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FDA s Frueh Says Agency is Open-Minded About Reviewing Proteomic Biomarkers

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Though they are still significantly behind genomic biomarkers, protein biomarkers appear to be gaining steam as components in molecular diagnostic and pharmacogenomics applications.

Last month, Correlogic, which uses bioinformatics to identify protein patterns, obtained an undisclosed equity investment from Quest Diagnostics, which happens to be a long-term R&D collaborator. And last week, Ciphergen, which identifies protein biomarkers by using its SELDI platform, said it is in discussions with Quest to develop its own diagnostic.

Despite these gains, protein biomarkers remain a poor relation for certain pharmacogenomics applications in part because the US Food and Drug Administration's thinking on the topic is still evolving. And as genomic biomarkers have shown, industry tends to wait for agency guidance before committing R&D dollars.

Pharmacogenomics Reporter this week caught up with Felix Frueh, associate director of the FDA's Center for Drug Evaluation and Research and head of the agency's Interdisciplinary Pharmacogenomics Research Group, to talk about the agency's current position on proteomic biomarkers and the role they can play as pharmacogenomics tools.

What is the FDA's current thinking on the use protein biomarkers or protein biomarker technologies as either stand-alone diagnostics, components of the drug-discovery process, or even as potential companions to new or existing therapeutics?

I think it's not going to be different from any [genomic] diagnostic that has been approved or that is in approval, or can be approved. The nature of the biomarker is different, but the fact is we're not approving or disapproving based on what the biomarker is as a protein or a gene, or blood pressure. We are basing our decision on the usefulness of the biomarker, regardless of its nature. … It's analytical performance and clinical performance and clinical usefulness.

It just seems that, as you said, the field is heating up rapidly, and developments can be seen very quickly. Perhaps also from a regulatory perspective, we are going to see submissions in that area.

Has the FDA been receiving data submissions from protein biomarker companies, compared to genomic biomarkers?

What we have seen coming in pre-IDE stage at CDRH is predominantly genomics. But we're starting to see proteomics as well. I wouldn't know the ratio, but it's twice genomics to proteomics at this time. I'm talking the new kind of proteomics, like mass-spec tests, not ELISA tests.

Conspicuously absent in the recently released pharmacogenomics guidance [see PGx Reporter 3/24/05] was any mention of protein biomarkers. Is the FDA right now considering a draft guidance for proteomic biomarkers, or has the agency not attained enough data to have a formal thinking on the matter?

There is a simple reason for that: We do believe that genomics in that sense as a science is more advanced than proteomics. Also, because writing such a guidance, it's not done. We also need the appropriate resources to review them once we solicit them. To do that, you need to create, one, an infrastructure, and, two, identify personnel and expertise that actually can do the work. So, what we assessed at the time the genomics guidance was written was that, most likely, the biggest boost in the — 'omics' field was coming from genomics. That's where we put the emphasis on.

However, if you read the guidance, and if you were to exchange the word 'pharmacogenomics' with 'proteomics,' a lot of what's written in the guidance holds true. In other words, the decision trees and the validity of biomarkers that now would be proteomic rather than genomics biomarkers would hold up. There is no reason why there shouldn't be any difference. Take that further to the [FDA's Voluntary Genomic Data Submission guidance, which is a part of the pharmacogenomics guidance document], I don't see a reason why voluntary submissions for proteomic could or should be any different than they are for genomics.

In other words — and we've been talking about this — you could imagine some kind of process where you exchange 'G' with 'X,' so it would not be a VGDS but rather VXDS, and that 'X' could stand for … 'Exploratory.' What we have created with the pathway for voluntary genomic submission is a pathway not necessarily only for genomic data, but for all exploratory early-stage research-type data. However, we encourage at this moment the submission of genomic data because we believe that this is the one field that is most ready for regulatory implications and we want to see and learn what the industry is learning.

You've also been receiving proteomic biomarker data within the VGDS pathway?

No, we have not. We have been contact several times for request about whether or not we accept them. What we've gotten so far really wasn't at the stage that we thought would warrant a submission at this point. But we definitely are open-minded. Let's put it this way. The process would be the same.

— Kirell Lakhman ([email protected])

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