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Effects of humic acid on DNA quantification with Quantifiler® Human DNA Quantification kit and short tandem repeat amplification efficiency

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Abstract

Correct DNA quantification is an essential part to obtain reliable STR typing results. Forensic DNA analysts often use commercial kits for DNA quantification; among them, real-time-based DNA quantification kits are most frequently used. Incorrect DNA quantification due to the presence of PCR inhibitors may affect experiment results. In this study, we examined the alteration degree of DNA quantification results estimated in DNA samples containing a PCR inhibitor by using a Quantifiler® Human DNA Quantification kit. For experiments, we prepared approximately 0.25 ng/μl DNA samples containing various concentrations of humic acid (HA). The quantification results were 0.194–0.303 ng/μl at 0–1.6 ng/μl HA (final concentration in the Quantifiler reaction) and 0.003–0.168 ng/μl at 2.4–4.0 ng/μl HA. Most DNA quantity was undetermined when HA concentration was higher than 4.8 ng/μl HA. The C T values of an internal PCR control (IPC) were 28.0–31.0, 36.5–37.1, and undetermined at 0–1.6, 2.4, and 3.2 ng/μl HA. These results indicate that underestimated DNA quantification results may be obtained in the DNA sample with high C T values of IPC. Thus, researchers should carefully interpret the DNA quantification results. We additionally examined the effects of HA on the STR amplification by using an Identifiler® kit and a MiniFiler™ kit. Based on the results of this study, it is thought that a better understanding of various effects of HA would help researchers recognize and manipulate samples containing HA.

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Acknowledgements

This work was supported by grant no 04-2010-0500 from the Seoul National University Hospital (SNUH) Research Fund and by Future-based Technology Development Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (No. 2010-0020631).

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Authors and Affiliations

  1. Department of Forensic Medicine, College of Medicine, Seoul National University, 28, Yongon-Dong, Chongno-Gu, Seoul, 110-799, South Korea

    Seung Bum Seo, Hye Young Lee, Ai Hua Zhang & Soong Deok Lee

  2. DNA Analysis Laboratory, Division of Forensic Science, Supreme Public Prosecutor’s Office, Seoul, 137-730, South Korea

    Hye Yeon Kim

  3. Department of Anatomy, College of Medicine, Seoul National University, Seoul, 110-799, South Korea

    Dong Hoon Shin

  4. Institute of Forensic Medicine, College of Medicine, Seoul National University, Seoul, 110-799, South Korea

    Dong Hoon Shin & Soong Deok Lee

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  1. Seung Bum Seo
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  2. Hye Young Lee
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  3. Ai Hua Zhang
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  4. Hye Yeon Kim
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  5. Dong Hoon Shin
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Correspondence to Soong Deok Lee.

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Seo, S.B., Lee, H.Y., Zhang, A.H. et al. Effects of humic acid on DNA quantification with Quantifiler® Human DNA Quantification kit and short tandem repeat amplification efficiency. Int J Legal Med 126, 961–968 (2012). https://doi.org/10.1007/s00414-011-0616-z

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  • DOI: https://doi.org/10.1007/s00414-011-0616-z

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