A performance study on three qPCR quantification kits and their compatibilities with the 6-dye DNA profiling systems

Forensic Sci Int Genet. 2018 Mar:33:72-83. doi: 10.1016/j.fsigen.2017.11.016. Epub 2017 Dec 2.

Abstract

DNA quantification plays an integral role in forensic DNA profiling. Not only does it estimate the total amount of amplifiable human autosomal and male DNA to ensure optimal amplification of target DNA for subsequent analysis, but also assesses the extraction efficiency and purity of the DNA extract. Latest DNA quantification systems even offer an estimate for the degree of DNA degradation in a sample. Here, we report the performance of three new generation qPCR kits, namely Investigator® Quantiplex HYres Kit from QIAGEN, Quantifiler® Trio DNA Quantification Kit from Applied Biosystems™, and PowerQuant® System from Promega, and their compatibilities with three 6-dye DNA profiling systems. Our results have demonstrated that all three kits generate standard curves with satisfactory consistency and reproducibility, and are capable of screening out traces of male DNA in the presence of 30-fold excess of female DNA. They also exhibit a higher tolerance to PCR inhibition than Quantifiler® Human DNA Quantification Kit from Applied Biosystems™ in autosomal DNA quantification. PowerQuant®, as compared to Quantiplex HYres and Quantifiler® Trio, shows a better precision for both autosomal and male DNA quantifications. Quantifiler® Trio and PowerQuant® in contrast to Quantiplex HYres offer better correlations with lower discrepancies between autosomal and male DNA quantification, and their additional degradation index features provide a detection platform for inhibited and/or degraded DNA template. Regarding the compatibility between these quantification and profiling systems: (1) both Quantifiler® Trio and PowerQuant® work well with GlobalFiler and Fusion 6C, allowing a fairly accurate prediction of their DNA typing results based on the quantification values; (2) Quantiplex HYres offers a fairly reliable IPC system for detecting any potential inhibitions on Investigator 24plex, whereas Quantifiler® Trio and PowerQuant® suit better for GlobalFiler and Fusion 6C.

Keywords: DNA quantification; Forensic DNA typing; Investigator quantiplex HYres; PowerQuant; Quantifiler trio.

Publication types

  • Evaluation Study

MeSH terms

  • DNA Degradation, Necrotic
  • DNA Fingerprinting*
  • Female
  • Hemin
  • Humans
  • Humic Substances
  • Male
  • Microsatellite Repeats
  • Real-Time Polymerase Chain Reaction / instrumentation*
  • Tannins

Substances

  • Humic Substances
  • Tannins
  • Hemin