Potential for wide-scale whole-genome sequencing in humans using nanopore approaches

Wellcome Trust Centre for Human Genetics and Genomics plc first to sequence multiple human genomes

By Oxford University | December 5, 2016

Oxford University’s Wellcome Trust Centre for Human Genetics (WTCHG) and the leading genome analytics company Genomics plc today announced the first sequencing and analysis of multiple human genomes using nanopore technology.  The announcement, made on Thursday at the Oxford Nanopore Community Meeting in New York City, marks a major breakthrough in sequencing technology in opening up the potential of wide-scale whole-genome sequencing in humans using nanopore approaches.

Today’s announcement raises the possibility of a major change to both the economics and the science of DNA sequencing.  Researchers at the WTCHG and Genomics plc used the MinION sequencer developed by Oxford Nanopore Technologies. The portable MinION is a hand-held device about the size of a Mars bar, and is powered by a laptop computer to which it connects via a USB port.  It is available for $1,000 plus the cost of consumables.  While nanopore sequencing has been available for two years, it has previously only been practicable to apply it to relatively small genomes or regions of DNA, such as the much smaller genomes of viruses and bacteria.  Recent upgrades to the technology have now made it possible for researchers to conduct larger-scale studies such as sequencing complete human genomes by using multiple MinIONs.

A key strength of nanopore sequencing is that reads can be much longer than is possible with other scalable sequencing technologies.  Longer reads offer significant advantages in human genome sequencing, enabling researchers to obtain good sequence data from certain biologically important regions of the genome which are difficult to study using existing sequencing technologies.  The long reads also appear to make it easier to detect large structural changes in individual genomes.

The WTCHG and Genomics team sequenced a standard human reference sample, NA12878. In addition, in collaboration with the NIHR Oxford Biomedical Research Centre, they sequenced the DNA from a clinical patient. 

Dr Rory Bowden, Deputy Head of High-Throughput Genomics at the WTCHG, and one of the leaders of the project, said: “It is a significant breakthrough to sequence multiple human genomes with nanopore technology.  Moving forward, the idea that there will be alternative technologies with new properties in this space will be very appealing to researchers and to clinical geneticists.

Professor Michael Simpson, Co-Head of Science at Genomics plc, another project leader, said: “It is particularly encouraging to show that nanopore sequencing works for routine clinical samples, where the amount and quality of DNA available for sequencing may be constrained.  Further, in the clinical sample, the long reads provided by nanopore technology were critical in confirming the genetic changes responsible for the patient’s condition.”

Professor Peter Donnelly, Director of the WTCHG and a Founder and Director of Genomics plc, said: “The WTCHG were one of the pioneers of whole-genome sequencing in clinical medicine.  We are delighted to be able to work with nanopore technology to sequence and analyse a reference and a clinical human genome, and to explore the potential for large-scale human sequencing using nanopore approaches.” 

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