Information on Low Template / Low Copy Number DNA Testing
Sessions were held at several recent international forensic DNA meetings* to discuss low template DNA (LTDNA) testing, which is widely referred to as low copy number or "LCN" typing. The purpose of this website is to provide further information to help readers better understand this topic.
*At the International Society for Forensic Genetics (ISFG) meeting (September 18, 2009) in Buenos Aires, three speakers presented their positions on this topic: Adrian Linacre (University of Strathclyde, member of the Caddy report), Bruce Budowle (University of North Texas, formerly of the FBI Laboratory), and Peter Gill (University of Strathclyde, formerly of the UK Forensic Science Service). At the International Symposium on Human Identification (ISHI or Promega) meeting (October 15, 2009) in Las Vegas, a panel discussion was held that included Charlotte Word (consultant, formerly of Orchid Cellmark), Bruce Budowle (University of North Texas, formerly of the FBI Laboratory), John Butler (National Institute of Standards and Technology), Theresa Caragine (NYC Office of Chief Medical Examiner), Brad Leventhal (NYC prosecutor), Gillian Tully (UK Forensic Science Service), and Angela van Daal (Bond University, Australia).
Presentations on LTDNA
John Butler - ISHI (Promega meeting) 2009 LCN Panel
Becky Hill - ISHI (Promega meeting) 2009 Technical Leaders session
Theresa Caragine - ISHI (Promega meeting) 2009 LCN Panel
Charlotte Word - ISHI (Promega meeting) 2009 LCN Panel
LTDNA Validation Data
Labs having validation data on this topic are invited to share it on this website - submit information to john.butler@nist.gov
NIST Sensitivity Data with low level DNA templates
10 replicate amplifications for each condition with two fully heterozygous, single-source samples
Click on links to see summaries and DNA profiles observed
STR kit - PCR conditions Sample 1 Sample 2 Identifiler - 28 cycles 100 pg 100 pg 30 pg 30 pg 10 pg 10 pg Identifiler - 31 cycles 100 pg 100 pg 30 pg 30 pg 10 pg 10 pg PowerPlex 16 HS - 31 cycles 100 pg 100 pg 30 pg 30 pg 10 pg 10 pg PowerPlex 16 HS - 34 cycles 100 pg 100 pg 30 pg 30 pg 10 pg 10 pg
LTDNA References
Butler, J.M. and Hill, C.R. (2010) Scientific issues with analysis of low amounts of DNA. Profiles in DNA (Promega), 13(1). Available at http://www.promega.com/profiles/.
Peer-reviewed literature (containing data)
Balding, D.J. and Buckleton, J. (2009) Interpreting low template DNA profiles. Forensic Sci. Int. Genet. 4: 1-10.
Benschop, C.C.G., van der Beek, C.P., Meiland, H.C., van Gorp, A.G.M., Westen, A.A., Sijen, T. (2010) Low template STR typing: Effect of replicate number and consensus method on genotyping reliability and DNA database search results. FSI Genetics (in press). DOI: 10.1016/j.fsigen.2010.06.006
Buckleton, J. (2009) Validation issues around DNA typing of low level DNA. Forensic Sci. Int. Genet. 3: 255-260.
Caragine, T., Mikulasovich, R., Tamariz, J., Bajda, E., Sebestyen, J., Baum, H., Prinz, M. (2009) Validation of testing and interpretation protocols for low template DNA samples using AmpFlSTR Identifiler. Croatian Med. J. 50: 250-267. [link to paper]
Dieltjes, P., Mieremet, R., Zungia, S., Kraaijenbrink, T., Pijpe, J., de Knijff, P. (2010) A sensitive method to extract DNA from biological traces present on ammunition for the purpose of genetic profiling. Int. J. Legal Med. (in press)
Findlay, I., Taylor, A., Quirke, P., Frazier, R., and Urquhart, A. (1997) DNA fingerprinting from single cells. Nature 389(6651): 555-556.
Gill, P., Whitaker, J., Flaxman, C., Brown, N., and Buckleton, J. (2000) An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA. Forensic Sci. Int. 112(1): 17-40.
Gill, P., Brenner, C.H., Buckleton, J.S., Carracedo, A., Krawczak, M., Mayr, W.R., Morling, N., Prinz, M., Schneider, P.M., Weir, B.S. (2006) DNA commission of the International Society of Forensic Genetics: Recommendations on the interpretation of mixtures. Forensic Sci. Int. 160: 90-101.
Gill, P., Puch-Solis, R., Curran, J. (2009) The low-template-DNA (stochastic) threshold -- its determination relative to risk analysis for national DNA databases. Forensic Sci. Int. Genet. 3: 104-111.
Gill, P. and Buckleton, J. (2010) A universal strategy to interpret DNA profiles that does not require a definition of low-copy-number. Forensic Sci. Int. Genet. (in press).
Kloosterman, A.D. and Kersbergen, P. (2003) Efficacy and limits of genotyping low copy number (LCN) DNA samples by multiplex PCR of STR loci. J. Soc. Biol. 197(4): 351-359.
Schiffner, L.A., Bajda, E.J., Prinz, M., Sebestyen, J., Shaler, R., and Caragine, T.A. (2005) Optimization of a simple, automatable extraction method to recover sufficient DNA from low copy number DNA samples for generation of short tandem repeat profiles. Croatian Med. J. 46(4): 578-586. [link to paper]
Taberlet, P., Griffin, S., Goossens, B., Questiau, S., Manceau, V., Escaravage, N., Waits, L.P., and Bouvet, J. (1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res. 24: 3189-3194. [link to paper]
Walsh, P. S., Erlich, H. A., and Higuchi, R. (1992) Preferential PCR amplification of alleles: Mechanisms and solutions. PCR Meth. Appl. 1: 241-250. [link to paper]
Wetton, J.H., Lee-Edghill, J., Archer, E., Tucker, V.C., Hopwood, A.J., Whitaker, J., Tully, G. (2010) Analysis and interpretation of mixed profiles generated by 34 cycle SGM Plus® amplification. FSI Genetics (in press). DOI: 10.1016/j.fsigen.2010.07.003
Whitaker, J. P., Cotton, E. A., and Gill, P. (2001) A comparison of the characteristics of profiles produced with the AMPFlSTR SGM Plus multiplex system for both standard and low copy number (LCN) STR DNA analysis. Forensic Sci. Int. 123(2-3): 215-223.
Reports (evaluating the methodology)
Caddy report - "Review of the Science of Low Template DNA Analysis" http://police.homeoffice.gov.uk/publications/operational-policing/Review_of_Low_Template_DNA_1.pdf
UK Forensic Regulator response to Professor Brian Caddy's Review of the Science of Low Template DNA Analysis: http://police.homeoffice.gov.uk/publications/operational-policing/response-caddy-dna-review
Review articles (commenting on other's data)
Budowle, B., Eisenberg, A.J., van Daal, A. (2009) Validity of low copy number typing and applications to forensic science. Croatian Med. J. 50: 207-217. [link to paper]
Graham, E.A.M. (2008) DNA reviews: low level DNA profiling. Forensic Sci. Med. Pathol. 4: 129-131.
Wickenheiser, R. A. (2002) Trace DNA: a review, discussion of theory, and application of the transfer of trace quantities of DNA through skin contact. J. Forensic Sci. 47(3): 442-450.
Non-peer reviewed literature (representing the authors' opinions only) - conference proceedings and letters to the editor
Buckleton, J. and Gill, P. (2010) A commentary on Budowle et al.: Low copy number has yet to achieve "general acceptance"; FSI Genetics supplementary series 2 (2009) 551-552. FSI Genetics (in press).
Budowle, B., Hobson, D.L., Smerick, J.B., Smith, J.A.L. (2001) Low copy number – consideration and caution. Proceedings of the Twelfth International Symposium on Human Identification. Available at http://www.promega.com/geneticidproc/ussymp12proc/contents/budowle.pdf.
Budowle, B., Eisenberg, A., van Daal, A. (2009) Low copy number has yet to achieve "general acceptance". Forensic Sci. Int. Genetics Suppl. Ser. -- Progress in Forensic Genetics 13 / Proceedings of the 23rd International Society for Forensic Genetics Congress 2: 551-552.
Budowle, B., van Daal, A. (2010) Low copy number typing is not a way of thinking; it is a methodology. FSI Genetics (in press).
Budowle, B., Eisenberg, A., van Daal, A. (2010) Concerns about low copy number typing. FSI Genetics (in press).
Budowle, B. and van Daal, A. (2010) Reply to Comments by Buckleton and Gill on “Low copy number typing has yet to achieve ‘general acceptance”’ by Budowle, B., et al., 2009. Forensic Sci. Int.: Genet. Suppl. Series 2, 551–552. FSI Genetics (in press).
Butler, J.M. and Hill, C.R. (2010) Scientific issues with analysis of low amounts of DNA. Profiles in DNA (Promega), 13(1). Available at http://www.promega.com/profiles/.
Caragine, T. and Prinz, M. (2010) Commentary on the paper: "Low Copy Number typing has yet to achieve 'general acceptance'". FSI Genetics (in press).
Gilder, J., Koppl, R., Kornfield, I., Krane, D., Mueller, L., Thompson, W. (2009) Letter to editor: Comments on the review of low copy number testing. Int. J. Legal Med. 123: 535-536.
Gill, P. and Buckleton, J. (2009) Low copy number typing -- where next? Forensic Sci. Int. Genetics Suppl. Ser. -- Progress in Forensic Genetics 13 / Proceedings of the 23rd International Society for Forensic Genetics Congress 2: 553-555.
Leventhal, B. (2010) Low copy number analysis from a legal perspective. Profiles in DNA (Promega). Available at http://www.promega.com/profiles/.
Linacre, A. (2009) Review of low template DNA typing. Forensic Sci. Int. Genetics Suppl. Ser. -- Progress in Forensic Genetics 13 / Proceedings of the 23rd International Society for Forensic Genetics Congress 2: 549-550.
Michel, S., De Bast, A., Vandenbroere, I., Froment, O. (2009) Interpretation of low-copy-number DNA profile after post-PCR purification. Forensic Sci. Int. Genetics Suppl. Ser. -- Progress in Forensic Genetics 13 / Proceedings of the 23rd International Society for Forensic Genetics Congress 2: 542-543.
Murray, C., Lowe, A., Richardson, P., Wivell, R., Gill, P., Tully, G., Whitaker, J. (2001) Use of low copy number (LCN) DNA in forensic inference. Proceedings of the Twelfth International Symposium on Human Identification. Available at http://www.promega.com/geneticidproc/ussymp12proc/contents/murray.pdf.
Whitaker, J., Tully, G., Sullivan, K. (2009) Letter to the editor: Response to low level DNA profiling. Forensic Sci. Med. Pathol. 5: 102-103.
Word, C. (2010) What is LCN?--definitions and challenges. Profiles in DNA (Promega). Available at http://www.promega.com/profiles/.
Last Updated: 09/21/2010