PRESIDENT & EXECUTIVE DIRECTOR’S MESSAGE
laboratory instrumentation has evolved to
point to enable “non-targeted” analysis—
where we can detect compounds we are
not specifically looking for. We can store
this data and, as we learn more about new
chemicals, we can go back and measure
compounds that were not on our radar
screens when we originally tested these
samples. Minnesota has one instrument
that can do this—a hybrid quadrupole
time of flight mass spectrometer
(Q-TOF-MS)—and we’re in the process of
purchasing a Thermo Orbi-trap, which
performs non-targeted analyses using
somewhat different technology. We
recently ran some water samples on the
Q-TOF-MS and detected PFAS that are
not detected by our standard method.
We in public health need to look toward
the future.
Scott: You mention the issue of data
storage. When I think about data storage
issues, I think about genetic sequencing
data, which is massive. How does this
compare?
Joanne: Good question! The answer
surprised even me. According to our IT
people, Q-TOF instruments generate
much more data than whole genome
sequencing of microbes. In fact, we get
bigger data files from one run on our
Q-TOF instrument than an entire day’s
worth of testing with DNA sequencers.
So that’s a problem. And it’s worth
mentioning because the focus is on “big
data” on the sequencing side, but we also
have “big data” on the chemistry side.
Scott: That reminds me of a new focus
area the APHL board has prioritized
for 2019—promoting, designing and
developing the laboratory informatics
infrastructure. And along with that is
to develop best practices for building
relationships with non-traditional
laboratory partners for data analytics.
Data issues really do span the entire
laboratory.
manually transfer data to the health
department network on flash drives,
which is inconvenient, to say the least.
Of course, the key to resolving any of this
is to work with our IT staff. Generating
data is what we do for a living, and we
need an IT infrastructure and a business
strategy to support data analysis across
the laboratory—newborn screening, whole
genome screening, chemistry, etc. We’re
in the midst of strategic planning with
our IT staff, so we don’t end up going in
different directions. They’re working with
us to come up with some creative ideas.
Maintaining that relationship is critical.
Scott: The laboratory is often a challenge
for IT folks. We’re not just using HelpDesk.
The laboratory has unique and uniquely
sophisticated needs. We can also view the
solution as letting the IT folks become the
champions, not just having the laboratory
yelling into the wind. Didn’t Minnesota
win an award for data innovations?
Joanne: We did. We won a government
IT award for interoperability for a
newborn screening system that went
live in 2018. It transfers infant hearing
screening data and critical congenital
heart defect data electronically from
the hospital (where that screening takes
place) to the laboratory. We worked with
Oz Systems and our LIMS vendor, Natus
Medical, Inc., to transfer the data into our
LIMS. IT was very helpful in that. It was
exciting for both the laboratory and IT
staff to demonstrate that you can work
cooperatively and come up with creative
solutions that reduce manual entry
reduce errors. That was very exciting for
both of us.
A new focus area the
APHL board has prioritized for
2019 is promoting, designing
and developing the laboratory
informatics infrastructure.”
Scott Becker, Executive Director, APHL
Scott: That’s great. What a wonderful
experience.
Joanne: The other thing we focus on
is workforce. We often talk about the
need for bioinformaticians, but we need
chemistry informaticians as well. Our
datasets are huge. n
Joanne: Absolutely. Another data
challenge is that our instruments don’t
always have the latest IT security, so
we have to run them on a network
that is separate from rest of the health
department. That means we have to
PublicHealthLabs
@APHL
APHL.org
Winter 2019 LAB MATTERS
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