PAGXXV Genomic Sequencing: New Machines, New Era for Illumina, Pacific Biosciences and Oxford Nanopore

Published: Jan 23, 2017

PAGXXV Genomic Sequencing: New Machines, New Era for Illumina, Pacific Biosciences and Oxford Nanopore January 23, 2017
By Josh Baxt, BioSpace.com Breaking News Staff

SAN DIEGO – The just-concluded International Plant and Animal Genome (PAG) conference highlighted a wide range of genomic success stories, including enhanced bioinformatics, new reference genomes and the next generation sequencers that drive the action.

Just a few days before the conference, Illumina launched their NovaSeq platform. The company displayed a NovaSeq 6000 at PAG, and more than a few people posed for pictures with the instrument.

But while Illumina has an enormous market share, there are other players, and they showcased their own recent advances. Here’s a quick survey of several technologies from Illumina, Pacific Biosciences and Oxford Nanopore Technologies on display at PAG.

Illumina

The Illumina team is more than a little excited about NovaSeq. The platform is superfast: according to the company, the 6000 can provide two billion reads in around two days, potentially accelerating population studies in animals, plants and people.

“It really let’s people in the ag space think about sequencing entire populations of animals or entire collections of germplasms for different crop species,” said Ryan Rapp, associate director of Agrigenomics at Illumina. “It opens up the door so people can tap into that catalogue of variation that’s out there, which until now has been a little bit hidden.”

Many of the discussions at PAG focused on assembling reference genomes for new species. While soybeans, corn, shrimp and salmon are known, hundreds of species remain black boxes. Wheat was finally sequenced in January 2016.

“Globally there are an enormous variety of plants and animals that make up the food supply chain for humans,” said Rapp. “As the price of sequencing becomes lower and the machines become more powerful and the bioinformatics gets better and better, it allows different crops to come online.”

Pacific Biosciences

Just around the corner from Illumina, Pacific Biosciences (PacBio) was generating a lot of interest in their Sequel System, which provides longer reads than Illumina’s technology. On January 16, PacBio announced they had sold ten Sequels to Novogene.

“The reason that everyone at the conference is so excited, and why the technology is so strong, is that it provides the longest reads, the highest accuracy and very little bias on what DNA it is sequencing,” said Jonas Korlach, chief scientific offer at PacBio.

Long reads can make it easier to discern structural variations, a compelling point for researchers studying large and complex plant genomes.

PacBio believes their technology is a clear winner at assembling new genomes, studying RNA expression, isoform sequencing, epigenetics and other applications. On the human clinical side, Korlach notes that PacBio machines are being used to characterize genes that influence how patients metabolize drugs—findings that could take the trial and error out of dosing.

Oxford Nanopore Technologies

Illumina uses sequencing by synthesis (SBS) chemistry to get their reads. As the genome is assembled, dyed nucleotides tell the instrument which base is sequenced. PacBio uses a different SBS method called single molecule real time (SMRT).

Oxford Nanopore Technologies takes a different approach. They pass DNA through a small hole (nanopore) while simultaneously passing a current through the nanopore. By measuring changes in the current, they can identify bases.

Like PacBio, Oxford Nanopore is hanging its hat on long reads. They also have a size advantage: their MinIon, with 512 nanopores, is not much larger than a candy bar. Their “big” box, PromethIon, has 48 flow cells and up to 144,000 nanopores, and is customizable to different applications.

Oxford Nanopore has steadily improved its accuracy, a problem early on. Their instruments were recently used to sequence a wild tomato species. But the technology’s greatest advantage may be its portability. Researchers from the Royal Botanic Gardens at Kew have taken MinIons into the field to study two Arabidopsis species. The technology also proved its value during the most recent Ebola. Disease surveillance may end up being one of Oxford Nanopore’s killer apps.

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