Tips, Tricks, and Best Practices for Gaining Efficiency in Your Forensic DNA Laboratory
This webinar will detail how new sample triage assays and automated methods can help forensic DNA labs reduce backlog, improve turnaround times, and increase efficiency. David Miller from West Virginia State Police Forensic Laboratory will discuss how the lab is using NaOH extraction and Applied Biosystems™ Quantifiler Trio DNA Quantification Kit as a Y-screen assay to improve efficiency in sexual assault kit workflow. Thermo Fisher Scientific will discuss how automated solutions, such as the ID NIMBUS® Presto using the Applied Biosystems™ PrepFiler™ Automated Forensic DNA Extraction Kit, address bottlenecks for each step in DNA processing. You will learn about: How the Y-screen assay can help determine whether enough male DNA is present to yield a probative STR profile How automation can optimize various steps in your workflow and improve efficiency in your laboratory
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Gaining Efficiency with Forensic Automation Solutions
Hello and welcome to Tips, Tricks and Best Practices for gaining efficiency in
your forensic
laboratory brought to you by Forensic and Sponsored by Thermophisher Scientific
This is the fourth webinar in the sixth part of future trends in Forensic DNA
technology
series.
My name is Michelle Taylor, Editor-in-Chief of Forensic and I will be your
moderator throughout.
For today's webinar, you can earn one hour of continuing education credit.
Following the conclusion of the webinar, you will receive an email with
information on
how to obtain CE Credit documentation.
We have a great line up scheduled to present to you today, but before we begin,
I'd like
to cover just a few logistics.
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Today, you will be hearing from David Miller, Forensic Scientist Supervisor at
the West Virginia
State Police Forensic Laboratory.
He has 26 years of experience as a DNA analyst and biological evidence
processor.
Miller is a member of the West Virginia Sexual Assault Forensic Examination
Commission and works
closely with the West Virginia Foundation for Rape Information Services to
improve collection
and testing of sexual assault evidence collection kits.
His education includes a BS in biology from West Virginia State College and an
MS in Forensic
Science from Marshall University.
You will also be hearing from Garrett Steed, Production Application Specialist
at ThermoFisher
Scientific.
Steed has held this role for the past eight years.
Prior to his work at ThermoFisher, Steed was a biochemist researcher with
Forensic Science
Service in the UK, as well as a laboratory analyst with A.B.
Bio in Agricultural and Food Services Business.
Steed received his Bachelor of Science Honors in Forensic Science from England
's University
of Kett.
Thank you for attending the fourth session in the six-part Future Trends in
Forensic
DNA Technology webinar series.
After this webinar, please be sure to check your email for more information on
CE Credit
documentation.
We look forward to seeing you on September 10th for the fifth part, Advances
and Analysis
of Human Remains.
And without further ado, I'm going to hand it off to David to get us started.
Good morning and thank you Michelle and ThermoFisher Scientific for the
opportunity and invitation
to speak to you today regarding how the West Virginia State Police Forensic
Laboratory
is using sodium hydroxide extraction and quantifiler trio as a Y-screen to
improve workflow
with regard to sexual assault evidence collection kits.
We'll discuss how our small laboratory ended up moving from a body fluid
identification
to a Y-screen process and keeping in mind the SWIG DAM report released this
past June
on Y-screen.
But first, a little bit about our state and our situation here.
West Virginia has a population of a little bit under 2 million, which our
laboratory serves.
The number of reported sexual assaults in our state is around 1100 a year.
And we have one standardized sexual assault evidence collection kit, which we
use statewide.
We also distribute that kit to several laboratories in Ohio and in Maryland for
use on West Virginia
victims kits that will be coming back to us.
And our kit is a pretty standard kit.
It contains two internal vaginal swabs, two external vaginal swabs, anal oral,
additional
swab for oral contact.
There's a pubic hair combing or pubic area swab envelope in there.
We also have various packaging items for clothing.
And we also include a toxicology kit with blood and urine collection materials
for direct
facilitated sexual assaults.
But we have 72 collection facilities in our state, including hospitals, child
advocacy
centers, and health care clinics.
One does not have to be a same trained nurse in West Virginia to collect a kit.
We have same trained nurses as well as non-same trained individuals collecting
kits.
So based on that training and experience of those individuals, we do see a wide
variety
of both quality and quantity of items collected in our kits.
To help with that situation, we use our in-house tracking software application,
not only to
track the location of kits, but to also record the quality of the kit
collection.
We will make comments if an individual says that there was oral contact with
her neck,
for example, but there were no next swabs collected.
We will provide a quarterly report back to that hospital saying that there's a
need
for improvement there.
And we will also provide that information to our same trainers so that it can
be used
in their trainings.
Our laboratory itself is made up of two sections with regard to DNA.
We have a biology and processing section with six full-time forensic scientists
, one of
which is in training and recently hired.
And our biology DNA section has 11 full-time scientists and three technicians,
a total
of four who are in training at this point.
And Yokoala just said that we have about 1,100 sexual assault reported in West
Virginia
a year.
Our sexual assault kits are distributed by the processing section of the
laboratory.
We custom order them through SIRCHI and distribute about 600 kits on average a
year over the
past eight years while we've been recording this information.
And we have received back about a third of those kits year after year
repeatedly, even
though we've requested repeatedly that all kits which are collected be
submitted to our
laboratory.
This was especially true following our DANNY grants and SAKI initiative
projects where
we are required to prevent kits from being unsubmitted to our laboratory.
So we can see from this chart that we have a problem getting the number of kits
that
we send out coming back to our laboratory.
To be fair, some of them are non-reported sexual assaults which go to another
offsite
facility at Marshall University for storage and we know that some kits are used
in training.
But we estimate that around 200 kits a year are collected and not submitted to
our laboratory.
Our laboratory supports the mandated submission of a sexual assault kit.
If it's collected it should be submitted here.
This is also supported by our state's sexual assault forensic examination
committee.
So we are in support of a mandatory submission and began several years ago
preparing for such
a thing to occur.
We increased our storage capacity at our lab.
We can now house upwards of 3,000 kits if we had to in a newly built evidence
storage
room.
And we began the hiring process of two new employees, one in the processing
section and
another in DNA to handle the expected increase in caseload that this would
bring them out.
And most importantly we began validating and looking into the why screen
process to change
our workflow with regard to moving from body fluid identification to a why
screen.
All of that really kicked off in 2019 when the West Virginia State Legislature
passed
Senate Bill 72 which was the sexual assault victims bill of rights.
That bill said among other things that a victim has the right to have a sexual
assault kit
tested and preserved by the investigating law enforcement agency.
That bill also said that the victim has the right to know the results of those
tests provided
that it does not interfere with the investigation.
That is the responsibility of the investigating law enforcement officer in the
case.
That was in 2019.
This year in 2020 in March the West Virginia Legislature passed House Bill 4476
which we
call a direct deposit bill dealing with the direct deposit of sexual assault
kits.
4476 says that upon collection sexual assault forensic examination kit shall be
submitted
for testing by the health care provider to the West Virginia State Police
forensic laboratory
within 30 days of collection or soon thereafter as practical.
That bill became effective on May of 2000, I'm sorry May the 18th of 2020.
Since then I've been able to look at the increase in the number of kits that we
're receiving
every month and I'm able to project that by the end of this year we will see
approximately
400 kits submitted to our laboratory.
I expect the increase this year will be about 150 cases.
Next year I expect we'll see a full 200 more cases on our past average.
It might be interesting to note here that we are receiving fewer requests this
year for
sexual assault kits.
I don't know if that's the case nationwide but we have speculated a little bit
that this
is perhaps due to some fear of going to the hospital in these times.
So you can see here we did have an increase and expected increase in the number
of kits
that we are having received at our laboratory.
I will say that House Bill 4476 had some teeth with it following a misdemeanor
crime if anyone
willfully neglects to follow this direct.
So prior to February of 19 our laboratory was performing body fluid
identification on
all items submitted in a sexual assault case.
Clothing items, swab items in a kit, bedding, whatever was submitted.
We tried to limit the items but for the most part our case submission policy
would allow
for multiple items to be submitted and we would perform that Leukomelikite
green presumptive
test, as a phosphatase presumptive test, an AB-A-R-P30 lateral flow amino assay
for prostate specific
engine followed by a Christmas tree stain and your occasional RSID saliva test.
If you are performing those tests you know that they take time and sample.
Time and samples both are consumed in this testing.
Notice that top slide in the center, the amount of material that we would
collect take from
the swabs for a acid phosphatase test.
Come back to that in a minute and here are the amounts of sample that we would
take for
AP-30 and then maybe another cutting for an RSID if it was requested.
Our laboratory at the conclusion of that testing would maintain our multiple
samples retained
for DNA testing, multiple extractions, quantitations and amplifications would
then be performed
in the DNA section on those samples.
This is the note our DNA section is using PyJENESI-1 advanced Excel for
extraction of those samples.
We did and still do prepare a report of our initial findings in the processing
section.
I would also say that in cases that were negative, if we had a negative
presumptive test or negative
confirmatory test, we would keep samples knowing that the DNA testing is more
sensitive than
our presumptive testing.
If there was an allegation of a contact, we would keep that sample even with a
negative
presumptive test.
After February of '19, we began doing a sodium hydroxide extraction and quantif
ylotrion amplification
on swab samples in male suspect and female victim sexual assault.
This is what we validated.
Let me thank Thermophisher and Jared for the work they did on that.
We benefited greatly from it, but we are performing the Y-screen on two swabs
per area tested.
I mentioned that our internal and external vaginal swabs, we typically request
two swabs
for every area, every body area that could be collected, and we test those
together.
We would take a tenth to an eighth of each swab and combine that into one Y-
screen test
for that area.
We have swabbed, most swabs in a case are tested, we're typically seeing
anywhere from
four to twelve sets in a usual case, and we are not performing serology unless
we're
specifically requested to do so.
We are a two report to extract workflow laboratory, so we are still writing a
report on our results.
Now that we're doing the Y-screen, we find that we are only retaining one to
two items
retained for DNA testing, and that's based on the result and the scenario that
we're
faced with.
If there is oral contact to the neck or breast, we will keep those swabs if
they're positive
for male DNA, as well as preferably an internal vaginal swab, if that's the
best sample.
The STR, Y-STR decision is made in the DNA section based on the quantation
values from
the full swab extraction, so we're not making a determination in processing
about the direction
the testing will go, that's made after the full extraction over in the DNA
section.
A little bit about a sodium hydroxide extraction, and what we're calling a
dirty extraction,
there is no purification of the samples that we're testing, so we are only
doing this on
swabs that are in sexual assault kits, no clothing items, we didn't validate
that.
But this test is performed in a Lysep column, which you see there in the lower
center, this
is just a column with a separation filter and membrane, which breaks with
centrifugation
allowing the Lysate to flow into an extraction tube.
We will put the two 1/10 to 1/8 swab cuttings in 100 microliters of one normal
sodium hydroxide,
and place that onto a thermoshaker set at 80 degrees Celsius for 10 minutes at
700 RPMs.
It's a very quick extraction.
That DNA is stable in the alkaline solution like that, and it is then centrif
uge for two
minutes separating the substrate from the extract, which is then neutralized
with four
microliters of glycerolocytic acid.
That is then diluted 1/5 dilution in TE-4 and is ready to amplify with the
quantifiler
trio.
We are using quantifiler trio on an AB7500 real-time PCR instrument, 96-walled
plate format.
It will take me about an hour and a half from setup to results.
From setup to results, I mean I've got my extracted DNA from the sodium hydrox
ide extraction.
We're going to set up the amplification and place it on the real-time
instrument.
Then about an hour and a half, we have results and are ready to collect samples
for DNA testing.
Typically, I'm assigning five to seven sexual assault kits per analyst per week
when we're
doing these runs, and we are able to set up, do all the paperwork necessary and
add the
samples to our limbs, take our bench notes, cut the samples, get them into,
perform that
extraction, and we will have a result at the end of about a two-day period.
If we start on Monday morning, I typically have results in five to seven cases
per analyst,
and I'm ready to go.
We will typically batch two to three analysts per plate and batch our work in
that fashion.
The real-time PCR itself is the quantifiler has four targets, really.
It has a small lot of similar target.
Of 80 base pairs, these are multi-copy conserved regions of DNA.
The large autosomal target is 214 base pairs in size.
The haploid y target is 75 base pairs in length.
There's also an internal PCR control, which is a 130 base pair synthetic strand
of DNA
that's amplified.
We rely on this amplification here to be a guide to assist whether or not we're
seeing
any inhibition in the sample.
We're routinely checking the IPC to make sure we're not seeing any inhibition
in our samples.
We have seen some, and I'll show you an example of that in a second.
But besides the quant values of those three top targets, small, large, and y
targets, we
are also able to determine a degradation index due to the size of those small
and large autosomal
targets as well as a male to female ratio in the case.
This can give us an idea as to whether or not that sample is going to end up
going towards
a YSTR analysis or perhaps differential extraction in global value.
Here I have an example of a multi-component plot.
This is fluorescence relative to cycle number.
You should be able to see here that the internal PCR control, which is this red
pair, kind
of took off at around 27 cycles across the cycle threshold there.
We have an IPC value there for 27.2 in this case, which is what we typically
see in an
uninhibited sample.
This particular sample was part of our validation and is a 10% male blood mixed
with female
blood, so 10% microliters of female blood, and that was diluted 100-fold.
You can see from the result that the small autosomal target, which is the
primary target
of the assay, wanted at 0.02 nanograms per microliter, and the Y value is
approximately
a tenth of that, which is what we would expect in a tenfold mixture like that.
This is what a typical run looks like.
The next three slides are real case examples where we have taken approximately
seven samples
from a sexual assault kit and performed the screen on, and I'll go over how we
are using
this information to select the samples that are going forward for DNA testing
and what
we would have done in the past with a body fluid identification.
This first case is a negative male DNA case where we receive seven samples.
These screen seven samples, the external vaginal swab and anal swab, a set of
anal swabs.
The nurse examiner in this case collected four oral swabs, so we divided those
into
groups of two and screened oral swabs one and two and oral swabs three and four
There was a pubic hair swab, a neck swab, and an unusual sample of inside the
ear swab.
And looking at the Y values for this, you can see that there was no male DNA
detected
in any of these samples, and that's exactly how we would have reported this
case in our
processing laboratory report.
We would say that no male DNA was detected in these samples.
With the exception of the inside the ear sample, which we would have reported
in this case
as inconclusive.
Take a look at the IPC value there, the internal PCR control across the cycle
threshold at
31 cycles.
This is a little bit high and can be an indication of an inhibited sample.
In this particular case, we would have called that inconclusive and sent the
sample over
for confirmation with a DNA extraction and purification before the trio run.
Had we been doing body fluid identification on this case, we would know, based
on the
scenario, what body parts were indicated as being affected in this case or
touched.
And we would have kept probably the external vaginal swab sample, an anal, an
oral, and
perhaps the next sample to begin testing with.
The next case, again, with seven samples is what we would call a low-level male
DNA case.
Again, we have an internal vaginal sample, which was two swabs.
A sample just labeled vaginal, which we don't know if that was the same area
collected as
the internal vaginal, which is labeled vaginal.
The cervix swabs, amons pubis swabs, two swabs labeled around left nipple, two
swabs labeled
around right nipple ring, and two swabs from a belly button ring.
In this case, we had relatively low amounts of DNA in all of these samples,
lowest of
them being the cervical swab, which is usually one of the better swabs.
But in this cervix sample, and based on our validation, we would call this one
a trace
amount of DNA because in our laboratory, we know that anything below .0004 nan
ograms
from microliter or .4 picograms from microliter, we would not expect routinely
to have repeatable
results on a full swab extract of this cervical swab sample.
Right now, we're still calling them positive.
We're just saying it's a trace amount, and we're looking into it a little bit
further
if we can say that an insufficient amount of male DNA was detected to continue
on with
testing.
Right now, though, this is a trace sample.
But you can see from these results that I can now make an educated decision
about what
is the best sample to send over for DNA testing.
I just don't have a weak AP and maybe a negative infirmatory test with body
fluid ID.
I can look at this and say, "Okay, the internal vaginal swab sample has the
highest quant
of male DNA as far as an internal sample goes, but I'm going to select the
around the right
nipple ring swab as an external body sample that has the best chance of giving
full DNA
profile."
So in this case, I've very neatly narrowed it down to the two best samples that
we can
send over for testing and have our best expectation for results.
Thirdly, we have a case with another seven samples that gave us pretty nice
results.
So I've got vaginal vaults swabs one and two, three and four, another cervical
swab,
an external vaginal swab, a pubic area swab, and then anal and oral swabs.
Of these, you can see the vaginal swabs three and four gave the highest Y value
of .2 nanogram
per microliter, better than the other two swabs of vaginal vault one and two.
The cervical swab is positive, but not quite as much as the vaginal vaults sw
abs, and
the external vaginal swab is very positive.
Now if this case involves someone who had had proconsensual intercourse, we
might then
make a decision to test both the internal and external vaginal swab samples,
but because
in our state, the sexual assault is defined by penetration of the vagina, then
we are
going to usually go with an internal sample if we believe that that sample will
give us
results.
The pubic area and anal swabs also positive, and then there's a nice clean oral
sample
with no male DNA detected.
One of the things that I've been able to do is to take a look at the last 2,000
samples
that we've done the Y screen on and make a comparison of the body cavity and
the amount
of times that we obtain a result.
I've done this for internal and external swabs, and you can see here that the
vaginal swabs
that we get about 47% of the time are positive, compared that to cervical,
where about 61%
of all the cervical swabs that we've tested have been above 0.0005 nanograms
per microliter.
So above 0.5 picograms per microliter, we're seeing that 61% of our cervical
sample.
Compare that to the oral, where only 7% of the time we're getting a result of
that.
That's that positive.
With regard to external body swabs, breast have been pretty good at 22%.
Neck over 56% of our samples are positive when they're collected, which is a
really great
sample.
So I can take this information back to our same trainers, back to our hospitals
, and
say be sure to collect that next swab.
She says there was oral on-tock with the neck.
Get that next swab.
Take that cervical swab.
Those are showing to be our best samples.
Some of the other things that I'd like to do in the future with this chart
would be to
add to that the post-assault interval and say how often are these samples
positive when
there was a shower?
How often are these samples positive from 24 to 48 hours after the assault?
48 to 76 and so forth.
And we say more about when we lose the ability to obtain a DNA result from a
sample based
on post-assault interval.
Can I make any conclusions about whether a sane trained nurse is doing a better
job with
quality of collection than a non-sane trained examiner?
That's something else that we can do to try to support the use of sains in our
state as
those who are collecting sexual assault evidence kits.
And lastly is a slide where I tried to make a little bit of a comparison
between the cost
of performing a body fluid identification which we have on the left and a Y
screen examination
which I have on the right.
Relatively speaking there's not a great difference in the cost here.
The cost savings and the time savings that we're seeing is coming post-
processing where
we're able to make a better informed decision about what is the best sample to
keep for
DNA testing.
I do think there is some cost savings.
I think we're seeing some time savings because I'm not having to wait for an
hour extraction
to do a P30 and then if that's negative selecting another sample to do or I'm
not spending an
hour at a microscope looking for sperm in a case where they don't exist.
We're going right to the Y screen learning if that male DNA is present and then
sending
the best samples over for DNA testing.
So I look forward to some conversation about what we're doing here and how we
're doing
it.
With regard to the SWIGDAMM report and with that I will give this to Gareth and
he can
continue the conversation and I do look forward to some conversation.
Thank you for your time.
Thank you for the introduction and hello everybody.
Today I'd like to speak with you about laboratory automation and how that can
be used to improve
the efficiency of your laboratory's workflow.
And in addition I'd like to speak about the HID Professional Services team
which I'm a
member and how we're able to partner with your laboratory to help in the
adoption of
new technology and new automation.
So when we think of workflow efficiency and the benefits of it, the first
points that
most people often think of are the two listed at the top here.
So this is an improvement in the amount of time it takes to process a sample
and secondly
the number of samples the ill laboratory is able to process.
You also need to think of some of the other benefits, for example precision and
accuracy
improvements and this is evidence in a reduced number of samples that need to
be repeated.
Again, improving time to result and increasing sample throughput.
There are also other benefits, for example data management, reduction of cost
as well
as optimising the tasks and tools and resources in your laboratory, for example
making best
use of the laboratory analysts that you currently have.
The equipment that you currently have and the space that you have in your
laboratory.
I'm thinking then about validation.
We often think of validation as one single item but if we dive down under the
surface
of a validation we'll see that there are actually many different components
that make
up a validation and this is everything from the initial developing a method and
testing
it through to what traditionally people think of as validation which is the
work, the
practical lab work to test the system, analysing the resulting data and
preparing reports that
are suitable for your regulatory requirements.
But then the validation doesn't end there.
We also need to think about how can we train your laboratory analysts in this
new technology?
How can we assess their competency in it and how can we help you in preparing S
OP documents,
for example.
So there's this whole raft of separate stages that make up a full validation
and the HPS
team is experiencing in all of this and we've partnered with multiple labs to
deliver some
all of these parts of validation.
So thinking about process efficiency improvements, one of the first steps that
we need to look
at is where is the bottleneck in your workflow and a bottleneck can occur
really anywhere
from the initial receipt of a sample right through until where we have the
final result
and we're able to produce a report on that sample result.
And the key here is that we need to identify the bottleneck but then we need to
not just
move it but to actually remove it from the system.
For example, there could be a bottleneck in the sample purification step if we
just address
that for example with adding new or additional automation then we may just move
that bottleneck
down to quantification where the existing systems that the laboratory has in
place just can't
cope with the extra level of samples that are placed upon it and so we've just
moved
the bottleneck to the quantification step.
So really the key here is that we need to be looking at the lab's workflow in
its entirety.
We can't look at each individual part in isolation.
We need to consider everything and how we can completely fix the system rather
than just
tweaking with certain elements of it.
And this slide, there are just some examples here of various liquid handling
robots on
the market that we've had some experience with here in the HPS.
These include instruments from Hamilton, from Tcan and from Beckman.
And by no means is this an exhaustive list.
We have worked with other instruments and we can support customers that are
running different
robots to be shown.
We are very lucky in the team that we have a lot of experience in-house in
working with
these multiple instruments.
We have good contacts within the robotic companies themselves.
So we are very well placed to be able to support you on these instruments shown
here and also
a wide range of other instruments.
If we just take a step back and think now, regardless of the technology that
you go with,
so regardless of whether it's a Hamilton robot, for example, or a Tcan robot,
there are definitely
core features that you need to be considering regardless of the technology that
you select.
The first is the ability for barcode tracking.
Barcodes are a very simple way of tracking samples and reagents throughout the
whole process.
It's a way of reducing errors and reducing operator hands-on time.
In the robotic system where everything is locked and recorded, it's a very
simple way
to be able to show that samples are processed as expected and that can be
demonstrated in
the results files that are generated.
You also need to consider worklists.
For example, is there a limbs that you need to integrate with?
Considering things such as run parameters, for example, you may currently be
working
with samples in tubes, but on switching to automation, it may actually become
apparent
that it's more appropriate to be working with plates in all or part of the
workflow.
So it's looking at what you currently have in your workflow, but also what
would be most
appropriate going forward.
And then we need to consider reports and files.
This is almost an extension of worklists.
So what do you need the robot and the software to be able to reduce for you?
For example, you may wish for it to generate not just a limbs file, but also a
file that
could be used on a downstream robot, for example, or possibly a plate map file
for a quant
studio 5 or a 3500 instrument.
This is just another benefit of automation, that these files automatically
generated.
So it's reducing operator time in generating these files.
It's also ensuring that there are no errors in these files also.
And then just thinking then about some of the systems that are on the market at
the
moment that we have supported and have experience with.
So thinking about the beginning of the process, so extraction, beginning with l
ysis.
So this is frequently a bottleneck in many laboratories because it's a very
hands-on
process.
And typically it is performed manually in the majority of laboratories.
And so this photograph here is actually taken from the Hamilton Autolyse robot,
which is
a very nice solution that is able to fully automate the lysis protocol.
And one of the real benefits here is that not only is this entirely operator
hands-off,
it means that one operator taking charge of this one instrument can process a
full batch
of 96 samples themselves.
And it's also freeing up their time as well.
So whilst this robot is running, they're able to be in the laboratory or
perhaps out
in the office kind of doing other tasks that they need.
So really it's kind of making the best use of the resources that you have and
making
the best use of people's time.
And then if we then think of the next stage of the process, so this is the
actual purification
step, so following lysis.
So again, we think here this photograph is taken from a Hamilton ID starlet.
This is able to process a batch of 96 samples at once.
So again, like with the autolyse, this is one operator able to take care of all
these
number of samples in one go.
And if we're comparing this, for example, to small scale instruments, so
perhaps an
automatic express or an easy one that working much smaller numbers, you can
really see the
benefit that one operator is able to process many full time number of samples
in one run.
And this nicely moves on then to just highlighting one of the newest solutions
that we have available
for extraction.
And that's the ID Nimbus Presto instrument.
And this actually achieves sample extraction through a different approach to
that that
may be achieved, for example, with a Hamilton ID starlet or a T can evo.
And rather than pipette transferring, we're actually using magnetic rods to
achieve particle
transfer.
So here we have a magnetic rod that is covered in a disposable plastic cover
that the magnetic
particles bind to.
And they are then moved between the various reagent containers.
So for example, they can be moved to the reagents for binding and then
subsequently to the reagents
necessary for the multiple wash steps and the final elution step.
And so here this is natural picture of the instrument.
So this is one of our newest solutions which we launched at the end of 2019.
So what we've done here is we've taken two instruments that already existed on
the market.
So on the left there we have the Kingfisher Presto and on the right is the
Hamilton ID
Nimbus.
So we've integrated a Kingfisher Presto into a Hamilton robot.
And yeah, we just have some parts that are highlighted here.
So on the left, which is where the Kingfisher Presto is located, this is where
the actual
chord, the extraction takes place.
And then on the right-hand side, which is the Hamilton deck, this, for example,
is where
you would load your samples, processing plates, pipette tips, and also
containers of the
top filer reagents.
And on the very bottom right there you'll see that we've highlighted the bar
code scanner.
So the robot includes an integrated barcode scanner coming back to what I was
mentioning
earlier, just about the importance of barcode scanning in automation.
And how then this instrument is able to ensure accurate and reliable sample
tracking.
And this is just a nice schematic of the instrument, just kind of showing it
from above so we
can quite clearly see on the left-hand side where we have the Kingfisher Presto
, which
is the region where the extraction is taking place.
And then in the middle then we have the processing area, which is where re
agents are added to
plates where the sample is transferred into a processing plate at the beginning
of a method,
for example, and then on the far right then we have a waste container and next
to the other
region where you would load your samples.
So like I said, this is a solution that is currently available.
It launched at the end of last year.
This is an extraction only instrument and the real benefit of this is the speed
in which
it can process.
So it can process a batch of 96 samples and it takes less than an hour for
those 96 samples.
So it's in the region of 50 minutes, it takes to process a full batch of 96
samples, which
if you compare it to some of the existing automation on the market, it's much
faster and obviously
considerably faster than if you're thinking about manual processing.
And just to highlight some kind of recent development work that's going on with
the instrument,
so as I said the instrument has launched, but we continue to develop and create
new solutions
for it based on customer demand.
So the latest project is that we are working with the Pratfiler BTA kit.
So this is the DNA extraction kit that has been optimized for working with bone
teeth
and adhesive samples.
So in addition to actually having a new protocol that can be installed on the
Nimbus Presto robot,
this will be supported also by the launch of a new kit, which will be the
automated Pratfiler
BTA kit.
And this will have all the ratings necessary for BTA extraction and they will
be provided
in large volume bottles, suitable for automation.
So this is currently being validated at the moment, so it's been co-developed
between
ourselves at thermophisher and by Hamilton robotics, and it's currently in our
validation
phase at the moment.
And based on the customers who we've spoken to, so as well as kind of testing
this to ensure
that it works well for the core bone teeth and adhesive samples, we will also
be looking
at, for example, touch DNA samples because we know that some customers do like
to use
this BTA kit for a wider range of sample types, perhaps they prefer one kit for
all sample
types.
So as I said, this is currently in development and we're hoping to launch this
in October
of this year.
So in a couple more months, this will be fully available as a solution.
So we will have the instrument supporting regular Pratfiler and then secondly
Pratfiler
BTA.
So that was thinking about DNA extraction.
If you can move on to the next stage in the process and automating the quant
ification step,
I think one of the real key features about quantification and automation for
quantification
and one of the real benefits for that is if we think about standard curves.
So a robot you can guarantee will always pipette in a consistent way repeatedly
So whether it's the first run of the day, whether it's your hundredth run
overall,
whether it's the thousandth run that a robot has ever performed, it will pip
ette consistently.
And we don't see differences.
So for example, you may see slight differences in pipetting, a biasing glal
analyst, a more
noticeable differences in pipetting between different analysts, but with a
robot it will
run consistently.
And so that is then removing any kind of worry that there may be about whether
a standard
curve would pass or not.
So the robot is able to create standards automatically for you.
If you already have some existing standards, perhaps they've been prepared on a
previous
run by the robot, then those can be used instead.
And also now that we have the ability to support a virtual standard curve, it
truly means that
we can process a batch of 96 samples on one plate.
So without needing to leave any additional space to allow for positioning of
standards
as we traditionally would have needed to.
And then if we think of the last step in the pre-PCR workflow, which is the PCR
setup and
normalization, again this is where we see a huge time saver.
Compared to manual processing.
So the software is able to automatically analyze a quantification results file,
perhaps a
Panchrio file from a Qantuio 5.
It's able to analyze that and then to determine how each sample needs to be
diluted to achieve
a particular target input for PCR.
And it's very easy to set variable targets per sample within the software.
So perhaps one sample is having a recommended one nanogram input, but for
another sample
you wish to have a slightly lower or perhaps a slightly higher input.
So that's all very easily entered into the software and in the background then
the required
calculations performed automatically.
You can decide what to do with each sample on a very much on a sample by sample
basis.
So not only input level, but you can easily choose for example to skip a
particular sample
based on quality criteria that you've defined in the software.
And also just kind of a final note that I should mention then is regarding
direct amplification.
So this is also another technology that we're able to automate and it's
something that we
have solutions already on the market for and something that we have a lot of
experience
of working with.
So whether that's working with blood or saliva as a sample type, whether the
substrate is
FDA cards or perhaps co-pattern nucleic cards or whether you're working with sw
abs, then
that's all entirely possible through automation.
The example shown in the photo on the bottom right here, this is a Hamilton
easy pantrobot
which is able to work with sample cards.
It's an imaging system that's able to take photos of the cards, it's able to
determine
the optimum position to take a punch and then automatically punch that into a
PCR plate.
And this technology is able to work with all of our direct amplification
chemistry kits.
So for example Global Father Express or perhaps Verifile Express, that's also
supported as
well.
And as a final note, I just wanted to talk about the HID Professional Services
team of
which I'm a member of and really how we can work with you as an implementation
and validation
partner.
Not only within automation but also within regular sample processing as well if
that's
what your laboratory needs.
So as I've said, we're able to work well with our internal team and also
robotic vendors
and their applications team.
So we're able to create methods for you, identify what we would consider to be
good solutions
for you based on your current workflow, what your workflow requirements in the
future would
be.
And then kind of once we have these instruments and these protocols in place,
then we can
work for example on performing verifications or validations or performance
check which
would be used where there are multiple instruments, multiple new instruments
and we're kind of
comparing the performance of all the instruments together to ensure that they
're all performing
to a similar standard as well as also then as I mentioned before performing,
training,
looking at things like competency, SOP documents as well.
So everything that's necessary.
And I'm just going to round off the presentation just by sharing some contact
details here.
So there's obviously my email address there and two of my colleagues, Jared and
Scott,
who are both based in North America.
So that's kind of really highlighting that we very much have a global reach.
So we kind of cover every territory globally, we have robotic experts available
within all
the regions.
So we're definitely able to support you and really we just need to know how we
can work
with you, how we can partner with you and what we can do to help you.
And with that I'd like to say thank you for your attention and please let me
know if you
have any questions.
Thank you.
Audience, it is almost time for the Q&A portion of our webinar.
If you have not already, please take a moment to ask our presenters a question
using the
Q&A dialogue box on your screen.
While you do that, we're actually going to throw up two polling questions for
you to
answer.
The first one, how does your lab currently triage sexual assault kit evidence,
a manual
sperm search via microscopy, serological assay, you already use the Y screen or
you do not
triage and test all samples.
Why don't you go ahead and take a moment to answer what your lab does and then
we will
see what everyone says and get some insight from our experts.
All right.
This is what we are looking at right now.
It looks like the majority of you already use Y screen.
So that's pretty great.
David, what is your thoughts on these interesting polling results?
Well we've seen such an improvement here with the quality of the sample that we
're sending
over for DNA.
I think it's the way that we're going to go in the future and we're looking at
the QAS
guidelines in our laboratory and are knowing that we're going to be seeing more
kits coming
into our laboratory based on the sake and danny grants that we've all been
through
here recently.
So we explore kits and we expect that this sort of a workflow is going to be
better for
everyone that's doing such a thing.
Absolutely.
That's great.
Those are some interesting results then and definitely tie back to what you
were talking
about.
All right.
Let's get one more poll in there before we proceed with our Q&A.
Which areas are the greatest need for automation?
DNA lysis, DNA purification, automated differential extraction, Y screen quant
ification setup, normalization
slash SPR setup, or maybe all of the above.
All right.
It looks like most of you need the most house with automated differential
extraction, followed
by Y screening.
So that's interesting.
Audience, we really appreciate you taking time to answer those polls.
So what we're going to do next is jump right into our Q&A.
So David, we have a bunch of questions already coming in for you.
So let's get this started.
So first, David, could you explain maybe in more detail the workflow regarding
the biology
screeners that you were talking about earlier?
Certainly our laboratory does have two sections here.
We have a biology processing unit and a biology DNA section.
We separated those out in 2005 so that we could offer investigators a
preliminary report
on the findings in sexual assault kits to say that they do or don't have
biological material
suitable for testing.
And we've been operating that way doing body food ID since 2005.
So we still have these two units.
And with the five individuals that we currently have in processing and one soon
to be completing
his training, we will have six individuals that examine all physical evidence
in our lab,
including sexual assault kits that prepare the samples for our DNA unit.
We, in the case of a Y screen, will actually go through and collect the samples
and put
them in a two milliliter tube ready for the EZ1 extraction.
And at that point, the DNA analysts just come over and take that sample and are
ready to
do the full swab extraction.
I saw a question about how we did that, which we'll answer in a second.
But so with the five of us looking at and taking those samples, we do prepare a
report.
So we are a two extract, two report laboratory.
And we are looking now into the best way for us to be operating most
efficiently at this
point.
But that's for now what we're still doing.
Okay.
All right.
Great.
Thanks.
Let's get on to those swabs.
Since you take a portion from both swabs per area tested for the Y screening,
have to
decide which of the swabs to submit for full purification and SPR processing.
The short answer to that is we don't.
We actually take half of each swab.
We know that the screening sample is not necessarily going to directly
correlate to
the amount of DNA that's obtained from the full swab extraction.
So we take our widescreen sample from the tip of the swab down the side a
little bit.
Most of our sexual assault kit swabs are a visible stain, but we do get your
occasional
body swab that it doesn't even appear used.
But we will try to get that fluffy end of the swab that may have been disturbed
, just
a portion.
And then when we get back that positive result, we don't know that it was from
one or both
of the swabs that we tested together.
So we will take half of each of those swabs or equivalent swabs being extracted
for the
DNA portion.
Okay, gotcha.
That makes sense.
Garrett, we got you back yet?
Yes, yes.
I'm sorry.
No, no worries.
That happens.
Let's get you involved.
We want to ask you about the ID Nimbus Presto.
So using that, can you also sample from...
Can you process samples from tubes instead of from a plane?
Yes, yes.
So I mentioned in the presentation that we have a new version being released in
a round
round of October time.
And that will have the necessary kind of software protocols and hardware to
support tubes and
plates as both the input and output for the robot.
So yes, we can work with tubes and plates depending on a lab's work flow.
Fantastic.
Okay.
And can a single robot handle multiple applications?
Yes, yes, definitely.
So I think a nice example of that if we think of the Hamilton ID Starlet robot,
which is
a robot designed with all the necessary hardware and software for working for
DNA purification,
the quantification step and the FDR and normalization step.
So yes, so multiple applications can be combined onto one robot.
And really that's a decision that we need to make looking at the lab's work
flow, the
number of samples that they're looking to process.
It may not always be appropriate to have one robot for everything.
It may make sense depending on the exact workflow to split that up and maybe
separate
those applications off onto different robots, but it is totally possible.
Okay, thanks.
That's helpful.
David, back to you quickly.
We have some more questions about your Y target.
So in addition to just the amount of DNA shown in the Y target, do you also use
the
male to female ratio as a cutoff to determine whether you will use a
differential selection
for a normal extraction?
Well that decision may not be based over on our section.
We would look at certainly the male to female ratio and the degradation index
to maybe make
an evaluation as to whether we're going to go with a global filer or a YSTR
analysis.
But we're also using the scenario, was it a vaginal sample in a sexual assault
case or
if we had that sample from a neck and an alleged licking type of a case, then
we might choose
that scenario based and not do a differential or do a differential.
But we would certainly take the ratio into consideration case by case basis.
Okay, and now, do you ever go direct to YSTR testing based on the Y screen
results?
Yes, yes, and we know from what we've seen in our laboratory that when we're
getting
what we call a trace result in that five-peakogram or less in the screen that
we are just not
getting enough DNA in the full swab extraction, which is normally about ten
times the screening
result to do a global filer.
So in that range, we are looking at taking it directly to YSTRs.
We'd also like to take this data and eventually determine can we determine a
point in the
screen where we can say there's insufficient amounts of DNA to continue any
testing, almost
a stop at quant in the screening side of things.
And in the 40 or 50 samples that we've taken through to DNA where our screening
result was
in the trace amount or five-peakograms or less, then we have only seen one
sample where
we obtained a repeatable full YSTR profile and that was in a fingernail sample
taken from
a victim.
And to me, a fingernail sample might be one where we'd expect a less homogenous
sample
to be on the tick swab.
We could easily expect there to be more DNA on one side or the other of the sw
ab depending
on how it was collected.
So we may have an outlier there, but most -- and that sample was .002 nanograms
per microliter.
So it was a low-level trace sample that gave a duplicate YSTR result.
And that's the only sample we've seen in 50 of those that gave a repeatable
result.
So we may be able to use the information even further to say we're going to
stop and just
report insufficient amounts to continue as we collect more data on that point.
>> Okay.
Gotcha.
Another question for you is before we switch to Garrett quickly.
Are you still performing any traditional serological testing in your lab or
have you completely
transitioned into widespreading?
>> Well, very little, but we are.
We do have an occasional request to go back and perform a body fluid idea.
The one that I'm thinking of was from a case where we did not obtain a usable
DNA result
even with YSTRs.
So there was a request to go back and test that swab to see if there was saliva
So we are doing an RSID saliva test for alpha amylase.
And we kind of felt that that was a request that we knew or we thought was
going to be
negative once we went ahead and did it based on knowing that these YSTR results
in male
DNA is more sensitive than the body fluid ID.
But it was requested so we went ahead and performed that test.
And we have had a very occasional request to go ahead and identify sperm cells.
This is a time though everyone has been very accepting of the results.
The prosecuting attorney's association understands what we are doing.
And at this point we haven't had very many cases at all where we will go back
and do that
body fluid ID.
But if it is a male on male sexual assault or a female on male which in our
state seems
to be mostly on child cases then we would go ahead and do the traditional ser
ology.
>> Got you.
And actually I do want to follow up on that real quickly because you mentioned
something
that we had a question about what have your feedback been from your partner
agencies like
the police and prosecutors about this to the two YSTR.
>> Overall positive we presented this information to our prosecuting attorney's
institute years
ago before we started doing this.
There was some initial concern.
But at this point we have not had many questions about it.
>> Great.
That's awesome.
All right, Gareth, let's get you in here.
One of our audience members said that she has heard a lot of good things about
HPS.
How do customers usually fund this?
She's afraid that it may be too expensive.
So what are your thoughts on that?
>> I'm glad that she's doing good things for HPS.
>> Yeah, so labs can send them in many ways.
So for example, they may receive government or a local government grant or
funding.
That's kind of something we're able to help with as well if a lottery needed to
prepare
grant applications, that's kind of something we also have some experience with.
But I think it's not solely just about thinking about the cost.
It's about looking at the value of the service that we offer.
So we're able to perform a validation in a way that would be quicker and more
efficient
to the customer.
So it's not taking up the time of your analysts.
It's not interfering with your current workflow.
So we're able to come in and do the work with that kind of interrupting
everything that
you've got currently.
>> I'm really don't be afraid that it's too expensive, get in touch with us,
talk with
us about what you need and we can help in any way we can.
>> Okay, great, that's awesome.
Another one for you guys.
How much grown heat sample goes on the robot for the prep filer BTA?
>> So we actually recommend the same as if it was being performed manually.
So we would suggest a maximum of around 50 milligrams of bone or tooth powder.
So yes, that keeps the protocol in comparison to what we have manually with the
BTA kit.
>> Perfect, okay, that makes sense.
All right, David, we've got a few more questions to you and then a few more
questions for
Dares before we round this up.
When setting up a live screening workflow, are you only testing samples for
semen or
do you use it for a contact DNA testing as well?
>> Well, we're testing every swab in a kit, every set of swab that come in our
sexual
assault kit and recall that we have 72 different collection facilities in West
Virginia with
a variety of qualified people collecting those kits.
So we see a great number of different types of swabs in our kit, body swabs,
internal
and internal swabs.
And sometimes they get very enthusiastic about the number of samples that they
collect
and will collect sometimes even up to 30 samples in a case.
So we are screening every swab in most cases, including those that are
submitted for touch
or where the scenario might suggest a touch or digital penetration type case.
And in some cases, we're just too many to do all at once.
We will select a subset of the kit to screen based on the scenario.
If all those are negative, we'll go back and screen the rest of the swabs.
If all that is then negative, then we're going to go ahead and do the innermost
undergarment
in the case with traditional serology in those types of negative cases.
But yes, we are looking for the screen to be used in any swab sample collected
in a male
suspect female victim case.
Okay.
And now we were talking about the swabs earlier.
Have you found that the screening results from the 1/8 of the swab correlate to
those
from the full swab that are processed thereafter?
There can be some variation.
It's not always a direct one-to-one correlation where we get 1/8 or 10 times
the amount of
DNA on the full swab extraction, but it is close, especially in those that are
well collected
at the hospital level.
It's those swabs where there's no apparent stain, that it can be difficult and
annoying.
You're almost taking a blind sample, but that is better than what we were doing
in the
past where we were just taking everything and sending it over to DNA to see if
there
was anything there at all.
Okay, right.
Yeah, that makes sense.
You mentioned earlier that you have some male/male cases.
Have you experienced any of the male/male mixed swabs from sexual assault?
And so how do you process them in your lab?
If it was a male/male case, we would look for semen, but that's going to go
directly
over to the DNA section and then they would use the known DNA profile to either
deduce
a foreign profile there, but we would not be doing a wash screen on a case
where we knew
it to be a male/male case.
Okay, I understand.
Now, how do the male/quant values from the regular DNA extraction correlate to
the
Y screen quantiles?
Again, that would be dependent on the homogeny sample on the swab, which we don
't know.
If we have not had a case in the swabs where we have identified male DNA above
that trace
amount where we did not identify DNA in the full swab extraction, we have had
samples
in that trace quantification amount where we're talking about 5 kilograms or
less in
the screen where there was no male DNA indicated in the full swab extraction.
And in that case, at that level, the better result is on the DNA side because
they have
been extracted the full set of swabs and have the ability to say that that's a
stop at
the point.
Got you.
Okay.
One more question, Corey, because then before we jump into our polling, our
final polling
question, David, have you encountered issues with investigators or prosecutors
requesting
information about presumptive testing or sperm ID now that those tests aren't
routinely
performed?
We haven't been the trial a lot with the wash screen yet.
We would like to look at a study saying having done a differential lysis and
only seeing
male DNA in the post differential fraction that we can say that sperm were
present, we
do not get a lot of requests about the presumptive test.
We might get just a few questions in the past having done that, but no, that's
not been
a great deal response there for us.
Okay.
Great.
Thank you, David.
And well then, Garrett, the last question for you here.
Can users process trace samples as well on the ID Nimbus Presto?
Yes, yeah, definitely.
So, in fact, there are several labs that are already using the ID Nimbus Presto
for trace
samples for things like touch DNA samples.
And, in fact, when we performed the internal developmental validation for the
instrument,
that was one sample type that we included in our validation.
And all that data has been published in the tech note that kind of accompanied
the release
of the instrument as well.
So, yeah, it can definitely work with trace samples.
We have customers using it, and it was included in the validation as well.
Fantastic.
Thank you, Garrett.
I actually wrapped up the time we have for our Q&A today.
If you'd like some more information, we have a final polling question.
So, before we wrap this up, if you would like to receive more information on
today's
webinar topics, and if so, which one?
We have a contact niece or demo on Y-screen.
So, you send me pricing info and technical specs on Y-screen.
Please send me pricing info and technical specs on automation.
Yes, I would like to discuss further with a live person.
Or no, not at this time.
If you could take just a minute to give us your final thoughts on that, we can
make
sure that there is a message on today.
And everyone on that great team follows up with you to show a question.
Otherwise, we thank you very much for answering our polling questions,
participating in our
Q&A, and just joining us for our webinar in this series.
Thank you, ThermoFasur Scientific for sponsoring this webinar, and thank you to
our speakers,
Dave and Garris, for all of the information that they provide us with today.
We hope you guys have a great rest of your day.
Thank you very much.
You too.