public laboratories perform a '100% technical review' of data generated by contract or vendor laboratories prior to uploading these STR profiles to the National DNA Index System (NDIS) of CODIS (see Chapter 18). Two independent analysis pathways - typically two different human analyst reviewers - are generally required to demonstrate that STR allele calls are the same between the two analysis pathways with the expectation that concordant information will be reliable (see Chapter 15).

With the CompareCallsSM approach, a human reviewer using Genotyper® and a human reviewer using a different analysis platform (in this case Myriad's SureLockIDSM allele calling software) generate data that is then compared for concordance. Thus, the CompareCallsSM software is not making the allele calls but rather checking them to ensure quality results between two independent reads of the STR data. Validation studies with 290 676 STR markers found Myriad's CompareCallsSM software to be at least as accurate as 100% human technical review of STR profiles (Ryan et al. 2004).

UNIQUE CHALLENGES WITH FORENSIC DNA AND NEW TECHNOLOGIES

DNA separations for the purposes of STR genotyping have been primarily conducted to date with electrophoresis, either in the form of slab gels or capillary instruments (see Chapters 12 and 14). However, a number of new methods are under development in research laboratories around the world. These methods involve techniques such as miniature electrophoresis separation systems, hybridization techniques, and mass spectrometry, all of which have been discussed briefly here. New genetic markers are also being investigated such as single nucleotide polymorphisms (see Chapter 8). We can expect that these new technologies will make DNA typing faster, cheaper, and easier to perform.

In the not too distant future, portable systems may be in use that would permit a rapid DNA test right at the crime scene. In addition, large laboratory centers are being established in many parts of the world that have the capability to perform thousands or even tens of thousands of DNA tests per day.

However, the adoption of new technology by the forensic DNA community takes time for several reasons. First and foremost, methods need to be carefully validated to ensure that results with a new technology are accurate and reproducible (see Chapter 16). Second, methods should yield comparable results to current technologies so that genotype information can be compared over time. The development of large DNA databases make it necessary to have a constant currency so that convicted offender samples have been analyzed with the same DNA markers as crime scene samples (see Chapter 18). A new set of markers or a new form of sample analysis, unless it gives an equivalent result to current technology, must have clear advantages and be very inexpensive to overcome legacy data in large DNA databases (Gill 2002, Gill et al. 2004). Now that millions of DNA profiles are present in national DNA databases (see Chapter 18) it is highly unlikely that the field will abandon the current STR loci in the next 5-10 years (National Commission on the Future of DNA Evidence 2000).

With the continued progress in biotechnology around the world will come better and better methods for DNA typing methods used in forensic DNA laboratories. We can expect that future DNA testing technologies will include the following desirable characteristics:

■ Improved capabilities for multiplex PCR, i.e., the ability to amplify more regions of the DNA simultaneously in order to improve further the number of markers examined and therefore the discrimination power of the test;

■ More rapid separation/detection technology;

■ More automated sample processing and data analysis/interpretation;

■ Less expensive sample analysis;

■ Accurate, robust methods.

REFERENCES AND ADDITIONAL READING

Applied Biosystems (2003) GeneMapper™ ID Software Version 3.1 Human Identification Analysis User Guide. Foster City, California.

Belgrader, P., Smith, J.K., Weedn, V.W. and Northrup, M.A. (1998) Journal of Forensic Sciences, 43, 315-319.

Butler, J.M., Li, J., Shaler, T.A., Monforte, J.A. and Becker, C.H. (1998) International Journal of Legal Medicine, 112, 45-49.

Butler, J.M. and Becker, C.H. (2001) Improved analysis of DNA short tandem repeats with time-of-flight mass spectrometry. Washington, DC: National Institute of Justice. Available online at: http://www.ojp.usdoj.gov/nij/pubs-sum/188292.htm.

Crouse, C.A. and Conover, J. (2003) Proceedings of the Fourteenth International Symposium on Human Identification. Madison, Wisconsin: Promega Corporation. See http://www.promega.com/geneticidproc/ussymp14proc/oralpresentations/Crouse.pdf.

Dunbar, H.N., Sparkes, R.L., Hopwood, A.J., Pinchin, R. and Watson, S.K. (1998) Proceedings of the Second European Symposium on Human Identification, pp. 55-58. Madison, Wisconsin: Promega Corporation.

Gill, P., Urquhart, A., Millican, E., Oldroyd, N., Watson, S., Sparkes, R. and Kimpton, C. (1996) International Journal of Legal Medicine, 109, 14-22.

Gill, P., Werrett, D.J., Budowle, B. and Guerreri, R. (2004) Science and Justice, 44, 51-53.

Goedecke, N., McKenna, B., El-Difrawy, S., Carey, L., Matsudaira, P. and Ehrlich, D. (2004) Electrophoresis, 25, 1678-1686.

Greenspoon, S.A., Ban, J.D., Sykes, K., Ballard, E.J., Edler, S.S., Baisden, M. and Covington, B.L. (2004) Journal of Forensic Sciences, 49, 29-39.

Hale, A.N. (1999) Building realistic automated production lines for genetic analysis. In Craig, A.G. and Hoheisel, J.D.(eds) Automation: Genomic & Functional Analyses, Methods in Microbiology, Volume 28, Chapter 5, pp. 93-129. San Diego: Academic Press.

Hayn, S., Wallace, M.M., Prinz, M. and Shaler, R.C. (2004) Journal of Forensic Sciences, 49, 87-91.

Hopwood, A., Brookes, J., Shariff, A., Cage, P., Tatum, E., Mirza, R., Crook, M., Brews, K. and Sullivan, K. (1997) Proceedings of the Eighth International Symposium on Human Identification, pp. 20-24. Madison, Wisconsin: Promega Corporation.

Kadash, K., Kozlowski, B.E., Biega, L.A. and Duceman, B.W. (2004) Journal of Forensic Sciences, 49 (4), 660-667.

Lagally, E.T., Emrich, C.A. and Mathies, R.A. (2001) Lab on a Chip, 1, 102-107.

McCormick, R., Nelson, R.J., Alonso-Amigo, M.G., Benvegnu, D.J. and Hooper, H.H. (1997) Analytical Chemistry, 69, 2626-2630.

Medintz, I.L., Berti, L., Emrich, C.A., Tom, J., Scherer, J.R. and Mathies, R.A. (2001) Clinical Chemistry, 47, 1614-1621.

Mitnik, L., Carey, L., Burger, R., Desmarais, S., Koutny, L., Wernet, O., Matsudaira, P. and Ehrlich, D. (2002) Electrophoresis, 23, 719-726.

Muller, O., Minarik, M. and Foret, F. (1998) Electrophoresis, 19, 1436-1444.

National Commission on the Future of DNA Evidence (2000) The Future of Forensic DNA Testing: Predictions of the Research and Development Working Group. Washington, D.C.: National Institute of Justice. Available at: http://www.ojp.usdoj.gov/ nij/pubs-sum/183697.htm.

Northrup, M.A., Benett, B., Hadley, D., Landre, P., Lehew, S., Richards, J. and Stratton, P.

(1998) Analytical Chemistry, 70, 918-922.

Paegel, B.M., Blazej, R.G. and Mathies, R.A. (2003) Current Opinions in Biotechnology, 14, 42-50.

Palsson, B., Palsson, F., Perlin, M., Gudbjartsson, H., Stefansson, K. and Gulcher, J. (1999) Genome Research, 9, 1002-1012.

Parson, W. and Steinlechner, M. (2001) Forensic Science International, 122, 1-6.

Perlin, M.W., Coffman, D., Crouse, C.A., Konotop, F. and Ban, J.D. (2001) Automated STR data analysis: validation studies. Proceedings of the Twelfth International Symposium on Human Identification. Madison, Wisconsin: Promega Corporation. Available at: http://www.promega.com/geneticidproc/ussymp12proc/contents/perlin.pdf.

Perlin, M.W. (2003) Simple reporting of complex DNA evidence: automated computer interpretation. Proceedings of the Fourteenth International Symposium on Human Identification. Madison, Wisconsin: Promega Corporation. Available at: http://www.promega.com/geneticidproc/ussymp14proc/oralpresentations/perlin.pdf.

Ross, P.L. and Belgrader, P. (1997) Analytical Chemistry, 69, 3966-3972.

Ross, P.L., Davis, P.A. and Belgrader, P. (1998) Analytical Chemistry, 70, 2067-2073.

Ryan, J.H., Barrus, J.K., Budowle, B., Shannon, C.M., Thompson, V.W. and Ward, B.E. (2004) Journal of Forensic Sciences, 49 (3), 492-499.

Schmalzing, D., Koutny, L., Adourian, A., Belgrader, P., Matsudaira, P. and Ehrlich, D. (1997) Proceedings of the National Academy of Sciences USA, 94, 10273-10278.

Schmalzing, D., Koutny, L., Chisholm, D., Adourian, A., Matsudaira, P. and Ehrlich, D. (1999) Analytical Biochemistry, 270, 148-152.

Shi, Y., Simpson, P.C., Scherer, J.R., Wexler, D., Skibola, C., Smith, M.T. and Mathies, R.A.

(1999) Analytical Chemistry, 71, 5354-5361.

Sosnowski, R.G., Tu, E., Butler, W.F., O'Connell, J.P. and Heller, M.J. (1997a) Proceedings of the National Academy of Sciences USA, 94, 1119-1123.

Sosnowski, R.G., Canter, D., Duhon, M., Feng, L., Muralihar, M., Radtkey, R., O'Connell, J., Heller, M. and Nerenberg, M. (1997b) Proceedings of the Eighth International Symposium on Human Identification, pp. 119-125. Madison, Wisconsin: Promega Corporation.

Swerdlow, H., Jones, B.J. and Wittwer, C.T. (1997) Analytical Chemistry, 69, 848-855.

Tereba, A., Mandrekar, P.V., Flanagan, L., Olson, R., Mandrekar, M. and McLaren, R. (2003) Proceedings of the Fourteenth International Symposium on Human Identification. Madison, Wisconsin: Promega Corporation. See http://www.promega.com/ geneticidproc/ussymp14proc/oralpresentations/Tereba.pdf.

Woolley, A.T. and Mathies, R.A. (1994) Proceedings of the National Academy of Sciences USA, 91, 11348-11352.

Woolley, A.T., Hadley, D., Landre, P., deMello, A.J., Mathies, R.A. and Northrup, M.A. (1996) Analytical Chemistry, 68, 4081-4086.

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CHAPTER 18

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