A Mathematical Approach to the Analysis of Multiplex DNA Profiles

Springer Science and Business Media LLC - Tập 73 - Trang 1909-1931 - 2010
Robert M. Goor1, Lisa Forman Neall1, Douglas Hoffman1, Stephen T. Sherry1
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA.

Tóm tắt

Multiplex DNA profiles are used extensively for biomedical and forensic purposes. However, while DNA profile data generation is automated, human analysis of those data is not, and the need for speed combined with accuracy demands a computer-automated approach to sample interpretation and quality assessment. In this paper, we describe an integrated mathematical approach to modeling the data and extracting the relevant information, while rejecting noise and sample artifacts. We conclude with examples showing the effectiveness of our algorithms.

Tài liệu tham khảo

Butler, J. M. (2005). Forensic DNA typing (2nd ed.). New York: Elsevier. Carlson, B. A. (1975). Communication systems (2nd ed.). New York: McGraw–Hill. Federal Bureau of Investigation (2010). CODIS—NDIS Statistics [Internet]. Washington, DC: U.S. Department of Justice; 2010 June [cited 2010 Aug 16]. Available from: http://www.fbi.gov/hq/lab/codis/clickmap.htm. Forman Neall, L., Sherry, S., Goor, R., Hoffman, D., Butler, J., Kline, M., Duewer, D., Carney, C., Coble, M., Della Manna, A., Murvai, J., Prinz, M., Northrup, T.P., Risch, G., Rogers, G.S., Riley, G., Scott, T., Sozer, A., Squibb, M., Zbicz, K., & Ostell, J. (2008). OSIRIS quality assurance software for multiplex STR profiles. In Proceedings of the 19th international symposium on human identification, Hollywood, CA, October 13–16, 2008. Sydney: The Promega Corporation. Forman Neall, L., Goor, R., Hoffman, D., Sherry, S., Zbicz, K., Coble, M., Kline, M., Hill, B., & Butler, J. (2009). The release of OSIRIS public domain software for DNA profile QA. In Proceedings of the 20th international symposium on human identification, Las Vegas, NV, October 12–15, 2009. Sydney: The Promega Corporation. Ghosal, S. (2004). Fluid mechanics of electroosmotic flow and its effect on band broadening in capillary electrophoresis. Electrophoresis 25, 214–228. Hall, C. A., & Meyer, W. W. (1976). Optimal error bounds for cubic spline interpolation. J. Approx. Theory, 16, 105–122. Poster from Promega 20th international symposium for human identification, October 12–15, 2009 (PDF). Available from: http://www.ncbi.nlm.nih.gov/projects/SNP/osiris/. Riesz, F., & Nagy, Sz.-B. (1955). Functional analysis. New York: Frederick Ungar. Stoer, J., & Bulirsch, R. (1976). Introduction to numerical analysis (2nd ed.). New York: Springer. Tomasi, G., van den Berg, F., & Andersson, C. (2004). Correlation optimized warping and dynamic time warping as preprocessing methods for chromatographic data. J. Chemom. 18, 231–241. Watzig, H., & Gunter, S. (2003). Capillary electrophoresis—a high performance analytical separation technique. Clin. Chem. Lab. Med. 41(6), 724–738.