Beyond Homopolymer Errors: a Systematic Investigation of Nanopore-based DNA Sequencing Characteristics Using HLA-DQA2

  • Péter Sárközy Department of Measurement and Information Systems, Faculty of Electrical Engineering and Informatics, Budapest University of Technology and Economics, Hungary
  • Viktor Molnár Department of Genetics, Cell- and Immunobiology, Semmelweis University, Hungary
  • Dóra Fogl Department of Measurement and Information Systems, Faculty of Electrical Engineering and Informatics, Budapest University of Technology and Economics, Hungary
  • Csaba Szalai Department of Genetics, Cell- and Immunobiology, Semmelweis University, Hungary
  • Péter Antal Department of Measurement and Information Systems, Faculty of Electrical Engineering and Informatics, Budapest University of Technology and Economics, Hungary

Abstract

Electronic, nanopore based single molecule real-time DNA sequencing technology offers very long, albeit lower accuracy reads in sharp contrast to existing next-generation sequencing methods, which offer short, high-accuracy reads in abundance. We provide a systematic review of the error characteristics of this new sequencing platform, and demonstrate the most challenging aspects in the field of whole gene sequencing through the human HLA-DQA2 gene using long-range PCR products on multiplexed samples. We consider the limitations of these errors for the applications of this technology, and also indicate prospective improvements and expected thresholds with respect to these errors.

Keywords: nanopore, DNA sequencing, next-generation sequencing, error characteristics
Published online
2017-05-23
How to Cite
Sárközy, P., Molnár, V., Fogl, D., Szalai, C. and Antal, P. (2017) “Beyond Homopolymer Errors: a Systematic Investigation of Nanopore-based DNA Sequencing Characteristics Using HLA-DQA2”, Periodica Polytechnica Electrical Engineering and Computer Science, 61(3), pp. 231-237. doi: https://doi.org/10.3311/PPee.10015.
Section
Articles