Nature Genetics Study Validates Seer’s Proteograph Platform as Essential for Turning Genetic Signals Into Reliable Drug Targets and Biomarkers

Rhea-AI Summary

Seer (NASDAQ: SEER) announced a Nature Genetics study (Nov 2025) validating its Proteograph product suite for population-scale, peptide-level mass spectrometry proteomics. The GWAS profiled ~1,600 blood samples (discovery n=1,260; replication n=325), detecting 5,753 proteins and quantifying 1,980 in ≥80% of participants. Researchers identified 364 pQTLs, 102 replicated, and 35 novel signals. The study found up to one-third of affinity-based pQTLs from single platforms failed mass spectrometry replication, showing peptide-level measurement reduces epitope-related artifacts and improves confidence for drug-target and biomarker discovery.

Implication: peptide-level MS can distinguish true protein regulation from assay artifacts, strengthening translational proteogenomics.

Positive

• Cohort size of ~1,600 samples supports population-scale analysis
• 5,753 proteins detected by Proteograph
• 1,980 proteins quantified in ≥80% of participants
• 364 pQTLs identified across the dataset
• 102 pQTLs replicated in independent cohort
• 35 previously unreported replicated pQTLs

Negative

• Up to one-third of single-platform affinity pQTLs did not replicate by MS

News Market Reaction

-1.04%

2 alerts

-1.04% News Effect

+2.0% Peak Tracked

-$1M Valuation Impact

$107M Market Cap

0.0x Rel. Volume

On the day this news was published, SEER declined 1.04%, reflecting a mild negative market reaction. Argus tracked a peak move of +2.0% during that session. Our momentum scanner triggered 2 alerts that day, indicating moderate trading interest and price volatility. This price movement removed approximately $1M from the company's valuation, bringing the market cap to $107M at that time.

Data tracked by StockTitan Argus on the day of publication.

Key Figures

Study samples: ~1,600 samples Discovery cohort size: 1,260 participants Replication cohort size: 325 participants +5 more

8 metrics

Study samples ~1,600 samples GWAS blood samples across multiple ethnic backgrounds

Discovery cohort size 1,260 participants Proteograph workflow discovery cohort

Replication cohort size 325 participants Independent replication cohort

Proteins detected 5,753 proteins Detected across all profiled samples

Proteins quantified 1,980 proteins Quantified in ≥80% of participants

pQTLs identified 364 pQTLs Genetic variants associated with protein abundance

Replicated pQTLs 102 variants pQTLs replicated in independent cohort

Novel signals 35 pQTLs Previously unreported replicated genetic signals

Market Reality Check

Price: $1.89 Vol: Volume 220,757 vs 20-day ...

normal vol

$1.89 Last Close

Volume Volume 220,757 vs 20-day average 165,583 (relative volume 1.33), showing modestly elevated trading. normal

Technical Price $1.81 is trading below the 200-day MA $2.06, indicating a weak longer-term trend pre-publication.

Peers on Argus

SEER traded down 0.54% while momentum peers showed mixed moves: BMEA down 6.58%,...

1 Up 2 Down

SEER traded down 0.54% while momentum peers showed mixed moves: BMEA down 6.58%, CRBP down 5.76%, and EQ up 4.43%. Sector scanner flagged broader dynamics with a median peer move of about -6.2%, suggesting the stock traded against a choppy sector backdrop.

Historical Context

5 past events · Latest: Dec 01 (Positive)

Pattern 5 events

Date	Event	Sentiment	Move	Catalyst
Dec 01	Platform validation news	Positive	-1.0%	Nature Genetics GWAS validates Proteograph for peptide-level proteomics.
Nov 07	Scientific data news	Positive	-3.2%	New HUPO 2025 data show Proteograph scalability and translational potential.
Nov 06	Earnings update	Positive	-0.5%	Q3 2025 results with revenue growth, improved loss, solid cash balances.
Oct 29	Investor conferences	Neutral	-3.1%	Announcement of participation in November healthcare investor conferences.
Oct 16	Earnings scheduling	Neutral	-2.3%	Notice of upcoming Q3 2025 results webcast and conference call.

Pattern Detected

Across the last five announcements, generally positive or neutral news was followed by negative 24-hour price reactions, suggesting a pattern of selling or muted response to news.

Recent Company History

Over the last few months, Seer reported Q3 2025 earnings with modest revenue growth and narrowed losses, alongside strong cash levels and ongoing share repurchases. It highlighted launch of the Proteograph ONE Assay and SP200 instrument, plus participation in multiple investor conferences and proteomics meetings. The current Nature Genetics publication extends this trajectory by providing peer-reviewed validation of the Proteograph platform’s population-scale, peptide-level mass spectrometry capabilities, reinforcing earlier translational and conference data.

Market Pulse Summary

This announcement highlights peer-reviewed validation of Seer’s Proteograph platform in Nature Genet...

Analysis

This announcement highlights peer-reviewed validation of Seer’s Proteograph platform in Nature Genetics, using a GWAS of ~1,600 samples to detect 5,753 proteins and identify 364 pQTLs, with 102 replicated and 35 novel. It underscores how peptide-level mass spectrometry can resolve epitope artifacts from affinity assays. In context of recent earnings and conference activity, key metrics to watch include publication uptake, translational collaborations, and how often Proteograph features in future large-scale studies.

Key Terms

genome-wide association study, GWAS, mass spectrometry, proteomics, +3 more

7 terms

genome-wide association study medical

"announced the publication in Nature Genetics of a large genome-wide association study (GWAS)"

A genome-wide association study scans the DNA of large groups of people to find small genetic differences that occur more often in people with a particular trait or disease. Think of it as scanning a crowd to locate which tiny pieces of genetic code are linked to a habit or condition. For investors, GWAS results can reveal potential drug targets, guide development of diagnostics and patient selection, and affect valuations and partnerships in biotech and healthcare.

GWAS medical

"a large genome-wide association study (GWAS) that used the company’s Proteograph"

A genome-wide association study (GWAS) is a large-scale research method that scans the DNA of many people to find small genetic differences that are linked to a particular trait or disease. Think of it like comparing thousands of books to spot recurring typos that correlate with a plot twist; for investors, GWAS can reveal biological targets, inform drug and diagnostic development, and help assess the commercial potential and risk of healthcare projects.

mass spectrometry technical

"provides the strongest evidence to date that mass spectrometry validation is essential"

Mass spectrometry is a laboratory technique that identifies and measures chemicals by giving molecules an electrical charge and sorting them by how fast they move, like weighing and separating coins to see which kinds are present. For investors, its results are evidence used in drug development, quality control, food and environmental testing, and diagnostics, so clear mass-spec data can affect regulatory approval, product reliability, costs and market confidence.

proteomics medical

"The Proteograph platform made it possible to perform population-scale mass spectrometry proteomics"

Proteomics is the large-scale study of all the proteins produced by a cell, tissue or organism, like taking a full inventory and watching how the workforce and machines inside a factory behave. For investors, proteomics matters because it helps identify drug targets, disease indicators and responses to treatments—information that can speed development, reduce risk, guide partnerships and reveal new commercial opportunities in biotech and diagnostics.

protein quantitative trait loci medical

"researchers identified 364 protein quantitative trait loci (pQTLs) genetic variants"

Protein quantitative trait loci (pQTLs) are specific locations in the genome where genetic differences influence the amount of a particular protein produced in the body. Think of them as dimmer switches on a circuit board that change how bright a protein’s signal is. For investors, pQTLs matter because they help link genetic causes to measurable protein biomarkers, guiding drug target selection, biomarker development and risk assessment for therapeutics and diagnostics.

Mendelian randomization medical

"For academic researchers conducting GWAS and Mendelian randomization studies, the message"

A research method that uses naturally occurring genetic differences as a kind of built‑in experiment to test whether one trait (like cholesterol level) actually causes an outcome (like heart disease) rather than just being linked to it. For investors, Mendelian randomization helps rank the most promising drug targets and public‑health interventions by increasing confidence that changing a specific biological factor will produce a real effect, which can reduce clinical trial risk and shape valuation and regulatory expectations.

affinity reagents technical

"Affinity reagents have been used in proteomics to measure a predetermined panel"

Affinity reagents are specially designed molecules—such as antibodies, engineered proteins, or short strands of DNA/RNA—that stick tightly and specifically to a chosen biological target, like a protein or virus. For investors, they matter because they are the key component in diagnostic tests, research tools and some therapies; their quality, availability and intellectual property can directly affect a product’s accuracy, regulatory approval and commercial value, much like a custom key that enables a specific lock to work reliably.

AI-generated analysis. Not financial advice.

Large-scale GWAS across ~1,600 samples shows how peptide-level mass spectrometry distinguishes true protein changes from potential binding artifacts resulting from affinity-based approaches, establishing accuracy as the foundation for downstream discovery

REDWOOD CITY, Calif., Dec. 01, 2025 (GLOBE NEWSWIRE) -- Seer, Inc. (Nasdaq: SEER), the pioneer and trusted partner for deep, unbiased proteomic insights, today announced the publication in Nature Genetics of a large genome-wide association study (GWAS) that used the company’s Proteograph^® Product Suite to measure proteins at peptide-level resolution and map their genetic determinants. The study, led by Karsten Suhre, PhD, of Weill Cornell Medicine–Qatar, with collaborators from Harvard Medical School/Brigham and Women’s Hospital, Seer, and TruDiagnostic, provides the strongest evidence to date that mass spectrometry validation is essential for turning genomic signals into reliable drug targets and clinical biomarkers. Without mass spectrometry validation, as many as one-third of protein–gene associations reported by affinity-based assays do not replicate, highlighting the necessity of accuracy in proteogenomics.

The analysis included ~1,600 blood samples representing multiple ethnic backgrounds. A discovery cohort of 1,260 and an independent replication cohort of 325 were profiled using Seer’s Proteograph workflow. Across these samples, 5,753 proteins were detected, and 1,980 were quantified in at least 80 percent of participants.

From these data, the researchers identified 364 protein quantitative trait loci (pQTLs) genetic variants associated with protein abundance. Of these, 102 replicated in the independent cohort. 35 of the replicated signals were previously unreported, extending the catalog of genetic regulation of proteins.

Affinity reagents have been used in proteomics to measure a predetermined panel of proteins in large cohorts and have generated thousands of reported pQTLs. But when protein-altering genetic variants change the binding site of affinity reagents, these methods can register erroneous signals as the binding strength of the affinity reagent to the protein is diminished. These so-called epitope effects can produce apparent associations between protein expression and genetic variants that do not represent true biology.

By measuring proteins directly at the peptide level, the Proteograph’s mass spectrometry approach made it possible to test whether a genetic variant truly altered protein expression, mitigating the confounding epitope effect.

“The Proteograph platform made it possible to perform population-scale mass spectrometry proteomics with the depth and reproducibility needed for genetic association studies,” said Dr. Suhre. “By measuring proteins directly at the peptide level, we could distinguish true biological effects from assay artifacts—yielding a more reliable map from genes to proteins to disease pathways.”

To contextualize the findings, the study compared mass spectrometry results with two of the largest affinity-based proteomics resources. The comparison revealed a clear pattern:

• pQTLs consistently reported across multiple affinity platforms were confirmed by mass spectrometry.
  
• Up to one-third of associations reported by a single affinity platform did not replicate when tested by mass spectrometry.
  
  

“This study demonstrates that mass spectrometry-based analysis is crucial for proteomics,” said Serafim Batzoglou, PhD, Chief Data Officer at Seer. “By providing peptide-level confirmation at scale, the Proteograph establishes protein measurements that lead to novel genetic associations and help annotate the accuracy of affinity-based pQTL predictions.”

For academic researchers conducting GWAS and Mendelian randomization studies, the message is direct: datasets built only on affinity reagents may contain a substantial fraction of associations that do not represent true protein abundance. Without validation, downstream analyses risk drawing causal inferences from epitope-induced artifacts.

For drug discovery and biomarker development, peptide-level validation strengthens confidence that selected targets represent genuine biology, not technical noise. Reliable associations reduce wasted effort and increase the likelihood that preclinical findings will hold in clinical settings.

For translational research, the study demonstrates how mass spectrometry and affinity reagents can be used together, with mass spectrometry stratifying the level of reliability of affinity-based predictions.

For patients, this rigor means a higher probability that tomorrow’s therapies are built on real biology. Together, they create a path toward comprehensive and trustworthy protein–genetic maps.

This publication marks the validation stage. The Nature Genetics study provides peer-reviewed evidence that mass spectrometry can systematically resolve artifacts and confirm which associations are robust.

The transformation comes in what this enables. As proteomics expands to larger populations and integrates with genomics, epidemiology, and clinical records, the utility of those datasets depends on accuracy. By anchoring discovery on peptide-level confirmation, Seer positions proteomics to become a population-ready science that supports drug targets, biomarkers, and translational medicine with the rigor required for clinical impact.

Article information

Title: A genome-wide association study of mass spectrometry proteomics using the Seer Proteograph platform
Journal: Nature Genetics, November 2025 (online)
Authors: Suhre K., Lasky-Su J., et al., including Seer scientists

About Seer

Seer, Inc. (Nasdaq: SEER) sets the standard in deep, unbiased proteomics—delivering insights with scale, speed, precision, and reproducibility previously unattainable by other proteomic methods. Seer’s Proteograph Product Suite uniquely integrates proprietary engineered nanoparticles, streamlined automation instrumentation, optimized consumables, and advanced analytical software to solve challenges conventional methods have failed to overcome. Traditional proteomic technologies have struggled with inconsistent data, limited throughput, and prohibitive complexity, but Seer’s robust and scalable workflow consistently reveals biological insights that others do not. Seer’s products are for research use only and are not intended for diagnostic procedures. For more information about Seer’s differentiated approach and ongoing leadership in proteomics, visit www.seer.bio.

Media Contact:
Patrick Schmidt
pr@seer.bio

Investor Contact:
Carrie Mendivil
investor@seer.bio

A photo accompanying this announcement is available at https://www.globenewswire.com/NewsRoom/AttachmentNg/ae65f47f-3263-4c92-ae93-f0f8d4ea62e4

FAQ

What did Seer (SEER) report in the Nature Genetics GWAS published Nov 2025?

The study used Proteograph to profile ~1,600 samples, detected 5,753 proteins, and identified 364 pQTLs with 102 replicated.

How many proteins did Proteograph quantify in the SEER GWAS?

Proteograph quantified 1,980 proteins in at least 80% of participants.

What replication results did the SEER Nature Genetics study report for pQTLs?

Of 364 pQTLs discovered, 102 replicated in an independent cohort and 35 were novel.

What does the SEER study say about affinity-based pQTL findings?

The study found up to one-third of associations from a single affinity platform failed to replicate by mass spectrometry.

How does peptide-level mass spectrometry affect drug-target selection for SEER (SEER)?

Peptide-level MS reduces epitope artifacts, increasing confidence that selected targets reflect true biology, not assay noise.

Which sample sizes were used in Seer's Proteograph GWAS (SEER)?

A discovery cohort of 1,260 samples and an independent replication cohort of 325 samples.