10X Genomics Announces a High-Throughput Platform for Synthetic Long Reads

January 14, 2015

By Aaron Krol 

January 14, 2015 | There is a growing appreciation in the genomics community that the next-generation sequencing revolution, which has led the pace of DNA sequencing to skyrocket and prices to plummet over the past decade, has come at some cost to accuracy. Illumina’s short-read sequencers, which generate well over 90% of all DNA data today, are the fastest and most efficient on the market, and remarkably accurate at calling DNA bases. But because they work by splitting the genome into millions of very small fragments, even the best computational pipelines can’t use their data to reassemble a perfect picture of the whole genome. Complicated rearrangements and duplications, and information on which fragments come from the maternal and paternal chromosomes, inevitably get left out.

“We’re getting lots of information, but it all has this fragmentary sense to it,” said Serge Saxonov, CEO of 10X Genomics, in an interview with Bio-IT World. “We know that we’re missing a lot, and we don’t even know necessarily everything that we’re missing.”

Today, the major genome centers are more and more turning to Pacific Biosciences to solve this problem. PacBio’s long-read sequencers, which can work with DNA fragments as much as 100 times longer than those read by Illumina’s instruments, have done a remarkable job patching the gaps while preserving most of the gains of next-gen sequencing. But they are cost-prohibitive for smaller labs that want to do sequencing at any significant scale. Saxonov’s company, which made its public debut at the J.P. Morgan Healthcare Conference in San Francisco this week and announced a Series B funding round that brings its total backing to $80 million, wants to bring PacBio-quality data to any lab with an Illumina sequencer.

“PacBio has been doing a great job of educating the market,” said Saxonov. “What we’re doing is leveraging the existing install base of Illumina sequencers, so people can make use of their existing investment.” To do that, 10X Genomics is releasing an as-yet-unnamed benchtop instrument that will work alongside a DNA sequencer, combined with proprietary software and chemistry. The instrument, around the size of a lunchbox, will retail at $75,000, a fraction of the price of any high-throughput sequencer; consumable prices have not been released.

While 10X is still cagey about the details of its technology, Saxonov did confirm the basics: the user places long DNA fragments in the 10X instrument, which separates each piece of DNA into its own microfluidic chamber. There, the DNA is labeled with a unique molecular tag. The user then retrieves her sample, fragments it into shorter pieces for sequencing, and runs an Illumina sequencer as usual. Finally, 10X’s software scans the raw sequence files for the company’s molecular tags, and uses them to digitally recover the original long fragments.

The process is very similar to Illumina’s own synthetic long-read technology, acquired with its purchase of Moleculo in 2013, and since rebranded as part of the TruSeq sample preparation line. A TruSeq long-read kit has been available to Illumina customers since summer 2014, and seems to offer real improvements over standard short-read sequencing, although it still struggles with highly repetitive regions of the genome.

Rob Tarbox, 10X’s Vice President of Marketing, acknowledged the similarity to Moleculo, but added that “what is different about our approach is that it is inherently more scalable, and a bit more friendly to customers’ existing workflows.” 10X claims that its platform’s proprietary microfluidics system can process a thousand times as many long fragments in a single run as the TruSeq protocol, with chemistry supporting hundreds of thousands of unique molecular barcodes. The 10X approach may also be able to handle much longer pieces of DNA. Saxonov said that the company routinely works with 100-kilobase fragments, roughly ten times longer than a typical synthetic long read with TruSeq — or, indeed, a true long read with PacBio.

The biggest test of 10X Genomics’ system will be whether it can perform de novo assembly: putting together whole genomes from scratch, without guidance from a reference genome. Such assemblies have become the gems in PacBio’s crown over the past two years, culminating in a whole human genome last fall. 10X is not yet sharing whether the company or its early access users have attempted an assembly, or which organisms they’ve been working with. “We have a number of customers working in a range of applications,” said Rob, “but we’re going to let them tell their story at AGBT,” the Advances in Genome Biology and Technology conference to be held in Marco Island, Florida, in February.

Saxonov, who started his corporate career as the founding R&D Architect at the personal genetics company 23andMe, ultimately hopes that filling the gaps left by short-read sequencing will help advance medical discoveries that rely on understanding the most difficult-to-sequence regions of the genome. “When we were at 23andMe, a perverse thing I kept running into was that the things that were most important to understand were the hardest to get at,” he said — things like the HLA locus, which is involved in the immune system and used to match organ donors with recipients. “Clearly, being able to unravel HLA is going to be very useful. Being able to detect gene fusions in cancer, and general structural variation, is going to be very important.”

It’s unclear how receptive Illumina will be to 10X Genomics’ service, which is exclusively compatible with Illumina’s instruments. On the one hand, 10X will compete directly with the Moleculo technology owned and heavily touted by Illumina. While the sequencing giant could do little to stop users from adopting the 10X platform, it does have important influence in pointing customers toward the best tools to improve their results.

On the other hand, the genomics community has a long history of collaboratively working on chemistry and software innovations that improve the power of standard tools in the field. Moleculo itself was a small, independent company trying to fill the same niche as 10X Genomics before it was acquired. It’s also worth noting that John Stuelpnagel, Illumina’s co-founder and first CEO, is now serving as Chairman of 10X’s Board of Directors.

A full product launch and data from early adopters is slated for announcement at the AGBT conference next month.