By Nava Whiteford
The first thing I imagine when asked to write about the future of sequencing is a young researcher gliding to her lab bench on a hoverboard, where she presses a single bright button labeled “Sequlite 10000.” A blur of motion and computer graphics engulf the lab. Ten seconds later, a monitor descends and a hologram proclaims “Paper submitted and accepted” (in the future all papers are written, submitted and reviewed by GPTChat 10).
When I woke up this morning, with the clarity of having slept on the idea, I realized that what I actually wanted was far more prosaic. I could talk about lab automation. Or sample prep innovation. Or long reads. Direct detection of RNA, methylation, and all the new exciting approaches that might exist … but then I started to think about what I actually want. And how most of those things are technologically feasible today.
Boring sequencers like boring qPCR machines
What I actually want is for a sequencer to be as boring and simple as a qPCR machine.
Nobody gets excited about buying a qPCR machine. Nobody feels a tingle of excitement when they put that new qPCR machine (which is the same as all the other qPCR machines) on a grant. No, qPCR machines are boring. It is stable technology that has not really changed much in the past 10 years. You cannot just buy a new fancy qPCR machine and assume you will get a few papers out of it because everyone else already has one and they just kind of work.
And that’s what I want from the future of sequencing.
I want to be able to buy a sequencer from a vendor (or grab one from a used lab supply company), stick it in my lab, and use it. I want to be able to buy reagents and consumables from one of tens (if not hundreds) of suppliers and throw them into my old sequencer, which may (or may not) have a service contract.
You can do this with a qPCR machine. In fact, your lowest cost of entry is incredibly low. You can buy an old Cepheid SmartCycler for $200. Even a BioRad or ABI OneStep will only set you back about $5,000. A brand new instrument will cost you about $20,000. Any of these will work well for basic research applications. If you are setting up a new lab, you can get competitive quotes from a number of different vendors, all of whom will provide equivalent machines. Sequencers? Not so much. Illumina dominates the market and the competitors are all a bit different. The workflow is different, the throughput is different, and the data quality is different. Competitive quotes are somewhat an artificial exercise … none of these platforms are drop-in replacements for the others.
But they could be! And that would be great! Imagine not being locked into a single vendor because you have built your whole workflow around them? Imagine being able to switch to another vendor because you do not like the support offered or the service contract they want to lock you into.
Imagine (shock, horror) not being forced to buy your sequencing reagents and consumables from the same vendor that makes the instrument! Imagine (like qPCR) being able to choose from literally hundreds of vendors willing to supply you.
The fact is that there is no technological reason for why this world cannot exist today. The fundamental patents for next-gen sequencing have all expired. Building generic sequencing instrumentation is a realistic possibility.
However, building this new eco-system around next-gen sequencing requires a significant shift in the market. We can only dream!
More and different ways of automation
Automation around sequencing currently seems to take two forms. Space-age digital fluidic solutions that also cost about as much to a trip to the moon, or pipette robots that seem to do their best to copy exactly what your lab tech does. They cost thousands of dollars, are only really useful when processing large numbers of samples, and usually come paired with their own automation specialist tasked with keeping them happy so they do not smash themselves (and your samples) to pieces.
I would like to see a very different kind of automation. One that is barely recognizable under that name. Taking another leaf out of the qPCR playbook, I would like to see sample-to-answer automation. The Cepheid GeneXpert is a good example of this in the qPCR space. Here, a user can pipette in a raw sample that is processed through a fixed workflow (extraction, reverse transcription, and qPCR amplification). GeneXpert cartridges are then used to give a quick molecular readout for infectious diseases and can be deployed in the clinic.
GeneXpert uses a simple injection molded cartridge that costs less than $20. The closest this in sequencing is the iSeq 100 (a shockingly unpopular sequencer). This also uses a self-contained injection molded cartridge without fluidic coupling to the instrument.
Can we build an iSeq that performs not just the fluidic steps required for sequencing on instrument but also the sample and library prep steps?
I do not see a huge technological barrier here. But so far vendors do not seem to have a compelling enough market to invest in these advances. In the research space, it might be “kind of interesting” to be able to stick a raw sample into an instrument and get a whole genome out the other end. But the approach really shines in the diagnostic space. Here, one would be driving sequencing towards diagnostic applications. Along with cost, fixing automation issue could be the key to making sequencing accessible to clinics.
My personal desire is to see sequencing ultimately displace qPCR. It may initially serve as a replacement for “high-plex” infectious disease panels that currently use molecular testing (like the BioFire Film Array), but it will hopefully make its way to wider applications.
This will require both vastly cheaper sequencing platforms and “sample-to-answer” platforms using tightly integrated and cheap approaches such as injection molded cartridges.
This will hopefully lead to …
More sequencing-based diagnostics
It has been both encouraging and disappointing to see how next-gen sequencing has been adopted for clinical applications. Encouraging because back when the first next-gen sequencers launched, their adoption rate in advanced diagnostics was zero. There was no existing application that was a good and easy fit for next-gen sequencing. However, Illumina recently reported that clinical applications were ~50% of their market. A good chunk of these applications is non-invasive prenatal testing, but the rest is oncology. The oncology field uses next-gen sequencing to classify tumors and monitor re-occurrences.
The disappointment comes from the difficulty in getting clinicians to adopt sequencing in other areas. Coming from a tech background, this has been hard for me to understand. But as I read more reports and personally interact with clinicians the picture has become clearer.
Clinicians do not view their jobs as finding out what is wrong with a patient. They view it as improving patient outcomes.
The clinicians reading this might find it confusingly obvious. But they have to understand the attitudes of scientists and engineers. We primarily want to understand systems, and we need to understand them then if we are to fix them. However, diagnosing and understanding comes first and has value in its own right.
Because the goal of clinicians is to improve patient outcomes, many of them may view a diagnostic test as unnecessary if it only increases understanding of an individual’s underlying condition and does not alter treatment. And in cases where there is only one viable treatment for the patients symptoms, why test at all?
This is usually the approach taken for conditions (like “flu-like symptoms”). It is also the cause for more serious conditions like intellectual disability for which, in many cases, clear genetic causes exist. Many clinicians are unwilling to test because despite having established genetic causes, treatments are not available.
However, my hope is that we are seeing a cultural change brought on in part by patient and clinician experiences during the COVID-19 pandemic. As one clinician put it:
“Frankly, patient experience scores increase when patients leave our care and have a name for the thing that is bothering them, even if there isn’t a targeted antibiotic or antimicrobial that has been identified, that would work against the pathogen. It still is comforting to patients and their families to have a name for the illness that they have.”—Emily Volk, MD, President, College of American Pathologists.
The reality is that patients like to know what is making them sick, even if an effective treatment is not available. One would hope that COVID-19 has made the general population aware of the fact that one can perform diagnostic tests cheaply and effectively. The broad adoption of sequencing is therefore unlikely to occur in a vacuum. We will either require a wide array of therapeutics to link the identification of underlying genetic causes or infectious diseases with improved patient outcomes, or we will need to instigate a cultural shift that makes it unacceptable for patients to leave a clinical setting without clearly identifying their condition.
At some point in the future, I hope it will be unacceptably weird to say “You’ve got a bit of a cold” instead of “You have an ‘HRV-A2 CA90-0150’ infection.” Or to tell a child they have an intellectual disability without identifying a clear genetic (or other) cause.
Nava Whiteford, s currently serving as a consultant at Whiteford Research Limited, where he specializes in life science tools, particularly DNA sequencing. Nava also runs a popular substack (aseq.substack.com) where he discusses technological approaches and developments in DNA sequencing technology.
