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Assessing the utility of quantitative and qualitative metrics in the DNA quantification process of skeletal remains for autosomal and Y-chromosome STR amplification purposes

  • Andrzej Doniec
    Correspondence
    Corresponding author at: Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31–033 Kraków, Poland.
    Affiliations
    Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31–033 Kraków, Poland

    Laboratory of Genetics and Evolutionism, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30–387 Kraków, Poland
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  • Miłosz Januła
    Affiliations
    Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31–033 Kraków, Poland
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  • Paweł Grzmil
    Affiliations
    Laboratory of Genetics and Evolutionism, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30–387 Kraków, Poland
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  • Tomasz Kupiec
    Affiliations
    Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31–033 Kraków, Poland
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      Highlights

      • Bone DNA samples from 80 skeletal remains were analysed using double qPCR and STR-typing.
      • Authors suggest to use at least two measurements of DNA concentration with kits with different primer variants.
      • Results may suggest a higher degradation rate of Y-chromosome comparing to autosomal DNA in some of the bone samples studied.
      • We strongly suggest that at least one of two qPCR should be based on an additional determination of the Y chromosome DI.

      Abstract

      In historical cases, ancient DNA investigations and missing persons identification, teeth or bone samples are often the only and almost always the best biological material available for DNA typing. On the other hand, DNA obtained from bone material may be characterized by a high degradation index (DI) or its low content, or DNA tests cannot be repeated due to bone piece size limitation. That is often the effect of the environment in which the material was placed and the time during which exposure to unfavorable environmental factors took place. Therefore, it is very important to use appropriate procedures related to STR analysis. For our study, we selected 80 challenging bone samples. The amount of DNA was compared in qPCR using Quantifiler™ Trio DNA Quantification Kit and Investigator® Quantiplex® Pro RGQ. All qPCR results were confirmed by PCR-CE. The results of DNA concentrations and the assigned degradation index (DI) differed significantly within analyzed samples (~10%). Additionally, the Y-chromosome DI also differed from the autosomal DI in the samples. The difference in degradation indexes could explain the lower Y-chromosome amplification success rate compared to autosomal e.g. during human identification process. The results indicate that performing two DNA quantifications with the use of two different kits (primers sets) allows for a much more precise evaluation of the DNA quality and quantity in the isolate. We suggest that at least one of two suggested DNA concentration measurements should be based on an additional determination of the Y chromosome degradation index. Altogether, it allows for rational isolate management, especially when the volume is limited and the sample is unique.

      Keywords

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