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. 2012 Jun;39(3):187-193.
doi: 10.1159/000338855. Epub 2012 May 11.

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

Thorsten Schwark  1 , Patrick Meyer, Melanie Harder, Jan-Hendrick Modrow, Nicole von Wurmb-Schwark
Affiliations

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

Thorsten Schwark et al. Transfus Med Hemother. 2012 Jun.

Abstract
in English, German

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.

Hintergrund: In der modernen Vaterschafts-und Spurenanalytik ist die Untersuchung sogenannter Short Tandem Repeats (STRs) heute das Mittel der Wahl. In bestimmten Fällen (Defizienzen, Mutationen in den STR-Systemen, sehr geringe DNA-Mengen) kann die STR-Analyse allein unter Umständen zur Klärung nicht ausreichen.

Methoden: Wir stellen als zusätzliche Methode einen von uns auf Basis der vom SNPforID-Konsortium vorgeschlagenen Single Nucleotide Polymorphisms (SNPs) entwickelten, 50 SNPs umfassenden Assay vor. Dieser neue Multiplex-Assay wurde in verschiedenen Routinefällen angewandt.

Ergebnisse und Schlussfolgerungen: Unsere Untersuchungen zeigen, dass die SNP-Analyse eine wertvolle Ergänzung der STR-Untersuchung darstellt und geeignet ist, zur Lösung komplizierter Spuren-und Vaterschaftsfälle eingesetzt zu werden.

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Figures

Fig. 1
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 (GeneRulerTM Low range DNA ladder, Fermentas GmbH, Germany).
Fig. 2
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
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.
See this image and copyright information in PMC

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