MinION™ device: latest advancements in next-generation DNA sequencing

Bethany Blank
Bethany Blank
University of Wisconsin
Stevens Point

Bethany A. Blank ¹, Scott J. Hebbring¹, Steven J. Schrodi¹, Zhan (Harold) Ye²
¹Center for Human Genetics, ²Biomedical Informatics Research Center

Research area: Genetics

Background: Advancements in next-generation sequencing (NGS) technologies are attempting to develop sequencing methods that are faster, more accurate, cheaper, and produce longer reads. The newest methods use single-molecule sequencing (SMS) to directly read DNA without the need of PCR amplification. As part of an early access program from Oxford Nanopore Technologies Ltd, we tested the capabilities and limitations of the MinION™ device, which uses nanopore technology for SMS, to determine the utility of the new technology.

Method: Seven DNA libraries were prepared from a lambda phage genome following the Oxford Nanopore Genomic DNA Sequencing Kit protocol. Libraries were loaded into the MinION Flow Cell and read using the MinKNOW™ software. Basecalling was performed using Metrichor™ software. Transformed data was then mapped to the reference sequence to determine quality, accuracy, and coverage.

Results: Quality of the MinION Flow Cells was quite varied ranging from greater than 100 to less than 400 active channels out of 512, greatly impacting the number of reads generated per library. Read length of fragments ranged from 5 to 109,320 bases, with an average of 4-5 kilobases compared to 200-300 bases using current NGS technologies. Basecalling quality averaged around a Phred score of 7 for bidirectional reads, which is significantly lower than current NGS technologies.

Conclusion: The MinION™ is a promising new DNA sequencing technology which after further development will likely be effective as a DNA sequencing device. The device’s ability to directly read DNA has many significant advantages, including eliminating the need for PCR and allowing more accurate de novo sequencing using longer DNA reads. However, issues relating to uncertain basecalling accuracy and quality, inconsistent flow cell quality, and development of compatible analysis tools must first be addressed.