Rapid short-read sequencing and aneuploidy detection using MinION nanopore technology

MinION™ is a memory stick-sized, nanopore-based sequencer primarily designed 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) and resulted in sequencing of 500 reads in 3 min and 40,000-80,000 reads in 2-4 hours at a rate of 30 nt/s. We then demonstrated the clinical applicability of this approach by performing successful aneuploidy detection in prenatal and miscarriage samples with sequencing in <4 hours. This method broadens the application of nanopore-based single-molecule sequencing and makes it a promising versatile tool for rapid clinical and research applications.