Hello and welcome to the Illumina customer solutions lab.
I'm Brian.
And I'm David.
We're here to give you an unprecedented behind the scenes
introduction to Illumina's newest innovation in the world of next generation
sequencing, the NovaSeq series of systems.
The NovaSeq platform leverages some of Illumina's greatest technological
advances in one complete package, utilizing the patent flow cell technology
from the HighSeq 3000, 4000 platform, and combining it with the two channel
chemistry and the simplicity of use demonstrated in our NextSeq platform.
What is now available to users is a highly flexible, easy to use, yet incredibly
powerful instrument capable of sequencing anywhere from 167 billion bases in
a single flow cell up, to upwards of 6 trillion bases in a single run.
With this new technology, Illumina can now offer a single solution that covers a
wide variety of library types at a very low cost per sample.
That's pretty impressive David.
What I'm most excited about is a simplified
workflow required to start the NovaSeq platform, which includes that onboard
cluster generation, as well as the fact that the platform has a lot of room to
grow.
Some of our legacy customers might remember that the HighSeq 2000
released in 2010, boasted an output of 200 gigabases per run.
That same
platform evolved over time to become that HighSeq X, which now produces
over 1.6 terabases per run.
Who knows how far we can take the NovaSeq series.
Brian, can you show us some of the features of the system including both the
consumables and the instrument itself, as well as demonstrate what the
workflow for a typical run might look like.
Not only did the development team combine the pattern flow cell and the two
channel chemistry technology, but they also optimized the workflow by utilizing
the cartridge based free agent delivery system used by the MiniSeq, MiSeq,
NextSeq systems making the process of setting up a run easier than ever.
We'll start with the cartridges.
The first cartridge, which has all of your frozen
reagents will be shipped on dry ice and stored at minus 20 degrees C. The
cartridge can be placed in the refrigerator overnight to thaw for a run to be
started the next day, or thawed at room temperature water bath for a few
hours just before the run.
There's an empty well, which is used to place the
prepared library tube just before you start the run.
Setting up the prepared
libraries is very similar and just as easy as with HighSeq instruments.
To start, we're going to push the sequence button, and then push okay.
The
flow cell door is going to open, and I've already loaded the library tube into the
cartridge.
My next step is to open the door, open the compartment for the
reagents, and then slide the tray open.
I'm then going to put the reagent
cartridge into the tray.
The second frozen cartridge is the SPS reagents.
This cartridge is shipped on dry
ice, and stored at minus 20 degrees, and for thawing you can follow the same
procedure as with your reagent cartridge.
You don't have to load a sample in
here, so you would just load this into the tray.
We then close the tray, and then
close the door.
The third cartridge contains your SPS buffers, which are shipped and stored at
room temperature.
This eliminates the need to acquire additional refrigeration,
which I really appreciate as a former lab manager.
There's no steps needed to
prepare the buffer cartridge, and it's ready to use as is.
I'm now going to open
the tray, place in the reagent buffer cartridge, and close the door.
Close the
door, and if I were going to start a run on the other side, I would repeat the
process here.
The last, and quite possibly most interesting consumable is the flow cell.
The
NovaSeq series is a comfortable fit for most researchers looking for a large
number of bases sequenced over a relatively short period of time.
The pattern
flow cells are a bit larger than even the NextSeq flow cell, packing a ton of
clusters between the two pieces of glass.
The reagent cartridge, buffer
cartridge, library tube, and flow cell all contain a unique radio frequency
identification or RF ID chip, making tracking of consumables automatic.
There's
no longer a need to use a barcode scanner for the information to be entered
into the run setup screen.
Now, let's take a look at that sequencer.
The first feature that you might notice
is that it's only 2 feet, 2.5 feet by 3 feet.
The footprint is smaller than a HighSeq.
There's no need to give up valuable bench space for the NovaSeq platform or its
computational components.
The self contained design incorporates everything
from the reagent cartridge and waste bottle compartments, to waste bottle
storage and onboard server for primary analysis.
The NovaSeq series even has
built in casters in case a field service engineer ever has to relocate your
instrument.
To set up a run, the prepared and denatured libraries was pipetted into that
library tube, which we then put into the cartridge.
Now, here on the screen
we'll have to first load the flow cell, and then close the flow cell door.
With the
intuitive user interface starting a run is stress free.
It's here where you're going to notice the similarities to previous workflows on
Illumina's other sequencers, from preparing samples for clustering, then
creating a sample sheet in Illumina experiment manager, and uploading it to the
instrument, the NovaSeq series will be an easy transition for any customer.
Some new additions introduced into the NovaSeq workflow like the run setup
file if you're using a LIMs system, updates to the loading concentration for
clustering and faster run times for the high throughput sequencer.
You can
expect to load your library at 200 to 300 picomole, which is a bit more than that
library than on a HighSeq.
What is most impressive is that the onboard cluster generation with the run
time for an S2 flow cell from start to finish for a 2 by 150 run will be 40 hours.
29 hours for a 2 by 100, and as little as 19 hours for a 2 by 50.
You can run a
massive amount of samples in a relatively short period of time enabling rapid
sequencing and data output with the minimal effort from the user.
I'm now going to tell the system that I've emptied out the waste trays, and I'm
going to push the run setup button.
Once you've entered all of the instructions
for the sequencer, you push review.
This may look very familiar from one of our
other sequencers.
After you've reviewed your run, press the pre-run checks
button.
The instrument will go through a series of pre run checks, which are
designed to diagnose potential problems before the run even starts.
One really cool feature is the ability to run different modes at the same time.
For example, if you want to run a whole genome sequencing with an S3 flow cell
on side A, and a whole exome sequencing with an S2 flow cell on side B, the
NovaSeq platform can accommodate it.
It's also possible to simultaneously use
the instrument in online mode on one side, stream your data to BaseSpace
Sequence Hub, and in local mode on the other side to stream data to the local
server.
And our team here at Illumina can always assist with custom
computation and storage solutions with Genomics IT services.
Once your run setup is finished, and it goes through that series of pre run
checks, we can push the sequence button.
You're now on your way to massive
amounts of sequence bases.
A big advantage to using one of Illumina's sequencers is the capability to
streaming and analyzing data on BaseSpace Sequence Hub.
If you don't have a
Base SpaceSequence Hub account, you can sign up for one on the Illumina
website by clicking the My Illumina tab at the top right of the screen.
Once you have an account, it's possible to monitor ongoing runs on any of our
sequencers analyzing data, using one of the many apps available in the app
store, access public data from previous runs, or further analyze data using the
Illumina correlation engine.
Laboratories frequently ask about customized bioinformatics support, including
custom app development, and Illumina professionals are happy to work with
you to manage your data needs.
To monitor an ongoing run, log into BaseSpace Sequence Hub, click the runs tab
at the top of the screen.
You will see a list of all your current and previous runs
to review the metrics.
This is where you can see metrics like cluster density,
clusters past, and filter percentages, and your Q30 metrics.
For the NovaSeq
series, a 65 to 75% passing filter rate is a successful run at the optimal cluster
density.
You’ll also notice that the clustering process will have a wider window
for optimal clustering when it comes to loading concentration.
This is just
another way that Illumina has made it easier to get to the high quality
sequencing data.
When your run is finished, the NovaSeq platform will automatically initiate a
post run wash, which will prolong the life of your instrument as well as help you
maintain high quality sequencing data.
For those customers that can further
benefit from instrument compliance services, for instance installation
qualification, operational qualification, and performance qualification services,
Illumina can help to ensure quality guidelines are met.
Analysis on Base Space Sequence Hub is also an intuitive process.
In this
example, I'll walk you through a typical whole genome analysis.
Under the apps
tab at the top of the screen in BaseSpace Sequence Hub, click on re-sequencing
on the right hand side.
Choose the whole genome sequencing app, all of the app
information and references are located on the application landing page.
To
choose this app, click launch.
On the next screen, choose your project.
Next,
select your sample fast queue files.
You also have the option of starting from
BAM files.
After that, choose the reference genome you would like to align your
samples with.
The application will then process your data, sending you an email
notification when it's finished.
The outputs are your VCF file, which contains your samples variance as well as
associated metrics like coverage and alignment.
We're happy to offer you a
chance to experience this sequencer's capabilities with your samples first-hand
through our proof of concept offering.
David.
Thanks Brian.
This is a really nice description of what the workflow on the
NovaSeq series looks like, and how easy it can be.
The NovaSeq series is built
from the ground up to accelerate your research, giving you the flexibility and
scalability to complete projects faster and more economically than ever before
across a broad range of applications.