Assessing Nanopore Sequencing for Clinical Diagnostics: a Comparison of Next-Generation Sequencing (NGS) Methods for Mycobacterium tuberculosis
Carol Smith, Tanya A. Halse, Joseph Shea, Herns Modestil, Randal C. Fowler, Kimberlee A. Musser, Vincent Escuyer, Pascal Lapierre
Abstract
and phenotypic drug susceptibility testing results when available. Our assessment of 431 sequenced samples over a 32-week period demonstrates that, when using the proper quality controls and thresholds, the MinION can achieve levels of genotyping analysis and phenotypic resistance predictions comparable to those of the Illumina MiSeq at a very competitive cost per sample. Our results indicate that nanopore sequencing can be a suitable alternative to, or complement, currently used sequencing platforms in a clinical setting and has the potential to be widely adopted in public health laboratories in the near future.
Topics & Concepts
Mycobacterium tuberculosisDNA sequencingNanopore sequencingTuberculosisComputational biologyBiologyMicrobiologyVirologyMedicineGeneticsDNAPathologyMycobacterium research and diagnosisTuberculosis Research and EpidemiologyInfective Endocarditis Diagnosis and Management