Low template STR typing: Effect of replicate number and consensus method on genotyping reliability and DNA database search results

Benschop, Corina C.G.; van der Beek, Cornelis P.; Meiland, Hugo C.; van Gorp, Ankie G.M.; Westen, Antoinette A.; Sijen, Titia

doi:10.1016/j.fsigen.2010.06.006

« Previous Next »Forensic Science International: Genetics
Volume 5, Issue 4 , Pages 316-328, August 2011

Low template STR typing: Effect of replicate number and consensus method on genotyping reliability and DNA database search results

Corina C.G. Benschop
- Netherlands Forensic Institute, Department of Human Biological Traces, P.O. Box 24044, 2490 AA The Hague, The Netherlands
Cornelis P. van der Beek
- Netherlands Forensic Institute, Department Dutch DNA database, P.O. Box 24044, 2490 AA The Hague, The Netherlands
Hugo C. Meiland
- Leiden Institute of Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333 CA Leiden, The Netherlands
Ankie G.M. van Gorp
- Netherlands Forensic Institute, Department of Human Biological Traces, P.O. Box 24044, 2490 AA The Hague, The Netherlands
Antoinette A. Westen
- Netherlands Forensic Institute, Department of Human Biological Traces, P.O. Box 24044, 2490 AA The Hague, The Netherlands
Titia Sijen
- Netherlands Forensic Institute, Department of Human Biological Traces, P.O. Box 24044, 2490 AA The Hague, The Netherlands
- Corresponding author. Tel.: +31 708886888; fax: +31 708886555.

Received 12 March 2010; received in revised form 25 May 2010; accepted 24 June 2010. published online 23 July 2010.

Abstract

To analyze DNA samples with very low DNA concentrations, various methods have been developed that sensitize short tandem repeat (STR) typing. Sensitized DNA typing is accompanied by stochastic amplification effects, such as allele drop-outs and drop-ins. Therefore low template (LT) DNA profiles are interpreted with care. One can either try to infer the genotype by a consensus method that uses alleles confirmed in replicate analyses, or one can use a statistical model to evaluate the strength of the evidence in a direct comparison with a known DNA profile. In this study we focused on the first strategy and we show that the procedure by which the consensus profile is assembled will affect genotyping reliability. In order to gain insight in the roles of replicate number and requested level of reproducibility, we generated six independent amplifications of samples of known donors. The LT methods included both increased cycling and enhanced capillary electrophoresis (CE) injection [1]. Consensus profiles were assembled from two to six of the replications using four methods: composite (include all alleles), n−1 (include alleles detected in all but one replicate), n/2 (include alleles detected in at least half of the replicates) and 2× (include alleles detected twice). We compared the consensus DNA profiles with the DNA profile of the known donor, studied the stochastic amplification effects and examined the effect of the consensus procedure on DNA database search results. From all these analyses we conclude that the accuracy of LT DNA typing and the efficiency of database searching improve when the number of replicates is increased and the consensus method is n/2. The most functional number of replicates within this n/2 method is four (although a replicate number of three suffices for samples showing >25% of the alleles in standard STR typing). This approach was also the optimal strategy for the analysis of 2-person mixtures, although modified search strategies may be needed to retrieve the minor component in database searches. From the database searches follows the recommendation to specifically mark LT DNA profiles when entering them into the DNA database.