Combining Two Technologies for Full Genome Sequencing of Human

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  • Authors: Skryabin KG1, Prokhortchouk EB1, Mazur AM1, Boulygina ES1, Tsygankova SV1, Nedoluzhko AV1, Rastorguev SM1, Matveev VB2, Chekanov NN3, Goranskaya DA3, Teslyuk AB1, Gruzdeva NM1, Velikhov VE1, Zaridze DG2, Kovalchuk MV1
  • Affiliations:
    1. Russian Research Centre Kurchatov Institute
    2. Institute of Carcinogenesis, Blokhin Cancer Research Center, Russian Academy of Medical Sciences
    3. Bioengineering Center, Russian Academy of Sciences
  • Issue: Vol 1, No 3 (2009)
  • Pages: 102-107
  • Section: Articles
  • URL: http://actanaturae.ru/2075-8251/article/view/10789
  • DOI: https://doi.org/10.32607/20758251-2009-1-3-102-107
  • Cite item

Abstract


At present, the new technologies of DNA sequencing are rapidly developing allowing quick and efficient characterisation of organisms at the level of the genome structure. In this study, the whole genome sequencing of a human (Russian man) was performed using two technologies currently present on the market - Sequencing by Oligonucleotide Ligation and Detection (SOLiDTM) (Applied Biosystems) and sequencing technologies of molecular clusters using fluorescently labeled precursors (Illumina). The total number of generated data resulted in 108.3 billion base pairs (60.2 billion from Illumina technology and 48.1 billion from SOLiD technology). Statistics performed on reads generated by GAII and SOLiD showed that they covered 75% and 96% of the genome respectively. Short polymorphic regions were detected with comparable accuracy however, the absolute amount of them revealed by SOLiD was several times less than by GAII. Optimal algorithm for using the latest methods of sequencing was established for the analysis of individual human genomes. The study is the first Russian effort towards whole human genome sequencing.

Progress in the development of novel DNA sequencing technologies allowing rapid and accurate determination of the distinctive features of an individual at the level of the structure of his genome has made genomics one of the most rapidly developing scientific disciplines. At present, three advanced technologies of DNA sequencing are in use: pyrosequencing based on the “sequencing-by-synthesis” principle and commercialized in a next-generation Roche GS-FLX capillary genome sequencing system (454 Life Science Inc./Roche), cyclic sequencing by oligonucleotide ligation and detection (SOLiD, Applied Biosystems), and high-throughput DNA molecular cluster sequencing-by-synthesis using proprietary fluorescently labeled oligonucleotides (Illumina GAII Genome Analyzer, previously known as SOLEXA). These platforms have already demonstrated their significant worth: in the last two years, five new genomes have been read – in addition to the reference genome sequence that was determined by several leading research groups at institutes in the U.S., United Kingdom, and Canada in the course of 10 years and at a cost of 3 bln dollars [1] – such as the genomes of outstanding biologists of our times[2, 3], that of a Nigerian man [4, 5], a Chinese [6], and a Korean [7], not to mention thousands of other eukaryotic and prokaryotic species sequenced [8]. All these projects only became possible thanks to advanced technologies allowing cost-effective and high-throughput sequencing.

K G Skryabin

Russian Research Centre Kurchatov Institute

E B Prokhortchouk

Russian Research Centre Kurchatov Institute

Email: prokhortchouk@biengi.ac.ru

A M Mazur

Russian Research Centre Kurchatov Institute

E S Boulygina

Russian Research Centre Kurchatov Institute

S V Tsygankova

Russian Research Centre Kurchatov Institute

A V Nedoluzhko

Russian Research Centre Kurchatov Institute

S M Rastorguev

Russian Research Centre Kurchatov Institute

V B Matveev

Institute of Carcinogenesis, Blokhin Cancer Research Center, Russian Academy of Medical Sciences

N N Chekanov

Bioengineering Center, Russian Academy of Sciences

D A Goranskaya

Bioengineering Center, Russian Academy of Sciences

A B Teslyuk

Russian Research Centre Kurchatov Institute

N M Gruzdeva

Russian Research Centre Kurchatov Institute

V E Velikhov

Russian Research Centre Kurchatov Institute

D G Zaridze

Institute of Carcinogenesis, Blokhin Cancer Research Center, Russian Academy of Medical Sciences

M V Kovalchuk

Russian Research Centre Kurchatov Institute

  1. Lander E., Linton L., Birren B., Nusbaum C., Zody M., et al. // Nature 2001. V. 409. PP.860–921.
  2. Levy S., Sutton G., N g P., Feuk L., Halpern A., et al. // PLoS Biology. 2007. Sep 4;5(10):e254.
  3. Wheeler D., Srinivasan M., Egholm M., Shen Y., Chen L., et al. // Nature. 2008. V. 452. PP. 872–876.
  4. Bentley D., Balasubramanian S., Swerdlow H., Smith G., Milton J., et al. // Nature. 2008. V. 456. PP. 53–59.
  5. McKernan K., Peckham H., Costa G., McLaughlin S., Fu Y., et al. // Genome Research. 2009. V. 19. № 9. № 1527–1541.
  6. Wang J., Wang W., Li R., Li Y., Tian G. // Nature. 2008. V. 456. PP. 60 – 65.
  7. Ahn S., Kim T., Lee S., Kim D., Ghang H., et al. // Genome Research. 2009. V. 19. № 9. PP. 1622–1629.
  8. http://www.ncbi.nlm.nih.gov/guide/genomes

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Copyright (c) 2009 Skryabin K.G., Prokhortchouk E.B., Mazur A.M., Boulygina E.S., Tsygankova S.V., Nedoluzhko A.V., Rastorguev S.M., Matveev V.B., Chekanov N.N., Goranskaya D.A., Teslyuk A.B., Gruzdeva N.M., Velikhov V.E., Zaridze D.G., Kovalchuk M.V.

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