A Comparison of Three Autosomal STR Amplification Kits

As DNA extraction, quantitation and STR amplification technologies have evolved, forensic DNA laboratories are now able to detect individual profiles from less DNA, even from challenging sample types. In 2017, the Combined DNA Index System (CODIS) increased the number of required loci from 13 to 20 and several new STR amplification kits have been developed to meet this need.

Tay et al. published a research paper that describes their evaluation of three of these kits.¹ The team evaluated the kits for baseline noise, sensitivity, peak height variability, and artefacts. All positive and negative controls were amplified according to the manufacturer’s recommendation on the Proflex Thermal Cycler. Samples were subjected to capillary electrophoresis on the Applied Biosystems 3500xL Genetic Analyzer with Data Collection Software 4.0 and analyzed with GeneMapper ID-X Software v 1.6.

Baseline noise: The Applied Biosystems VeriFiler Plus PCR Amplification Kit* produced the cleanest baseline overall when considering both the negative and positive controls.

Sensitivity: All kits were evaluated with a serial dilution of total DNA input that ranged from 8 pg to 2 ng. VeriFiler Plus kit detected the highest percentage of alleles recovered at the 8, 16 and 32 pg, while all three kits performed comparably at higher amounts of input DNA.

Peak height variability: The peak heights and peak height ratio were comparable at most of the DNA input amounts. There were differences at 8 and 16 pg where the Promega Fusion 6C System had higher values than the VeriFiler Plus kit; however, the VeriFiler Plus kit had a lower Analytical Threshold setting.

Artefacts: The VeriFiler Plus kit did produce a higher number of artefacts at the recommended DNA input, though when the peak heights were also considered, the ratio of artefacts to peak height was comparable for all three kits.

In conclusion, the authors state “Overall, the VeriFiler Plus kit was found to be most suitable for low template DNA samples, with high sensitivity and low levels of baseline noise. These performance characteristics provide a higher degree of confidence for differentiating trace DNA alleles from noise related artefacts.”¹

With a total of 25 markers, including 11 mini-STRs, VeriFiler Plus kits are specifically designed for challenging sample types such as touch, inhibited, or degraded samples, with improved sensitivity and robustness to inhibition. In addition, an Internal Quality Control (IQC) system assesses the presence of inhibitors in the sample to enable distinction between degraded and inhibited samples, which can help forensics analysts make better decisions on how to further process problematic samples. The IQC system also verifies successful PCR amplification. Although optimized for casework samples, direct amplification of single-source reference samples using the VeriFiler Plus kit is also supported to enable laboratories to process all sample types with one amplification kit.

The VeriFiler Plus kit is approved for use by laboratories generating DNA profiles for inclusion in the US National DNA Index System (NDIS) CODIS database.

*The data in this publication is based on the original Verifiler Plus kit, which was redesigned in Aug 2020.

Reference:

1.      Forensic Science International: Reports 1 (2019) 100049

 For research, forensic or paternity use only. Not for use in diagnostic procedures.