Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology

Abstract

MinION is a memory stick–sized nanopore-based sequencer designed primarily for single-molecule sequencing of long DNA fragments (>6 kb). We developed a library preparation and data-analysis method to enable rapid real-time sequencing of short DNA fragments (<1 kb) that resulted in the sequencing of 500 reads in 3 min and 40,000–80,000 reads in 2–4 hr at a rate of 30 nt/sec. We then demonstrated the clinical applicability of this approach by performing successful aneuploidy detection in prenatal and miscarriage samples with sequencing in <4 hr. This method broadens the application of nanopore-based single-molecule sequencing and makes it a promising and versatile tool for rapid clinical and research applications.

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

“…The typical turnaround time for aneuploidy detection in such samples is 1–3 weeks when using NGS platforms [59]. Wei and Williams [38] used the MinION to detect aneuploidy in prenatal and miscarriage samples in under 4 h. They concluded that the MinION can be used for aneuploidy detection in a clinical setting.…”

“…To date, only MinION-based strand sequencing has been successfully employed by independent genomics laboratories. Where possible, this review focuses on peer-reviewed research performed using the MinION [1, 7–38]. …”

Oxford Nanopore MinION Sequencing and Genome Assembly

“…Future diagnostic support could revolutionize the ability of the researchers working in the public health sector to perform sequencing during future disease outbreaks. Other diagnostic applications have also been reported, including prediction of antibiotic resistance by sequencing the genomes of Staphylococcus aureus and Mycobacterium tuberculosis [62]; real-time strain typing and analysis of antibiotic resistance [63]; and aneuploidy detection in prenatal and miscarriage samples with sequencing reads generated in less than 4 h [64] just to name a few. Please visit https://publications.nanoporetech.com for an up-to-date list of applications and publications using ONT sequencing.…”

Technological advances in precision medicine and drug development

“…Both of these technologies are more error-prone than current NGS systems, but workarounds are possible with a hybrid sequencing effort, using high-quality NGS short read information for error correction in the longer TGS reads [141]. Furthermore, despite these error rates, it has been demonstrated that even at extremely low coverage (58,000 reads compared to Illumina or Ion’s millions of reads typically generated), MinION has potential clinical applications in prenatal testing, accurately assessing aneuploidy in 2–4 hours using a short read sequencing library preparation [142]. …”