The SNPforID Assay as a Supplementary Method in Kinship and Trace Analysis

Abstract

OBJECTIVE: Short tandem repeat (STR) analysis using commercial multiplex PCR kits is the method of choice for kinship testing and trace analysis. However, under certain circumstances (deficiency testing, mutations, minute DNA amounts), STRs alone may not suffice. METHODS: We present a 50-plex single nucleotide polymorphism (SNP) assay based on the SNPs chosen by the SNPforID consortium as an additional method for paternity and for trace analysis. The new assay was applied to selected routine paternity and trace cases from our laboratory. RESULTS AND CONCLUSIONS: Our investigation shows that the new SNP multiplex assay is a valuable method to supplement STR analysis, and is a powerful means to solve complicated genetic analyses.

Fig. 1

Checking of amplification success prior to single-base extension (SBE). Aliquots of 5 μl of each PCR product from 6 different samples were separated on a PAG and detected using a modified silver staining. Left: Results from the 21-plex; right: the 29-plex amplicons. NTC = No template control, L = molecular weight marker (GeneRuler^TM Low range DNA ladder, Fermentas GmbH, Germany).

Fig. 2

Sensitivity of the established 29-plex. Electropherogram after separation of specific reaction products on an ABI3130. Different DNA concentrations were subjected to the described 29-plex. The figure shows that with as little as 25 pg template DNA some SNPs are still detectable.

Fig. 3

Genetic analysis of single hairs using STR and SNP typing. Amplification success in percent of successfully typed markers after analyzing 17 STRs or 50 SNPs. Every analysis was done using 1 μl pure DNA extract as template.