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Method for the Search for the Size Standard Peaks in Fragment Analysis of DNA

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Abstract

Fragment analysis of DNA by the capillary gel-electrophoresis method is an effective tool for studying the DNA structure, which has a large number of applications (in particular, for genetic expertise of breeds and breed samples of a number of important crops). Fragment analysis of DNA is carried out in several stages. The stage of processing of the results of investigations includes the procedure of detection of peaks for standard DNA fragments. We list the features of the spectrum of the DNA fragment distribution, which necessitate the development of a new method for detecting peaks of a standard. We propose a method for their search based on comparison of the aggregate of standard lengths of DNA fragments and spectral peaks and describe the algorithm for implementing this method. We also consider in detail the critical stage of the algorithm, i.e., the choice of the threshold for the procedure of detection of peaks in the spectrum. The advantages and disadvantages of the method are enumerated and the results of testing are considered.

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ACKNOWLEDGMENTS

The study was supported by the Federal Agency of Scientific Organizations of Russia under the subprogram “Development of Selection and Potato Seed Farming in the Russian Federation” of the Federal Scientific and Technical Program of Development of Agriculture for 2017–2025 “Development of Software for Genetic Enterprise of Potato Breeds and Breed Samples,” and additional state assignment no. 007-02-2014 of the Institute of Analytic Instrument Making of the Russian Academy of Sciences dated November 18, 2017. The research was performed on high-cost equipment “NANOFOR 05” genetic analyzer of the Collective Use Center Biotechnology, Federal State Budget Scientific Enterprise, All-Russia Research Institute of Agricultural Biotechnology.

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Authors and Affiliations

  1. Institute for Analytical Instrumentation, Russian Academy of Sciences, 190103, St. Petersburg, Russia

    I. V. Zarutskii, V. V. Manoilov, N. S. Samsonova, A. I. Petrov, V. E. Kurochkin & I. A. Leont’ev

  2. ITMO University, 197101, St. Petersburg, Russia

    I. V. Zarutskii & V. V. Manoilov

  3. Ioffe Institute, Russian Academy of Sciences, 194021, St. Petersburg, Russia

    N. S. Samsonova

  4. OOO Sintol, 127550, Moscow, Russia

    Ya. I. Alekseev

  5. All-Russia Research Institute of Agricultural Biotechnology, 127550, Moscow, Russia

    Ya. I. Alekseev

Authors
  1. I. V. Zarutskii
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  2. V. V. Manoilov
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  3. N. S. Samsonova
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  4. A. I. Petrov
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  5. V. E. Kurochkin
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  6. I. A. Leont’ev
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  7. Ya. I. Alekseev
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Correspondence to I. V. Zarutskii.

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Translated by N. Wadhwa

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Zarutskii, I.V., Manoilov, V.V., Samsonova, N.S. et al. Method for the Search for the Size Standard Peaks in Fragment Analysis of DNA. Tech. Phys. 63, 1364–1369 (2018). https://doi.org/10.1134/S1063784218090244

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  • DOI: https://doi.org/10.1134/S1063784218090244

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