title: The application of Nanopore sequencing for variant calling on the human mitochondrial DNA
metadata.name: dc.contributor.author
metadata.value: Shikov, Anton
metadata.lang: -
metadata.name: dc.contributor.author
metadata.value: Tsay, Viktoriya
metadata.lang: -
metadata.name: dc.contributor.author
metadata.value: Fedyakov, Mikhail
metadata.lang: -
metadata.name: dc.contributor.author
metadata.value: Eismont, Yuri
metadata.lang: -
metadata.name: dc.contributor.author
metadata.value: Rudnik, Alena
metadata.lang: -
metadata.name: dc.contributor.author
metadata.value: Urasov, Stanislav
metadata.lang: -
metadata.name: dc.contributor.author
metadata.value: Sherbak, Sergey
metadata.lang: -
metadata.name: dc.contributor.author
metadata.value: Glotov, Oleg
metadata.lang: -
metadata.name: dc.date.accessioned
metadata.value: 2021-08-20T19:45:39Z
metadata.lang: -
metadata.name: dc.date.available
metadata.value: 2021-08-20T19:45:39Z
metadata.lang: -
metadata.name: dc.date.issued
metadata.value: 2021-06
metadata.lang: -
metadata.name: dc.identifier.citation
metadata.value: Shikov, A., Tsay, V., Fedyakov, M., Eismont, Y., Rudnik, A., Urasov, S., Sherbak, S., and Glotov, O. 2021. The application of Nanopore sequencing for variant calling on the human mitochondrial DNA. Bio. Comm. 66(2): 109–123.
metadata.lang: en_GB
metadata.name: dc.identifier.other
metadata.value: https://doi.org/10.21638/spbu03.2021.202
metadata.lang: -
metadata.name: dc.identifier.uri
metadata.value: http://hdl.handle.net/11701/32813
metadata.lang: -
metadata.name: dc.description.abstract
metadata.value: The emergence of long-read sequencing technologies has made a revolutionary
  step in genome biology and medicine. However, long reads are characterized
  by a relatively high error rate, impairing their usage for variant calling as a part
  of routine practice. Thus, we here examine different popular variant callers on
  long-read sequences of the human mitochondrial genome, convenient in terms
  of small size and easily obtained high coverage. The sequencing of mitochondrial
  DNA from 8 patients was conducted via Illumina (MiSeq) and the Oxford
  Nanopore platform (MinION), with the former utilized as a gold standard when
  evaluating variant calling’s accuracy. We used a conventional GATK3-BWA-based
  pipeline for paired-end reads and Guppy basecaller coupled with minimap2
  for MinION data, respectively. We then compared the outputs of Clairvoyante,
  Nanopolish, GATK3, Longshot, DeepVariant, and Varscan tools applied on longread
  alignments by analyzing false-positive and false-negative rates. While for
  most callers, raw signals represented false positives due to homopolymeric
  errors, Nanopolish demonstrated both high similarity (Jaccard coefficient of
  0.82) and a comparable number of calls with the Illumina data (140 vs. 154)
  with the best performance according to AUC (area under ROC curve, 0.953) as
  well. In sum, our results, despite being obtained from a small dataset, provide
  evidence that sufficient coverage coupled with an optimal pipeline could make
  long reads of mitochondrial DNA applicable for variant calling.
metadata.lang: en_GB
metadata.name: dc.language.iso
metadata.value: en
metadata.lang: en_GB
metadata.name: dc.publisher
metadata.value: St Petersburg State University
metadata.lang: en_GB
metadata.name: dc.relation.ispartofseries
metadata.value: Biological Сommunications;Volume 66; Issue 2
metadata.lang: -
metadata.name: dc.subject
metadata.value: next-generation sequencing
metadata.lang: en_GB
metadata.name: dc.subject
metadata.value: Oxford Nanopore
metadata.lang: en_GB
metadata.name: dc.subject
metadata.value: Illumina
metadata.lang: en_GB
metadata.name: dc.subject
metadata.value: variant calling
metadata.lang: en_GB
metadata.name: dc.subject
metadata.value: mitochondrial DNA
metadata.lang: en_GB
metadata.name: dc.title
metadata.value: The application of Nanopore sequencing for variant calling on the human mitochondrial DNA
metadata.lang: en_GB
metadata.name: dc.type
metadata.value: Article
metadata.lang: en_GB
resources.filename: 109-123.pdf
resources.url: https://dspace.spbu.ru/bitstream/11701/32813/1/109-123.pdf
resources.format: Adobe PDF
resources.size: 5,58 MB