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EFFICIENCY ASSESMENT OF CHELEX® AND QIAGEN® METHODS FOR BLOOD AND BUCCAL DNA ISOLATION AND STR ANALYSIS

Aim: Efficient isolation of DNA from various biological samples is the basis for successful forensic DNA profiling. Chelating resins and silica-based methods are commonly employed affinity and non-affinity methods for DNA extraction using limited amounts of biologic material. We aimed to evaluate DNA isolation efficiency of the commercially available non-affinity (Chelex® InstaGene™ Matrix) and affinity (Qiagen® QIAamp Mini) isolation procedures by comparing DNA yield and quality metrics of STR profiling data obtained from blood and buccal samples. Materials and methods: Ten buccal swabs and 10 blood stains collected on FTA cards were used as a starting material. Both buccal and blood DNA samples were isolated with the use of InstaGene Matrix and QIAamp Mini kit. Qubit fluorometer was used for DNA quantification and 16 STR loci were amplified with the AmpFlSTR® Identifiler PlusTM kit and the ProFlex 3x32 well PCR system. Following capillary electrophoresis on an ABI310, STR profiles and relative fluorescence units (RFU) were collected and analyzed in relation to buccal (B) or blood (P) sample DNA yield obtained with either InstaGene (IB or IP) or QIAamp Mini (QB or QP) isolation method. Kruskal Wallis and Dunn's post hoc test, adjusted by the Benjamini-Hochberg FDR were used for statistical data analysis. Results: The highest RFU (mean±SD, 3800±1315) and DNA concentration values (1.22±1.45 ng/ul) were seen in buccal samples isolated with InstaGene Matrix, when compared to IP RFU (1153±489, P=1.6x10-3) or DNA (0.06±0.012, P=4.8x10-3), and QP RFU (910±614, P=2.2x10-3) or DNA (0.02±0.035, P=9x10-5) levels. Moreover, QB RFU (3592±831) and DNA values (0.83±0.4) were significantly higher than QP RFU (910±614, P=6.9x10-4) and DNA (0.02±0.035, P=8.8x10-5) measures, which contained the highest number of DNA measurements below the lower Qubit sensitivity limit. Conversely, no difference in RFU and DNA values were observed between IP and QP, or IB and QB sample groups. Conclusion: Compared to blood stains, buccal samples provide greater DNA yield and higher STR peak values, regardless of DNA isolation method used. Conversely, InstaGene Matrix might be more reliable for blood stain DNA extraction and subsequent STR processing.

DNA isolation, Chelex, Qiagen, Instagene, STR

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