Massively parallel sequencing

Ronan, what's your approach to biomarker testing? I'm curious.

Are you sending just like a broad NGS panel? Are you doing multiple different tests? How do you approach that at diagnosis?

Yeah.

For metastatic disease, I often send next-generation sequencing right away.

And so in somebody where you have a need to initiate therapy right away, that can be a helpful guide.

I'm curious if there's any scenarios where you're starting treatment on someone before getting all of the molecular testing results back.

Yeah, so in my practice, actually, I only do chemotherapy for cycle one while waiting for the NGS results.

And once NGS results, either this is liquid biopsy or this is tissue biopsy, I added the target drugs in the second dose.

Now, the last area I want to ask you about is, are you familiar with something called NGS? Answer, yes.

Question, what is NGS? Answer, NGS stands for Next Generation Sequencing.

It's a DNA technique that sequences your DNA so it looks at the individual sequence of your DNA.

Question, and is it true, in your field, that whole area of NGS is something that's at the forefront of everybody's attention? For instance, when you go to seminars and you look at the presentations, there's a lot of talk about NGS, right? Answer, that's correct.

Question, and the reason it's designed to look at this is because it has been found that there are DNA areas that are different in sequence, even though they're the same length.

Is that true? Answer, I think the reason for developing NGS software is to add another tool to a forensic biologist's tool belt.

Question, okay.

Now, could you go to 154, please, for the witness only? You're familiar with this chart.

Yeah, that's the point, is that she didn't do it, and therefore she's not in a position to draw conclusions.

Judge Graff, prosecution.

Prosecution, the proffer is inaccurate and she's not able to draw conclusions because she did not do the NGS or the sequencing analysis.

She's testified that her lab and the analysis she did here is not sequencing analysis.

His work spans everything from solid tumor biomarker testing to liquid biopsies.

In our conversation, Javier shares incredible insights into biomarker classifications, assay designs, and how technologies like DPCR, qPCR, and NGS all have their moments to shine in the lab.

It's a thoughtful and engaging discussion, so let's get started.

Javier, thank you so much for joining us on today's episode of Absolute Genius.

And MRD is definitely something that we've seen an increase in interest as well in terms of research.

Is there any technology considerations looking at these types of studies? I mean, I can imagine, you know, you're looking, like you said, you know, a drop in the sea sometimes for some of these biomarkers.

How do you consider technologies to use like a qPCR or dPCR or NGS in your laboratory?

Yeah, usually I think that depending on the intended of use or maybe what are you searching in terms of, say, lead technology for these purposes.

Thanks for having me on.

I love talking to, you know, directors of pathology because that's really where the rubber hits the road in most, you know, of what we're talking about, applying NGS or molecular diagnostics to the clinic.

Yeah, absolutely, especially in this day and age where it seems as though genomics has kind of taken over for helping us to diagnose and prognose and treat our patients.

So it's been like a decade we were talking before we turned the mic on that I've talked to someone at Roswell Park.

So for every gene or every mutation that was important, you'd have to run a single analyte assay, like a PCR or pyro sequencing.

And that is really cumbersome, you know, to run, especially as more and more molecular targets are identified.

um you know if you're looking at 50 60 100 200 genes um that gets extremely cumbersome so using next generation sequencing we have these capabilities to multiplex all these gene mutations into a single assay but even more importantly instead of looking at copy number variations at the chromosome level or at the arm level or even at the gene level using things like fish or cytogenetics, we can do that within this NGS panel.

We can actually look for these rearrangements at the exact same time that we're looking for these point mutations.