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. 2012 Jun;39(3):195-201.
doi: 10.1159/000338957. Epub 2012 May 12.

Kinship Analysis with Diallelic SNPs - Experiences with the SNPforID Multiplex in an ISO17025 Accreditated Laboratory

Claus Børsting  1 , Martin Mikkelsen, Niels Morling
Affiliations

Kinship Analysis with Diallelic SNPs - Experiences with the SNPforID Multiplex in an ISO17025 Accreditated Laboratory

Claus Børsting et al. Transfus Med Hemother. 2012 Jun.

Abstract
in English, German

BACKGROUND: The mutation rate of single nucleotide polymorphisms (SNPs) is estimated to be 100,000 times lower than that of short tandem repeats (STRs), which makes SNPs very suitable for relationship testing. The SNPforID multiplex assay was the first SNP typing assay that was a real alternative to the commonly used STR kits in kinship and crime case work and the first SNP assay to be validated in a forensic laboratory accredited according to the ISO17025 standard. METHODS: A total of 54 crime case samples were typed with the SNPforID multiplex assay. 30 samples from relationship cases were sequenced in selected SNP loci. RESULTS: It was demonstrated that mixtures were easily detected with the SNPforID assay by analyzing the signal strengths of the detected alleles. Unusual imbalances in signal strengths that were observed in a few individuals could be explained by unexpected SNPs in one of the primer binding sites. A complicated relationship case with four closely related individuals is presented. CONCLUSION: Mixtures can be detected with bi-allelic SNPs. The SNPforID assay is a very useful supplement to the STR kits in relationship testing.

Hintergrund: Die Mutationsrate von Single-Nucleotide-Polymorphismen (SNPs) ist 100 000 Mal niedriger als die Mutationsrate von Short-Tandem-Repeats (STRs). Die kleine Mutationsrate macht SNPs sehr nützlich für die Abstammungsbegutachtung. Der SNPforID-Multiplex war der erste SNP-Typisierungstest, der eine gute Ergänzung und vielleicht ein echte Alternative zu STR-Kits in der Abstammungsbegutachtung war, und der erste forensische SNP-Test, der nach dem ISO17025-Standard akkreditiert worden ist.

Methoden: Insgesamt 54 Proben von Kriminalfällen wurden mit dem SNPforID-Multiplex-Test untersucht. Weiterhin wurden 30 Proben von Abstammungsfällen in ausgewählten SNP-Loci sequenziert.

Ergebnisse: Es wurde gezeigt, dass DNA-Mischungen leicht mit dem SNPforID-Test durch die Analyse der Signalstärke der detektierten Allele erkannt werden konnten. Ungewöhnliche Ungleichgewichte in SNP-Signal-stärken in einigen Proben konnten durch zusätzliche/unerwartete SNPs in einer der Primer-Bindungsstellen erklärt werden. Ein komplizierter Abstammungsfall mit vier eng verwandten Individuen wird als Beispiel vorgestellt.

Schlussfolgerung: DNA-Mischungen können mit bi-alleli-schen SNPs erkannt werden. Der SNPforID-Test ist eine sehr nützliche/wertvolle Ergänzung zu STR-Kits in der Abstammungsbegutachtung.

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Figures

Fig. 1
Fig. 1
Case example. a Hypothesis H1: The father of the mother is the father of the child. b Hypothesis H2: The brother of the mother is the father of the child. c STR and SNP typing results at the three loci where mismatches were detected between C and AF2.
Fig. 2
Fig. 2
Normalized peak height ratios from a 30 single source samples b and 20 two-person mixtures typed with the SNP for ID multiplex assay. program was used: denaturation at 95 °C for 5 min followed by 30 cycles of 95 °C for 15 s, 60 °C or 58 °C for 15 s and 72 °C for 30 s followed by 5 min at 72 °C. PCR products were sequenced using the BigDye Terminator Kit (Applied Biosystems) as recommended by the manufacturer. The results were analyzed on a 3130xl Genetic Analyzer (Applied Biosystems) with a 36 cm capillary array and POP-4 polymer (Applied Biosystems).
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