Opentrons User Interview with Gina Faraci of Keck Medicine, University of Southern California

Gina Faraci does viral RNA sequencing for HIV genomics assays at Keck Medicine USC. This involves a lot of PCR—and two OT-2 liquid handling robots.

Gina Faraci is a research analyst studying HIV at Keck Medicine of the University of Southern California. Her lab purchased its first Opentrons OT-2 in April 2019, and added a second OT-2 a few months later.

Gina-Faraci
Gina Faraci in her lab with her OT-2. CREDIT: Gina Faraci

OPENTRONS: Please tell me a little about your background.
GINA FARACI: I became interested in biological research as an undergraduate studying bioinformatics at the University of California San Diego, where I also gained a strong background in research, programming, and analysis skills.

OPENTRONS: What kind of research do you do?
GINA: We do HIV genomic incidence assays, integrating high-throughput next-generation sequencing, bioinformatics pipelines, and statistical analyses. At its very core, we’re doing viral RNA sequencing to target and sequence specific genes. We’re looking at how long the HIV has been in the body, because the longer it has been there, the longer it has had to evolve. We can estimate how long someone has been infected with HIV by testing how different the HIV in their body is from itself. The more different it is, the longer the person has been infected.

This involves a lot of PCR techniques—and that’s where the OT-2 robots come in. We wanted an automation platform to increase throughput from 36 samples a day to maybe a couple of plates. We already had a machine to setup RNA extraction, but we needed another machine to amplify PCR because it’s really tedious and makes a mess! I have to transfer volume, then transfer the product. We wanted a way to standardize it to free ourselves to increase our throughput and do more research. Our lab is rather small; we don’t have a whole host of lab techs devoted specifically to do these studies. The robots are taking the place of another person in our lab. While the robot is doing something, the rest of us can do other things.

OPENTRONS: Tell me about a typical day in your lab.
GINA: A typical day includes setting up RNA extraction using our Thermo Scientific KingFisher Duo Prime purification system and transferring the samples into the OT-2. We set up the thermosynthesis and PCR synthesis, and do bead-based PCR cleanup. At the end of the day, we freeze samples for library preparation, pooling, and sequencing.

Now that we have our OT-2 robots, I can set them up and walk away. The only intervention I need to make manually is if a robot fails at some point, but that doesn't often happen—especially since we've been optimizing our protocols and calibrations. We’re still optimizing the robots, particularly the PCR setup and cleanup so that it approximates the efficiency of a human being. It's going well so far, but there are still more features the robot could have to make this process easier.

We ordered our second OT-2 robot so we have two separate, dedicated machines to prevent contamination. It’s working out well. They have become so important, I like to call them my babies! It's nice to be able to have two dedicated machines and really make sure we’re doing everything right.

OPENTRONS: Had you used lab automation prior to Opentrons?
GINA: We had no liquid handling robots prior to our first OT-2. We did a lot of demos with the expensive companies. We went with the OT-2, first due to its price point. We are a smaller lab, so price makes a big difference for us. Second, we like the open-source API code that enables the robot to do whatever you want it to do. It is good that we don’t have to rely on Opentrons to make all the updates to the code. Also, having that accessibility to Opentrons is important. I request a protocol, and in a couple of weeks, I get back a skeleton for the code. I’m fairly familiar with Python now that I’ve had some exposure to it, so that’s nice. Learning the OT-2 API was a bit of a learning curve, but I feel like I've mastered the machine. That said, I would love it if you make the undocumented API "tricks" that I have seen coded by your technicians available to your community.

OPENTRONS: What did you expect the process of automating your lab to be like?
GINA: I was expecting to request code and get the machine up and running the first time. We requested the code, and it did work on the machine for the first time, but it didn't work with our sample volumes or sample types. We needed to optimize liquid transfer, mix volumes, mix speeds, and so on to meet our needs. It’s hard to explain to other people exactly what we want to do. It would be nice if the code were more universal. Maybe we have a different container than the one specified in the protocol, or maybe I have to adjust the height. Either way, it’s not a big deal to fix.

OPENTRONS: What was it like to get the OT-2 up and running?
GINA: We bought it for the magnetic bead cleanup, which is the hardest thing to get up and running. We make a version of the code to test, do a water run to make sure the code is in a working state, then test this version on samples measuring concentration before and after. Then we make a new version of the code increasing mix time, incubation time, and so on based on the observed performance and yield, and start the process again.

During the long incubation period, we couldn’t leave the machine, because the magnet was so strong that it would separate the beads and suck them up into the elution. It was a mess. I probably spent 10 to 15 hours tinkering with it. I adjusted the volumes based on the volumes we used, not on the ones in the protocol, and optimized the code for our lab. That solved the problem.

OPENTRONS: What’s next?
GINA: Ultimately, our goal is to create a method that’s really cheap that could be used in the field, specifically in disadvantaged communities. We want to take the whole setup to Africa. Our hope is that clinicians who have zero experience with running a lab robot would be able to plug and play to start treating people in the field. Thanks to the OT-2, I would say we are closer to this goal. Although we are still in the testing phase, we plan to use the OT-2 to complete a large cross-sectional survey.

OPENTRONS: Is there anything else you'd like to say about working with the OT-2?
GINA: It could be a little faster. Right now, the arm can go about as fast as a person can go. I don’t know if making it faster would mess up the accuracy, but if you guys ever roll that out, that’d be great! With two OT-2s, though, we can do two things at once now and maintain sample integrity.