Expanding Your Toolbox with Rapid DNA to Drive Actionable Investigative Intelligence
Crime fighting in the 21st century necessitates improved investigation methods, and increased partnership between crime labs and investigation units. Rapid DNA technology emerged over a decade ago, but continues to evolve to meet the changing needs of the criminal justice community. This webinar will provide viewers with insight into recent improvements to the Applied Biosystems™ RapidHIT™ ID platform for crime scene evidence sample processing. Join Peterjon McAnany, senior technical applications specialist, and Rob Lagacé, senior staff scientist, as they explore: •Chemistry and cartridge enhancements to improve peak height ratio balance, and identifying samples for low quantity, degradation, and inhibition •Improved system and analysis software to quickly flag challenging samples for review •Impact of an improved investigative lead solution on crime
Hello and welcome to Expanding Your Toolbox with Rapid DNA to Drive Actionable
Investigative
Intelligence.
Brought to you by forensic and sponsored by Thermo Fisher Scientific.
My name is Michelle Taylor, Editor-in-Chief of Forensic and I Will Be Your
Moderator Throughout.
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Following the conclusion of the webinar, you will receive an email with
information on
how to obtain CE Credit Documentation.
We have a great lineup scheduled to present to you today, but before we begin,
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Today, you will join Peter John McEnae, a senior technical application
specialist at ThermoFisher
Scientific, at the Human Identification Headquarters, as he interviews senior
staff scientist Robert
Legasse about recent improvements to rapid DNA technology amid the increase in
crime
seen throughout the country.
Peter John has 16 years of forensic DNA experience, including 10 years as a
forensic DNA analyst
between two law enforcement agencies.
In his current role with ThermoFisher Scientific, he divides his time between
the management
of global, escalated support cases, and new product initiatives to bring
innovative forensic
technology to the field.
His previous positions at ThermoFisher Scientific include staff scientists and
field application
scientists.
Robert has over 35 years of experience in the genomic field, from cancer
research to
the human genome project, gene discovery, and targeted assay development.
Here's current role at ThermoFisher Scientific, involves STR assay design for
the rapid DNA
platform, as well as leading collaborations efforts with key opinion leaders
throughout
the world to enhance the rapid DNA platform and massively parallel sequencing
solutions
for forensics.
We thank you for joining us for today's webinar, and please keep your eyes open
for our invitation
for their next one.
Now, without further ado, I'll hand it over to Peter John to get us started.
In the criminal justice community, there's only one mission, the relentless
pursuit of
the truth.
All it takes is one case that keeps you up at night.
One persistent investigator who never gives up, one dangerous criminal still on
the street,
one precious sample that changes everything, one innocent suspect who's
counting on justice.
One tenacious analyst who won't stop without an answer.
One brave victim who's not afraid to speak their truth.
All it takes is one.
One match.
One community.
One world made safer.
And there's one trusted partner who's been there from the beginning.
For over 30 years, ThermoFisher Scientific has provided forensic laboratories
all over
the world with gold standard forensic tools so you can protect your communities
, bring
justice to those who seek it, identify the missing and help prevent tomorrow's
victims.
We never stop because you never stop.
Individually we're strong.
But together, together we're unstoppable.
We find the truth.
Hi, I'm Peter John McEnany and one of my roles as a technical application
specialist
is to bring your voice to our new product developments.
Today, that brings me here to Pleasanton, California and the site of our Human
Identification
Headquarters where our development teams are working tirelessly to bring you
the next
generation solutions for rapid DNA.
Come with me and let's take a peek behind the curtain.
Hey Rob, nice to see you again.
It feels like it was just yesterday that we were working on a 3500 software
improvement
and GMAP or IDX solution to help DNA analysts streamline processing time.
And here we are again working to drive system improvements addressing the
growing crime
rates and resource limitations.
Hi Peter, John.
Nice to see you too.
I know in the past few years, crime has increased significantly in my
neighborhood.
I live on a street 10 hours long and I'm seeing multiple incidences of crime
every month.
I don't think police departments are equipped to handle this increase or
frequency in the
crimes I'm seeing.
Yeah, forensics labs seem to be overburdened with more samples and to make
matters worse,
we keep hearing of staff shortages and this combined with an expanding set of
challenges,
including natural disasters and other situations that demand focus and
resources.
It is more important than ever that we deliver tools that help with efficiency.
You know, I joined the applied biosystem in 2005.
We were just starting work on our third, what I call a new generation kit, mini
filer.
Profiling co-filer have emerged to become identifiler.
White filer would just come out.
I was running a single cap 310 in the 3130 at the time, not even an XL for gen
otyping.
I then helped work on the development of the 3500 series instruments and the
introduction
of the six-dye system.
For us, this was a significant improvement of the five-dye system and the 3130
instrument.
It allowed us to move from the 16 markers and identifiler to the 24 markers and
global
filer as we worked to improve workflow and make a better customer experience.
And this change was required to meet the expanded codus marker requirements.
Now, I hear some reasons why the more markers, or they want a specific set of
markers for
centralized high volume workflows.
And then again, I'm hearing people want decentralized workflows and small sets
and
screening of samples.
Well, rapid DNA enables a ladder.
With rapid DNA, labs can quickly triage their samples.
They can generate investigative leads early on in search for local databases.
And that enables them to take action while a suspect is still in custody.
So I hear that rapid assays are having an impact in the world.
And you know, it's really great for the R&D folks who work really hard to build
these
assays and develop them to hear feedback.
So I'd love to hear from you some feedback on the rapid assays and their impact
And the program showing the biggest impact are those developed in partnership.
The true power of rapid DNA is its ability to bring together key members of the
criminal
justice and human identification communities to obtain answers faster and help
prevent
or solve crimes.
So Rob, we call our next big rapid DNA solution, our enhanced investigative
lead solution.
But what does that entail?
If a new solution is really a completely redesigned workflow, we have updated
the three critical
components of this system.
Biggest one is we have a new investigative leads crime scene cartridge.
We have new software on the instrument and we have a new rapidly software.
Now all of this is compatible with the current rapid head idea instrument.
We're not going to change anything on the hardware of the instrument.
And what did the project team set out to accomplish with the development of our
enhanced investigative
lead solution?
A goal we started the project was to design a new assay that would improve on
the current
intel cartridge.
Basically, we wanted more green check marks than the intel system.
Now so we started the program.
But soon after a paper was published in SSFIG, a better task group made up of
the FBI,
Srigdam, and ENFSI with a set of recommendations for rapid casework systems and
how to upload
their results into CODIS.
So we pivoted and we actually enhanced our system.
So to meet these new requirements, we added indicators for PCR inhibition,
sample degradation,
sample load, and the possibility of an allele dropout, their potential.
These additions were added to the original goal of improving the p-kite balance
for low
input samples.
So Peter, John, what do you think customers are going to think of all these
changes we're
making?
I think those are some major changes and major improvements.
And I think customers always appreciate improved performance, especially when
it comes to balance
or sensitivity and the potential for future access to CODIS will be a game
changer.
I think it is all very exciting.
And you mentioned adding indicators of DNA quantity, DNA degradation, or PCR
inhibition,
I should say.
Can you elaborate on how we are achieving this and how those features were
developed?
To evaluate PCR inhibition, we used the same IQC chemistry that was developed
for the global
filer IQC kit.
We just incorporated the same system into the Intel Plus assay.
And since the system already functioned well within the global filer's T.R. set
of targets,
our work was then to optimize the IQC reaction to work well within a rapid
cartridge.
And adding the new human non-STR target systems, well that was way more
challenging.
We explored two systems.
We tried a multi-copy system and a single target copy system.
We quickly found the single target system was way more accurate in evaluating
DNA load
and sample degradation.
So the challenges in adding these new markers to an existing assay, they were
manyfold.
You have to have no cross-reactivity with any existing markers.
You have to have consistent target amplification to do the job their toes
supposed to do with
quantification.
And they've got to be human-specific.
So the target of primer locations, you can't have any SNPs or polymorphisms in
the targets
of the primers.
And the target amplicon itself has to be free of indels or any SNPs are going
to change
the mobility of the amplicon.
So I think we went through over 20 target candidates that failed just for peak
morphology in the
design.
The process for getting into the assay is quite rigorous.
In the end, we added two targets to the system for quantification degradation.
One at the front of the assay, around 65 nucleotides.
We found this is an ideal size for estimating the amount of sample loaded into
an assay.
And we have one near the end of the STR-read regions at 408 nucleotides.
So here we are.
We span the assay with targets that are immune to any PCR type of amplification
issues.
No allele size changes.
They're one size.
So this allows us to use the same slope concept we use with the IQC peaks for
inhibition to
predict how degraded the sample is.
And in addition to indicating the level of degradation of the sample, having
that large
target, which is out there at the end, to estimate how much DNA is present in
the reaction
at the larger STRs.
This is also a good indicator for how much impact inhibition has on the
amplification
of larger markers.
Because inhibition will also impact the large STRs.
And this is a good indicator for how severe that impact is.
Absolutely.
And I have to challenge in a good way.
You said that the multi-target quant markers, we quickly identified that the
single copy
was going to be better.
I have to give the R&D team credit for spending actually a lot of time trying
to optimize
that multi-copy target and really reap the benefits of that before having to
move to
the single copy target for the performance of the assay.
So props to you and the team.
But you also mentioned improved performance.
So as far as performance, can you expand on that for our audience today?
Yeah, remember I mentioned we started the project before the SwigDAM
recommendations
were announced and published.
We had already begun to look at ways to improve the performance of the Intel
assay, which
is extremely sensitive, but it's subject to stochastic effects.
So you could say our goal of the project at the beginning was to change the
yellow check
marks of Intel to green with Intel Plus.
So to accomplish this, we needed to system to have better p-type balances and
be more
immune to the low sample inputs, which causes amplification artifacts.
So how did we do this?
We did it by increasing the amount of DNA available in the PCR by reducing the
lysis solution
volume and capturing twice as much lysate, which is where we get the DNA, with
an additional
punch in the PCR chamber of the cartridge.
Of course, this changed Intel optimizing all our primer mix and a master mix in
the cartridge
to have the best performance.
So with the additional capture DNA, we were able to reduce the number of PCR
cycles further
reducing the amplification artifacts while keeping what our target sensitivity
of the
system was and what we wanted.
So while the GFE and ACE and Intel cartridges had made use of the GFE CE
chemistry kit formulation,
the Intel Plus cartridge, we re-optimized everything to work specifically with
the rapid
hit ID platform.
Just to try and summarize what you just said there and emphasize to the
audience how challenging
it is to make a change to SCR kit chemistry, it's no easy feat to just tweak a
single
marker, much less add new markers or add markers that are in flanking regions
kind of outside
of the typical SCR read region within a dye channel or within the host of dye
channels
within an entire kit.
So all of these changes are going to benefit the customer.
Are there any other changes to going to benefit the customer?
I hear that the user will be able to use a new swap to maximize performance.
I think that might have to do something with the lysis buffer that you
mentioned earlier.
Is that part of the new cartridge?
Yeah, that's right Peter, John.
The Intel Plus cartridge will support two protocols.
So we have a general protocol which has the same lysis volume as the ACE
cartridge and
we wanted to keep this so you can use standard size swabs.
But in addition, we've added a specialized protocol for these low input samples
So it does have certain requirements to use the protocol.
To use that specialized protocol, the user needs to use a micro or a mini fl
ocked swap
as a specialized protocol uses that reduced lysis volume to deliver more
concentrated
DNA to the PCR chamber.
So the sensitivity of the specialized protocol also enables the user to save
the primary
swap if they want for other processes.
As the user can, what we call sub-sample, the primary swap.
This is done by transferring a small amount of sample to the micro flocked swap
And you can do this by simply putting the micro flocked on a table and pressing
the
primary swap against it to transfer some small amount of material.
So now you can use the micro flocked swap to run the Intel Plus system as
either a screening
method or as a primary method for taking a genotype.
And then the result can help inform the lab that the sample is maybe
challenging, degraded,
inhibited before initiating their downstream workflow.
You touched on something there that I do want to elaborate on a little bit.
There's not necessarily a difference in the amount of transfer from a
traditional or general
cotton swab that you mentioned to the micro flocked swap with regards to
whether you're
transferring from one to the other.
But when it comes to ease of use, it's actually easier to put the blank micro
flock or mini
flock or what a hydro flocked swab on the bench on some paper and rub the maybe
wooden
handled swab, the stiffer swab that has the sample on it, rub that onto the
micro flocked
swap.
Instead of trying to rub the micro flocked swab onto the general cotton swab,
right?
It might not change the amount of transfer, but it's much easier to use.
Is that true?
Yeah, because of the flexible handle on that micro flocked swab, yeah, it's
really we
found out the best way to do transfer was to put the micro flocked down and
hold the
primary swab with the stiffer handle against it to transfer the DNA.
And all you need is a small amount.
This protocol is highly sensitive.
Anywhere between 0.2 to 0.4 microlears of blood is usually enough to pull a
full profile.
So that's why I said you can save that swab that has a decent amount of
material on it,
prefer the use and not use it up in the rapid instrument by doing the sub
sampling.
Absolutely amazing.
And the sensitivity there is wonderful.
So we talked mainly about the new chemistry and the cartridge and a little bit
on the
software with regards to the two instrument protocols.
Are there any other changes that the customer should expect with our new
solution?
Yeah, there's going to be quite a few.
So good news is for a lot of our early customers in the GMapper world and using
the chemistry
kits that are on the 3100 and 3500 instruments, is this system will go back to
using GMapper
ID extra genotyping.
And moving to GMapper on the instrument itself for its software update.
So this effect will have some changes for the user and how they do their work.
Now the system will require the running of a positive control swab after
insertion of
a new primary cartridge followed by the latter.
This requirement is really a kit level requirement.
So each kit that's going to be run on the primary cartridge will need to have
its positive
control run before running samples.
However, it does only need to be done once per kit per primary cartridge.
So the reason for this is the new system on the new system.
The positive control is going to establish the spectral die matrix which is
needed for
reduction to pull up events.
So another thing, this new software will only support GFES and Intel plus
cartridges along
with the 150 run primary cartridge.
The current HID, rapid hit HID software will not support the Intel plus kit and
neither
will the current rapid link software.
So you're going to have to upgrade your software versions for both rapid link
and the instrument
to version 2 to run the new Intel plus cartridges.
Now just so people know the GFES cartridges will still run under the same
protocols as
the previous version.
All we are changing is new signal processing software and the data analysis
again is migrated
to GMIDX for sizing and genotyping.
So rapid link.
Rapid link version 2 is a complete rewrite of the software.
It's a web-based browser interface now and it has features to manage what the
instruments,
user profiles, workflows and sample data.
In addition, a lot of things had to be added to rapid link to support the new
Intel plus
cartridges new features.
So we've introduced, I'm going to call them notifications or flags that were
added to
the profiles display screen in rapid link.
So for instance, for the things we've been talking about for inhibition and
degradation.
Based on the peak height differences of the smaller IQC and amplification and
quantification
markers, their respective larger counterparts.
The ratio difference will be displayed on the system as if you have inhibition
as a yellow
triangle next to the letters INH or if you have degradation, a yellow triangle
next to
the letters DEG.
If it is determined to be inhibited or degraded.
If no flags are generated, we detect no inhibition or degradation, you'll see
nothing.
There'll be no flags.
So based on the results of a measurement system analysis study we did, we can
now estimate
the amount of DNA present at both the small quantification target and then
again at the
larger quantification target, all based on their peak heights.
And when we do this, again on the display screen, we will show you the picogram
estimate
display for the small target next to letters QTS.
And then the estimate for the amount of DNA at the larger target next to the
letters QTL.
And the final swig dam recommendation for our systems meet was what is the
likelihood
of having a leo dropout in a sample.
And this was really interesting and challenging for us.
So through lots of evaluation of the assays response to very low level inputs
that induced
dropouts, we determined actually the best way to predict a dropout was to use
the peak
heights of a select set of the large STRs themselves, one from each dye channel
This proved to be much more accurate than looking at the quantification markers
, which
surprised us.
But we ran hundreds of samples and this had the best method, was the best
method.
So how this gets reflected to the user is on the profile screen of RapidLink.
The user is going to see the letters STO, followed by either a green, yellow,
or red flag.
A green flag indicates there should be no dropouts due to sample load.
A yellow flag that the sample may display various like peak height imbalances
and other
artifacts a little bit in the profile itself, but it should see no dropouts due
to sample
load.
The red flag indicates we have a very high likelihood that this sample will
have a dropout.
And in our studies, we saw a 75% positive rate call for dropout events when the
flag
went yet red.
So basically 75% of the samples that had a red flag also contained a dropout.
So Peter Don, I have to ask, you know, we've done R&D, has done a lot of work
redesigning
this cartridge to satisfy all the requests in this position recommendation
paper.
You have been the primary part of contact for the FBI during this work on
developing
the Intel Plus project.
Can you explain a little bit about the FBI's visions for these changes?
Maybe the future of where they see rapid DNA going?
And since really this is to access CODIS with crime scene samples, can you give
us a little
more on that?
So the position paper was the first step in the FBI's vision for how we as a
community
will get to the point where rapid DNA users can upload DNA profiles generated
from crime
scene samples on rapid DNA instruments.
The second step is the multi-lab study in which the FBI, along with its SWIG
dam counterpart,
will evaluate the suitability of these rapid DNA solutions for future CODIS
access with
crime scene samples.
Then steps three and four are involving the publication of the MLS data or the
multi-lab
study data and developing some new SWIG dam guidelines for CODIS access via
crime scene
evidence from a rapid hit instrument.
So there's a lot that went into it and there's actually a lot that you
mentioned in that
last segment about those enhancements.
And we tried to partner and work together with the various groups to try and
meet all
of those requirements.
Can you tell us a little bit about or do you have any questions about what this
might
mean for the community, whether it's forensics or law enforcement?
Yeah, so we know that booking stations now have approval to upload directly
into CODIS.
And that's great.
But now we're going to investigate of leads.
And I'm really wondering when the bar for investigative leads will we reach
where they
can upload those data into CODIS.
I think they use now local databases, but they can't go to CODIS.
So can you talk a little bit about that and the ability and what you see and
when will
that be available for the law enforcement?
At this point, labs will be able to upload crime scene samples to CODIS using
only the
modified rapid DNA analysis method, meaning all profiles will need to be
reviewed by a
qualified DNA analyst, even when the new crime scene evidence processing
solutions are going
to be available.
And that is after the study results have been published and the SWIGDAM
requirements have
been posted and everything has been enabled for any kind of crime scene sample
profile
upload to a CODIS index.
So this doesn't preclude the sample from being run at a law enforcement agency
or location,
but the data will still need to be transferred to a crime lab for review and
potential upload.
Any questions about that?
No, I'm just thinking this is so great.
I mean, it's great for the friends of community.
We've come along with rapid and honestly as a developer of these assays, it
really is
rewarding to hear that what we're doing is having an impact, that our work is
getting
traction and that just makes us want to do this more and do the next step for
the community.
Yeah, it's been a long road.
The journey is not over yet.
Our partnership with the FBI has been invaluable for the criminal justice
community and our
close partnership and cooperation brought testing the arrestee samples in the
booking
station to a reality and upload into CODIS for those specific samples and that
specific
sample type.
Now we are on a similar path with crime scene samples and I couldn't be more
excited about
our solution and what it's going to mean for the criminal justice and
investigative communities.
I really look forward to the future.
Thank you so much for joining me today Rob to discuss this with our Forensic
Magazine community
and I look forward to working with you in the future.
Thanks again Peter John for having me.
This has been great and very informative.
Thank you.
I hope you're as excited as I am about all the new developments and
enhancements in rapid
DNA technology at Thermo Fisher Scientific.
Standby, after this, there's a live Q&A session.
Thank you.
Thank you Peter John and Robert for those interesting and informative
presentations
and your own little Q&A there.
Now it is time for the regular Q&A with our wonderful audience.
If you have a question, please submit it through the Q&A panel on your screen.
You can do so right now.
And then while we wait and give everyone a second to submit their questions, I
have
a polling question for you guys.
So our first polling question should be on your screen.
It says, "When do you think your agency or jurisdiction will start using rapid
DNA?"
Next 12 months, next 24 months, in 3 to 5 years or NEP.
You could go ahead and take a moment to log your answer.
All right, we will go on to our next one.
Our last poll question quickly.
Would you like to receive more information on today's topic?
Yes, please contact me to discuss how to implement rapid DNA.
Yes, please contact me for a demo of the rapid hit ID system.
Yes, please send me pricing info and technical specs on the rapid hit ID system
or no, not
at this time.
Let's move on then to our Q&A with our audience.
All right, I would like to welcome back Peter John, right on time there, to our
Q&A.
And Rob, do we have you on audio?
Yeah, my connected.
Yes, you are.
Perfect.
I'd love to hear your voice.
All right.
Well, let us get the ball rolling then.
So Peter John, what specifically makes the mini flocks swab work so well with
the Intel
Plus cartridge?
Yeah, it's a fantastic question.
So the mini flocks swab or the micro flocks swab, they're both with a non-spunk
cotton
tip.
So they're much smaller, hence the mini or micro name, and they're capable of
absorbing
less liquid and releasing most of that liquid or releasing essentially the DNA.
So when we marry those characteristics of the swab or the swab tip with our
specialized
protocol on the rapid hit ID, we're essentially optimizing DNA collection and
then passing
that more concentrated lysate on to the PCR chamber where a lot of things are
happening
or occurring in concert to better the sensitivity and the balance of the
subsequent DNA profile.
As Rob mentioned, so there's now two punches in the PCR chamber to essentially
collect twice
as much DNA as predecessor cartridges.
Excuse me.
The combination of a more concentrated lysate and then more lysate collected
has actually
allowed us to change or reduce the PCR cycling for the Intel Plus cartridge so
that we don't
have as many stochastic effects just caused by PCR cycle so that we can get
more reproducible
and reliable DNA profiles and we get that better balance and increased
sensitivity.
So it really is the characteristics of those mini and micro hydroflox swabs
that allow for
that collection of a small amount of sample, DNA, liquid, however you want to
look at it
and then a good release of that into the much smaller volume of lysus buffer
that the rapid
Intel Plus cartridge and instrument protocol take advantage of.
Gotcha.
Okay.
Now our next question, at what percentage does the instrument lose the minor
component
of a mixture?
Oh sure.
So right now the system overall is basically identifying mixtures and it really
does that
based on the allele number or a combination of allele number and p-type
imbalance at a
certain number of loci.
So it's a very basic identification of a mixed sample or a mixture and right
now there aren't
any calculations being performed to alert the user to X ratio or major minor or
de-convolute
anything at the moment.
It's really just identification of a mixed DNA source or mixture.
Okay, I understand.
So at a crime scene.
How would you recommend collecting low lower level crime scene evidence on
porous surfaces?
Great.
Great question.
Okay, so porous surfaces.
I'll get to that in just a second.
Low level I think was mentioned first and already regardless of many or micro
flockswabs.
So there are a number of different ways to collect a DNA sample, right?
But now with the addition of our proposed collection or sub sampling solution,
we're
opening up additional avenues to get the most out of your sample in the rapid
system.
So as far as purely collecting from a crime scene sample or a crime scene
location, you
could use either swab, your traditional spun cotton swab which has a much
larger tip or
that hydro flock, micro or mini swab.
The big difference there is the shaft of the hydro flock mini or micro swab is
a little
bit more flexible.
It's a little bit longer because that tip is so much smaller, there's a little
bit of
a longer swab shaft.
It is very flexible.
So it can be a little bit tedious to really collect the sample and rub as hard
as you
want to.
However, it's really good for those hard to get to type of locations that a
traditional
swab that doesn't bend because of its wooden or harder plastic shaft.
So you can collect it however you want, but the beauty of being able to use
that hydro
flock mini or micro swab and the specialized protocol downstream on the rapid
hit ID is
that as mentioned and as you saw in the video, you can sub sample.
If you only have one swab collecting DNA from a crime scene sample, we have
found the easiest
thing to do is hold that mini swab down on a clean surface and rub that general
cotton
swab on the mini swab to transfer a small amount of that stain or that DNA.
Not only does this allow the user to retain that traditional cotton swab that
was used
at the crime scene, but also it takes very little amount of DNA on that hydro
flock mini
or micro swab and the specialized protocol to generate a beautiful full
balanced DNA
profile.
So as far as collecting, all of the options and then some are available to all
users,
crime scene operators, et cetera.
As far as processing, it really is about, okay, in the arena of collection, now
there is the
possibility of sub sampling in order to use that sub sampled swab, the hydro fl
ock mini
or micro in a specialized protocol on the rapid hit ID to get a good balanced
full DNA
profile from a much smaller amount of sample or DNA.
Perfect.
Thank you.
You know, there are some questions about cotton swabs that everyone's used to
in the flock.
So that's perfect.
Thank you for that info.
Our next question, what can we expect to see in the data, EPG with Intel plus,
especially
around the increased sensitivity?
Sure.
We did provide a few screenshots in the video that really showed off the new
features, the
new flags, the new, what I call like an informative, like the quant estimates.
So the electropharium itself, right, is going to display the new markers as we
saw the QQS
for quant quality small, the quant quality large or QQL, and then the
traditional global
filer, global filer express, STR and non-STR low side.
As far as with rapid Intel plus, we expect to see more balanced profiles and
more DNA
from less concentrated samples or lower level samples.
There's always going to be a limitation to every system, but comparative to
Intel and
other STR kits out there, we expect to see more sensitivity and better balance,
which
is really key to reproducing and making a more reliable DNA profile in a rapid
DNA
system.
Perfect.
Got it.
All right.
Our next question, are the fragments used to assess degradation and inhibition
different?
And if they are, what is the difference between the two?
Yeah, that is a great question.
And Rob, I might rely on you a little bit for this, but I'm going to take a
stab at it.
As Rob detailed in the video, the IQC or internal quality control piece, those
are the exact
same from our global filer IQC kit.
So those are basically not human DNA.
Those are synthetic or man-made DNA sequences that are added to the primer mix
so that we
have an abundance of that synthetic DNA in the PCR reaction.
If there is an inhibitor that is affecting PCR, then we expect to see an
imbalance between
the small and the large IQC peaks.
But we can also see an imbalance in the quant peaks when we're dealing with
degraded DNA
samples.
Now, that's because the quant markers are amplifying off of the sample or human
DNA
from the collection of that crime scene evidence.
So if those quant markers are imbalanced, it likely means that DNA degradation
is present
or a combination of degradation and inhibition as inhibition would decrease
that larger quant
peak as well.
So in concert with each other, the IQC markers and the quant markers can be
used visually
to determine am I seeing DNA degradation and inhibition or am I just seeing one
or the
other DNA degradation or PCR inhibition?
Does that answer the question?
I think so.
Rob, is there anything that you want to ask that though?
Sure, yeah.
The quant marker and the IQCs really are a tandem pairing to look at inhibition
degradation.
And one of the things is when you have an inhibited sample, it will also
display degradation
because inhibition impacts the PCR performance and the peaks will drop.
So you really can never tell if a sample is degraded when it is also inhibited.
But you can tell if there's no inhibition, the quant markers are very good at
indicating
whether that sample is solely degraded because the IQC markers will not be
impacted.
So that's kind of how the system works in a pairing.
So inhibition will usually trigger degradation, but degradation does not have
to trigger inhibition.
Got it.
Thank you for that follow-up.
That's helpful.
And if you don't mind, I'll just add to not to make it confusing, but those new
markers,
QQS and QQL.
When we look at the two peaks that are present at each marker, one of them is a
quant and
one of them is an IQC.
They're actually independent of each other even though they're underneath the
same marker
header QQS or QQL.
So just to differentiate the peak height of the quant small peak or the IQC
small peak,
they shouldn't affect each other.
They're within the same umbrella or marker header, but they're acting
independently and
they are being amplified off of completely different templates.
Same thing goes with the large, the quant and quality large header or marker
having two
separate loci underneath it, the quant and the IQC large.
If that helps as well kind of distinguish that these peaks at both loci or both
markers
are being amplified independently, they're just under that same marker header
for simplicity
and actually the performance of the assay.
Okay, got it.
Thank you.
All right.
Next question is, how is the Intel Plus cartridge being evaluated and how does
it compare to
the current Intel cartridge?
Great question.
So evaluated.
Obviously, we do our own internal verification and validation studies.
Those are completed.
Our additional developmental validation studies are still underweight.
And of course, that is not just for our developmental validation, but also for
the purposes of seeking
end disapproval of the rapid Intel Plus chemistry and getting that labeled as
an end disapproved
chemistry, as I mentioned in the video, a little choppy, but that has to be
done before you
can even get to modified DNA analysis for the purposes of uploading to a codist
database.
That Intel Plus chemistry has to be an end disapproved chemistry.
And then there are a number of other hurdles, right?
So that's one evaluation, right?
The FBI, NIST and NIJ, they are working on the FBI's multi-lab study.
So that multi-lab study, and I don't want to speak for the FBI, but essentially
, you
know, evaluates the vendor's solutions for crime scene analysis following and
judging
against those position statement requirements to see, hey, are these
requirements being
met, and if so, if not, how can we move forward with a solution to get crime
scene evidence
into a state or national database?
So we have our own evaluation.
The FBI's MLS study is kind of a separate evaluation, although completely
independent.
We are not involved in the publications that are going to come out of the multi
-lab study.
We have no input or effect on that, but we will be receiving feedback from that
multi-lab
study, and we will try and work that feedback into our solution, whether it is
the solution
that we launch or commercialize or an updated version of that shortly
thereafter.
So those are the main sources of evaluation.
Perfect.
Thank you.
I think that answers another question we had coming up.
So two and one there, Peter John.
Great.
All right, we have a few questions about crime scene samples now.
So let's get to those quickly.
Are there crime scene samples that you recommend not to run with rapid?
Well, I mean, we are testing a wide range of sample types in our verification
validation
and developmental validation studies.
So we're looking at almost everything, but it's really hard to look at every
single possible
crime scene sample.
Like I mentioned, there are limitations in a quantity, but our system is very
sensitive.
When it comes to where you should and should not use rapid DNA is really up to
the user
and their own validation studies, right?
But what we definitely recommend, and this is more of a larger thought process,
is rapid
DNA should not be used to consume a sample, right?
Especially a crime scene sample where you need to run that in the traditional
workflow
to provide confirmation or without access to a state and national database
currently
to get that investigative lead into a state or national database, depending on
where you
are, right?
To get a hit, hopefully, if you have no developed suspects and to try and
figure out what is
the source of this DNA?
So the samples, I mean, we'd have to go through a long list, right?
But optimal samples for rapid DNA are, of course, blood and saliva.
Mainly, they have the most amount of DNA for crime scene samples, and they're
frequently
found at crime scene samples.
And all of that plays well into a rapid DNA solution for crime scene samples.
Can you process all sorts of other samples, like hair, gum, you name it, other
biological
fluids?
I'll just leave it at that.
Those can all be processed.
We are in the process of evaluating those as well, and we will be tapping into
other
resources to evaluate those sample types and look forward to publishing that
developmental
validation as soon as we can.
Thank you.
That's awesome.
We will definitely be on the lookout for that.
So it was mentioned that both of positive control and ladders need to be run
for each
cartridge.
How many samples can be run per cartridge?
So, for a sample cartridge, there's single use.
They're really only meant to be used once.
You don't want to run a sample, take out a swab or whatever substrate was used
in there,
and then put into another sample into that same cartridge.
The sample cartridges are single use only.
Now, for our system, there's also a primary cartridge.
That supplies the bulk reagents that are needed for lysis and electrophoresis
on the
system.
These are not single use.
The ones that are going to be used on the 2.0 system are up to 150 samples.
Those can be used for multiple samples, and they work tandem with each other.
Remember, the sample cartridge is single use only, and the primary cartridge is
up to 150
samples, depending on the expiration date of those chemicals or the actual
cartridge itself.
Gotcha.
Okay.
Since crime scene profiles will all need analyst review.
Will mixtures generated on the rapid instrument be potentially suitable for
manual deconvolution
and interpretation?
Well, I would leave that up to the laboratory and their procedures or protocols
It's essentially kind of open at the moment, but as I mentioned before, m
ixtures that show
up in rapid right now are basically just going to be presented to the user as,
hey, we think
that this is a mixture.
That mixture flag is going to fire based on the genotypes at the different loci
So right now, it's not going to do any deconvolution, but it is wholly
dependent on the laboratory's
standard operating procedures for mixture analysis or deconvolution or
establishing a
major, minor, mixed major, whatever you want to put into a state or national
database.
Of course, also limited to that database as well.
So it all depends on how it's interpreted.
If it is a partial major, it's up to the database itself and the laboratory's S
OPs, whether
or not they would put that in.
But right now, the expert system, the system as a whole really just identifies
whether
it's a mixture or not.
Okay, perfect.
One of our attendees today, their lab is already, they're already experimented
on their own
with Intel cartridges.
Okay.
However, trying to bring this to the crime scene has yet to happen for the
sheriff's office.
She says she's hoping with the FBI study, there will be stronger guidelines and
access
to codus so that there's more value to the collection samples at the scene.
Obviously, you do not have a crystal ball, but do you envision something like
that happening
or what can you tell us about that?
Oh, absolutely.
But before I get into that, I would just say that, you know, right now, our
testing is
really just related to the cartridge and the software.
And that is what we are going to be releasing as soon as we can.
Our testing with RapidIntoPlus and the multi-lab study really doesn't focus on
mobility or
taking a rapid instrument to a crime scene.
Of course, that is possible, right?
And there are agencies all over the globe that are doing that with RapidHit ID
instruments,
whether it is in a mobile vehicle or building a crime lab, if you will, not a
whole crime
lab.
But let's just say a DNA testing facility using on-site or on-disaster location
to do DNA
processing on-site with Rapid.
Again, driving that actionable intelligence to get a DNA profile in about 90
minutes to
help identify victims to really exclude individuals, et cetera.
So the studies that we are doing and that the FBI doing are centered around
performance.
And how can we take the solutions and ensure that the user is getting all the
information
that they need to make a really good decision on whether or not this profile
should go to
a state and national database?
I hope that answers the question.
Absolutely.
I think it's the best of the abilities that we know now.
That answers the question.
Okay, next question then.
Is there going to be an option to take raw data from the system and put it into
GMID?
Absolutely.
Absolutely.
There are different levels of raw data as part of the position statement from
the FBI,
GM, MC, you know, one of the requirements is to be able to export raw data for
secondary
analysis.
So similar to traditional workflow, right?
With our new system, we're providing a whole different suite of applications or
avenues
of using that raw data all the way back to literally just the values of what
are the
peaks, whether it's baseline, everything.
Now for your traditional crime lab that has GMAP or IDX, they don't necessarily
need that
far back in the data analysis pipeline, if you will.
They really want the .fsa file, right, which is an output of the rapid hit ID.
You can easily obtain or export that from the instrument or from RapidLink 2.0
and you
get as well the .fsa file for the ladder that was used to call the alleles
present in the
sample.fsa file.
So you have both raw data files, if you will, or non-analyzed .fsa files.
Now those have been analyzed by the system and displayed to the user in Rapid
Link 2.0.
We are also, because we are now moving to GMAP or IDX as an analysis software
solution
for Rapid, we're also providing the user the .ser file, which most laboratories
are going
to be familiar with back in the day.
GMAP or IDX, if you wanted to technically review, you had to export it at SER,
import
it at SER.
You can still do that now, but with IDX, obviously you can just open up the
project.
You don't have to import export.
With Rapid, that .ser file allows you to see analyzed data.
But again, the question was about raw data.
Those FSA files, sample and ladder are available and the analysis methods will
automatically
import if you import a .ser file or you can get them from the run folder so
that you have
everything that you need to import the sample and the ladder into a new project
or an existing
project in IDX.
And do analysis with your own thresholds if you want to.
Again, subject to your laboratory standard operating procedures and validation
of the
system.
So yes, the short answer is absolutely the data files are present for every
single run
to do analysis, however you want to do it in GMAP or IDX.
Perfect.
And Rob, I know that was-
Thank you, Peter John.
Yeah.
Just to add to that.
So it will require GMAP IDX 1.7 to handle this upgrade to have the new features
IDX currently, however, will not display the SCO degradation or inhibition flag
That's not incorporated yet.
You need to use RapidLink.
But to get the full analysis and the benefit of the new sort of panel
definitions and the
mods that we've built, you need one seven IDX.
Yes.
And I'll just add to that we're going to keep building.
So the .ser file can be opened in 1.6 or 1.7 of GMAP or IDX.
If you want to actually analyze or reanalyze the .fsa files, you do have to
have GMAP
or IDX 1.7.
Thank you.
That was a very comprehensive answer, both of you.
So we all appreciate it, I'm sure.
All right.
Last few questions as we wrap up our time.
Sure.
Does the Rapid Instrument automatically search a profile?
Or is there a way to intervene and keep the instrument from searching a profile
that matches
a victim?
Yeah.
So current systems, 1.x or 1.3.x, RapidLink has a certain suite of applications
and one
of those is matching.
We're currently working on a similar application suite for RapidLink 2.0 to do
that as well.
But even the software as it is today will allow you to connect to an external
database.
That could be anything.
That could be a homegrown database.
That could be an application such as small pond, or that could be a database
that another
company or another agency has put together to work in concert with the
collecting agency
or the agency that's actually doing the DNA kind of running or processing.
And then the information gets shuttled automatically to the support laboratory.
And the searching matching occurs there.
So there are a lot of options.
But at a very minimal RapidLink 2.0, we'll be able to connect to an external
database seamlessly
and very easily to do all of those matching or other type of application
analyses.
Perfect.
Thank you.
All right.
So the FBI will allow a remote instrument installed outside the lab, such as at
a police
station, of course, to be covered under the lab's accreditation.
Can you discuss this and how that works?
That's a really, really great question.
And I know some people in the audience are probably smiling about that too.
So I recently learned about the upcoming sort of accreditation changes to allow
for external
agencies running rapid instruments to fall under the umbrella of the acc
reditation of
the main processing laboratory, if you will.
So I know some of that is still in process and in progress and will be updated
soon.
So that that answer will really be that answer.
That question will really be answered outside of the scope of our chemistry and
software,
if you will.
But those answers are absolutely coming.
And feel free if anybody else wants to, any other attendee wants to answer that
question.
All right.
Well, then with that, we will take our last question at the top of the hour.
So rapid DNA technology is often referred to as a vital tool to help drive
actionable
intelligence for investigations, just like we talked about earlier.
Can you elaborate on exactly how rapid fits with the existing technologies?
Yeah, absolutely.
I know we're right at the end of our time, but so this all goes around actions,
right?
Actionable intelligence, these kind of keywords.
We talked about that a little bit in the video and it's all about going a
little bit outside
of the traditional DNA analysis workflow or the traditional kind of crime lab
that is
set in a specific area and runs DNA samples a specific way, uses separate
instruments
for collection, extraction, amplification, quantification and genetic analysis.
Rapid really brings all of that together.
And not only can you have an instrument at a specific location, but you can't
actually
move that instrument around, you can take that instrument to a crime scene, to
a disaster
location, you name it and drive actions like establishing matches, identifying
victims
or identifying suspects or confirming a sample or just simply weeding out
samples that shouldn't
go to the laboratory or should go to the laboratory.
There are so many different options there to drive those actions like triaging
samples
and determining, hey, in 90 minutes or less, what should be run here?
What should be run at the laboratory?
And can we get an investigative lead?
Can we identify a victim?
Can we get some intelligence right now instead of sending that additional swab
or the remainder
of the swab onto the crime laboratory for eventual confirmation, right?
The rapid DNA instrument allows almost immediate feedback and drives those
actions that intelligence
to establish a connection.
Perfect.
Well, thank you so much, Peter John.
Audience, unfortunately, that wraps up all the time we have for our Q&A today,
but we
do appreciate all the questions and we, of course, appreciate all the insight
provided
by Peter John and Rob today, so thank you and thank you to Thermo Fisher
Scientific,
the sponsor for today's webinar.
In 24 hours or less, this webinar will be available on demand if you'd like to
watch
it again or maybe share it with friends and colleagues.
But until then, thank you so much for attending and we hope to see you next
time.