World first: continuous DNA sequence of more than a million bases achieved with nanopore sequencing.
Wed 27th December 2017
The first >1Mb DNA sequence (more than a million DNA bases in one continuous sequence) has been achieved using Oxford Nanopore sequencing technology, a landmark in the history of DNA sequencing.
Martin Smith, a researcher at the Kinghorn Centre for Clinical Genomics (at the Garvan Institute, Australia), has sequenced the first single fragment of DNA greater than 1Mb. The analogy used today by researchers is: if a nanopore was the size of a fist, a 1MB strand of DNA passing through that nanopore would be 3.2km long (credit Adam Philippy).
The read, from Chromosome 19, is 1.015 Mb in length and the alignment co-ordinates are: chr19 55982604 57017360e4f54091-8303-4643-8e5d-e07bfa1ef17360 - chr19 57018389 57021968e4f54091-8303-4643-8e5d-e07bfa1ef1731
The read ID is e4f54091-8303-4643-8e5d-e07bfa1ef173. It is available online here.
The method used the open RAD003 protocol provided by Nick Loman and Josh Quick, which can be found here: lab.loman.net/protocols
Why long reads, and why ultra-long reads?
Traditional short-read DNA sequencing technologies may provide data that is harder to assemble into a complete genome or dataset, like a jigsaw puzzle made from a large number of small pieces.
Nanopore sequencing is dependent on sample preparation, sequencing the fragment that is prepared. Researchers are now routinely sequencing fragments of 10s or 100s kb.
With long reads, and even more so with ultra-long reads that are 100s of kb long, it is easier to assemble genomes. For more information, read this white paper on genome assembly (registration may be required).
With long reads, it is also possible to span tricky regions or even characterise regions that have not been sequenced. It is estimated that ~8% of the human genome remains unsequenced (1). For a flavour of the use of nanopore sequencing for this purpose, watch Karen Miga’s talk on spanning the centromere, review these human genome assemblies from the nanopore consortium and Wigard Kloosterman, or review other papers that make use of nanopore long reads.
Long reads are also critical when resolving structural variation. This structural variation white paper reviews the use of nanopore for SVs.
1. Miga et al Nucleic Acids Research 43(20) e133