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Indel analysis by droplet digital PCR: a sensitive method for DNA mixture detection and chimerism analysis

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Abstract

Several methods have been developed to determinate genetic profiles from a mixed samples and chimerism analysis in transplanted patients. The aim of this study was to explore the effectiveness of using the droplet digital PCR (ddPCR) for mixed chimerism detection (a mixture of genetic profiles resulting after allogeneic hematopoietic stem cell transplantation (HSCT)). We analyzed 25 DNA samples from patients who had undergone HSCT and compared the performance of ddPCR and two established methods for chimerism detection, based upon the Indel and STRs analysis, respectively. Additionally, eight artificial mixture DNA samples were created to evaluate the sensibility of ddPCR. Our results show that the chimerism percentages estimated by the analysis of a single Indel using ddPCR were very similar to those calculated by the amplification of 15 STRs (r 2 = 0.970) and with the results obtained by the amplification of 38 Indels (r 2 = 0.975). Moreover, the amplification of a single Indel by ddPCR was sensitive enough to detect a minor DNA contributor comprising down to 0.5 % of the sample. We conclude that ddPCR can be a powerful tool for the determination of a genetic profile of forensic mixtures and clinical chimerism analysis when traditional techniques are not sensitive enough.

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Acknowledgments

We thank Dr. Piris and his team for their help in the development of this study.

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Authors and Affiliations

  1. Unit of Legal Medicine, Department of Physiology and Pharmacology, University of Cantabria, Av Cardenal Herrera Oria s/n, 39011, Santander, Spain

    Ana Santurtún, Jana Arozamena & María T. Zarrabeitia

  2. Department of Internal Medicine, Hospital U.M. Valdecilla, IFIMAV, University of Cantabria, 39011, Santander, Spain

    José A. Riancho

  3. Service of Hematology, Hospital U.M. Valdecilla, Santander, Spain

    Mónica López-Duarte

Authors
  1. Ana Santurtún
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  2. José A. Riancho
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  3. Jana Arozamena
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  4. Mónica López-Duarte
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  5. María T. Zarrabeitia
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Correspondence to Ana Santurtún.

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Santurtún, A., Riancho, J.A., Arozamena, J. et al. Indel analysis by droplet digital PCR: a sensitive method for DNA mixture detection and chimerism analysis. Int J Legal Med 131, 67–72 (2017). https://doi.org/10.1007/s00414-016-1422-4

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  • DOI: https://doi.org/10.1007/s00414-016-1422-4

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