Lab Matters Winter 2019 - Page 5

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 3