NanoVar: accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing

Genome Biol. 2020 Mar 3;21(1):56. doi: 10.1186/s13059-020-01968-7.


The recent advent of third-generation sequencing technologies brings promise for better characterization of genomic structural variants by virtue of having longer reads. However, long-read applications are still constrained by their high sequencing error rates and low sequencing throughput. Here, we present NanoVar, an optimized structural variant caller utilizing low-depth (8X) whole-genome sequencing data generated by Oxford Nanopore Technologies. NanoVar exhibits higher structural variant calling accuracy when benchmarked against current tools using low-depth simulated datasets. In patient samples, we successfully validate structural variants characterized by NanoVar and uncover normal alternative sequences or alleles which are present in healthy individuals.

Keywords: Long reads; Low depth; Oxford Nanopore sequencing; SV characterization; Structural variants; Third-generation sequencing; WGS.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cells, Cultured
  • Genetic Testing / methods*
  • Genetic Testing / standards
  • Genomic Structural Variation*
  • HCT116 Cells
  • Humans
  • Leukemia, Myeloid / genetics*
  • Leukemia, Myeloid / pathology
  • Nanopore Sequencing / methods*
  • Nanopore Sequencing / standards
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Sequence Analysis, DNA / methods*
  • Sequence Analysis, DNA / standards