International Journal of Legal Medicine

, Volume 127, Issue 1, pp 55–61 | Cite as

A real-time PCR-based amelogenin Y allele dropout assessment model in gender typing of degraded DNA samples

  • Kyung-Yong Kim
  • Younghyuk Kwon
  • Munkhtsetseg Bazarragchaa
  • Ae-Ja Park
  • Hyowon Bang
  • Won-Bok Lee
  • Junyoung Lee
  • Kwang-Ho Lee
  • Bum-Joon Kim
  • Kijeong KimEmail author
Technical Note


Allelic dropout due to stochastic variation in degraded small quantity DNA appears to be one of the most serious genotyping errors. Most methods require PCR replication to address this problem. The small amounts of valuable samples are often a limitation for such replications. We report a real-time PCR-based amelogonin Y (AMELY) allele dropout estimation model in an AMEL-based gender typing. We examined 915 replicates of AMELY-positive modern male DNA with varying amounts of DNA and humic acid. A male-specific AMEL fragment (AMELy) dropped out in 143 genuine male replicates, leading to gender typing errors. By graphing a scatter plot of the crossing point versus the end cycle fluorescence of the male replicates, a standard graph model for the estimation of the AMELy allele dropout was constructed with the dropout-prone and dropout-free zones. This model was then applied to ancient DNA (aDNA) samples. Nine samples identified as female were found in the dropout-prone zone; with higher DNA concentrations, six were shifted to the dropout-free zone. Among them, two female identifications were converted to male. All the aDNA gender was confirmed by sex-determination region Y marker amplification. Our data suggest that this model could be a basic approach for securing AMELy allele dropout-safe data from the stochastic variation of degraded inhibitory DNA samples.


AMELY allele dropout Ancient bone Real-time PCR Melting curve analysis Amelogenin 



We thank Jehyeok Lee and Yeong-mi Chang for their kind assistance in administration work and purchase of laboratory materials. We also thank Jee-hyun Yoon for the maintenance of the real-time PCR system. This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2010-0021367).

Ethical standards

All sampling was done according to Korean laws and ethical standards.

Conflict of interest

The authors declare that there is no conflict of interest.

Supplementary material

414_2011_663_MOESM1_ESM.pdf (149 kb)
ESM 1 (PDF 149 kb)
414_2011_663_MOESM2_ESM.pdf (228 kb)
ESM 2 (PDF 228 kb)


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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Kyung-Yong Kim
    • 1
    • 3
  • Younghyuk Kwon
    • 2
  • Munkhtsetseg Bazarragchaa
    • 2
  • Ae-Ja Park
    • 1
    • 4
  • Hyowon Bang
    • 1
    • 5
  • Won-Bok Lee
    • 3
  • Junyoung Lee
    • 7
  • Kwang-Ho Lee
    • 6
  • Bum-Joon Kim
    • 8
  • Kijeong Kim
    • 9
    • 10
    Email author
  1. 1.Institute for Medical SciencesChung-Ang UniversitySeoulSouth Korea
  2. 2.Department of Microbiology, College of Medicine and Medical SchoolChung-Ang UniversitySeoulSouth Korea
  3. 3.Department of Anatomy, College of Medicine and Medical SchoolChung-Ang UniversitySeoulSouth Korea
  4. 4.Department of Laboratory Medicine, College of Medicine and Medical SchoolChung-Ang UniversitySeoulSouth Korea
  5. 5.Department of Physiology, College of Medicine and Medical SchoolChung-Ang UniversitySeoulSouth Korea
  6. 6.Department of Life Science, College of Natural ScienceChung-Ang UniversitySeoulSouth Korea
  7. 7.The Hun School of PrincetonPrincetonUSA
  8. 8.Department of Microbiology, College of MedicineSeoul National UniversitySeoulSouth Korea
  9. 9.Institute for Medical Sciences, College of Medicine and Medical SchoolChung-Ang UniversitySeoulSouth Korea
  10. 10.Department of Microbiology, College of Medicine and Medical SchoolChung-Ang UniversitySeoulSouth Korea

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