Next-generation sequencing platform

DNA bases are separated by only 3.4 angstroms, the width of a few atoms. DNA sequencing methods cannot easily resolve this dimension. Sequencing by expansion technology, or SBX, overcomes this limitation by creating a surrogate molecule called an Xpandomer. This molecule is more than 50 times longer than its target DNA and encodes the DNA sequence information in large, high signal-to-noise reporters. 

The building blocks for the Xpandomer are novel nucleotides called X-NTPs. A modified DNA replication process synthesizes the Xpandomer by sequentially linking the X-NTPs along a target DNA template using a proprietary enzymatic process. This forms a double-stranded helix. Each of the four X-NTP types depicted as A, C, G, and T has a tether that is linked between the base and the alpha phosphate. The tether supports a high signal-to-noise reporter that mirrors the base sequence identity. 

Located in the center of each reporter is the translocation control element, or TCE, that modulates Xpandomer movement during sequencing. As the extension proceeds, only an X-NTP that correctly complements the next base on the DNA template will be incorporated. 

The sequence information of the DNA is now expressed in the reporter sequence of the X-NTP. This process of linking X-NTPs is continued sequentially and extends along the entire length of the DNA template. After synthesis, a reagent is added, which degrades the DNA template, and the cleavable bond between each of the X-NTP bases is broken, allowing the backbone to expand. This product is called the Xpandomer. The Xpandomer is then threaded electrically through a biological nanopore in a deterministic manner. The translocation control element holds the reporter in the nanopore, altering the electrical resistance of the pore to provide one of four signals that uniquely identify the corresponding base in the original DNA sequence. 

After measurement, a short high-voltage pulse is applied, and the Xpandomer is reliably advanced to the next reporter. This process is performed in a highly parallel manner across millions of wells on a single (complementary metal-oxide-semiconductor) CMOS-based sensor module and can provide for remarkable real-time sequencing rates of hundreds of millions of bases per second. 

Roche's innovative SBX technology can flexibly scale to satisfy a broad range of applications, setting a new paradigm for next-generation sequencing technology.

Next generation sequencing has revolutionized our understanding of biology. For years, sequencing by synthesis or SBS has been the most widely used technology. However, the invention of sequencing by expansion, or SBX, promises a new approach to shape the future of genomics, but what's the difference? And why does it matter? Let's start by looking at how DNA sequencing works. Sequencing a DNA sample generates its unique sequence of bases. The order of A's, T's, C's, and G's and the faster you can spot the differences that make a sequence unique, when compared to a reference, the sooner you can gain insights. This could mean driving quicker progress in oncology-related research and making faster breakthroughs that shape healthcare for the next generation.

Now, imagine DNA sequencing as a game of spot the difference. Your reference sequence is the original picture, the DNA from our sample is our difference picture. Our goal? To spot the differences between them. When you have both your reference and sample pictures together side by side, comparing them is very straightforward, but the key differences lie in how that sample picture is created, namely, how sequencing reads are generated.

Let's start with the SBS sample picture. SBS sequences the sample in iterative cycles, building the sequence piece by piece. Imagine this like a printer which prints the image line by line. You have to wait until the the image sufficiently appears before you can begin to see the full sample picture. Only then can you begin to spot all of the differences against the reference picture.

SBX works in a dramatically different way. First, samples are converted into molecules called Xpandomers. Then, after loading the Xpandomers onto the sequencer, full length reads begin to be measured within seconds of sequencing the converted sample. SBX achieves this speed by separating synthesis and sequencing steps. Instead of printing out our sample picture line by line, SBX begins to generate the full picture right from the start, with rapidly increasing clarity and that means you can compare against the reference picture with confidence almost immediately.

By looking at SBS and SBX side by side over the same period of time, we can see the differences in action. On the left is our SBS sample picture, we can only see a small portion of the image, we're still waiting for the printer to finish its job. In contrast, on the right, the SBX sample picture is visible in its entirety, you can compare the sample picture to the reference from the beginning, even as the picture gains increasing detail.

But what does this mean in the real world of genomics? With SBX, as the initial view of the full picture is available within within minutes, to even seconds, downstream analysis can begin almost immediately. This is in comparison to SBS, which must wait, until sequencing has sufficiently progressed to begin downstream analysis. This ability to generate data and move from sample to data analysis in a fraction of the time, while delivering high accuracy and flexibility, marks a fundamental shift in the sequencing workflow.

SBX will ultimately accelerate scientific discovery, unlocking possibilities in sequencing, that were previously unattainable. We're advancing towards a time where fast, accurate genomic understanding sets new standards in personalized medicine, health, and our collective well-being. So make space, because the future of genomics is here here and it's faster than ever before.