Case Studies of Seer’s Proteograph Product Suite

Explore three case studies showcasing the transformative impact of Seer’s Proteograph^™ platform in advancing scientific understanding.

From groundbreaking genomic research to comprehensive aging studies, and novel insights into rare diseases, these real-world applications demonstrate the power and versatility of our technology in pushing the boundaries of human health research.

Technology

Tackling Proteome Complexity to Advance Genomics Research

Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping

Overview

Bring together the power of genome-wide association studies and the insights of proteomics and the possibilities for genetics-based discovery are limitless. In this first-of-its-kind study, Seer’s Proteograph technology offered unparalleled proteome visibility and enhanced pQTL analysis to analyze the impact genetic alterations have on proteins and offer new understanding into the research and development of therapies to improve disease treatments.

Highlights

• The first external pQTL study to use the Proteograph to perform pQTLs analysis.
• From a cohort of 345 individuals, the Proteograph detected ~3,000 proteins and >18,000 peptides.
• The Proteograph measured variant peptides that affinity-based methods can’t.

Study Design

The Proteograph workflow and a novel bottom-up proteomics approach was used first to account for protein altering variants in the detection of pQTLs and then to explore the impact genetic variations have on protein levels and human health.

Results

In the end, genetic variants linked to GIP and ApoB levels associated with conditions such as Type 2 Diabetes and cardiovascular disease were identified, helping significantly advance the goal of the study and the scientific community’s ability to improve human health.

Having unbiased access to the proteome with peptide-level insights is necessary to truly understand the proteome, its variants, and its connection to human health and disease. Myself and my colleagues at WCM-Q were very satisfied that the Seer Proteograph technology was able to provide this.
— Karsten Suhre, Ph.D., Professor of Physiology and Biophysics and Director of the Bioinformatics, Core Weill Cornell Medicine – Qatar
Publication Pending

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Data

Tackling Workflow Challenges with High Throughput

OMICmAge: An integrative multi-omics approach to quantify biological age with electronic medical records

Overview

In our mission to understand the intricacies of aging, robust data is critical, however, since it involves complex interactions of both cellular and biochemical processes, both molecular and clinical data needs to be collected to truly measure and comprehend the variations. In this insightful study, the Proteograph™ platform’s unique capability to generate and analyze this powerful combination of data was leveraged.

Highlights

• The Proteograph facilitated unbiased discovery of proteomic associations.
• The Proteograph offered an increased number of quantified proteins – 2,805 non-unique, or 536 unique, protein groups, across 1,789 samples.
• Seer’s nanoparticles helped to isolate and extract peptides and proteins.

Study Design

A predictive biological aging phenotype, EMRAge, was created using clinical laboratory measures in ~30,000 individuals from the MGB-Biobank. The Proteograph combined with LC-MS was used to quantify relative protein levels for 2,000 samples, which were incubated with five Seer nanoparticles and quantified with Seer’s Proteograph Analysis Suite.

Results

Not only were novel proteins and peptides related to chronological and biological aging discovered but relevant low abundant proteins were revealed. The identified biomarkers demonstrated strong associations with chronic diseases and mortality, outperforming current biomarkers across the discovery and validation cohorts.

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Biological Insights

Tackling Sample Types with Low Volume, Non-Human Samples

Longitudinal Deep Multi-Omics Profiling in a CLN3Δex7/8 Minipig Model Reveals Novel Biomarker Signatures for Batten Disease

Overview

The molecular function of CLN3 disease, a rare and fatal autosomal recessive disorder caused by mutations in CLN3, has yet to be fully demonstrated. Looking to unlock new biological insights, Seer partnered with Sanford Burnham Prebys Proteomics Core, Sanford Research, and Amicus Therapeutics, to conduct a deep multi-omics study in the serum of wild type and transgenic CLN3^Δex7-8 Yucatan miniature pigs.

Highlights

• Integrated multi-omics analysis provided unmatched biological insights into CLN3.
• The Proteograph™ enabled deep proteomic profiling of serum, helping identify over 3400 analytes, 769 metabolites and 2634 proteins.
• Protein with metabolite biomarkers improved the differentiation of disease age/progression.

Study Design

The Proteograph platform with TMT 18plex labelling was used to enable deep serum proteomics profiling of Batten disease using a porcine model system. The serum was collected over the span of 36 months in both CLN3^Δex7-8 and control mini pigs. To analyze the study data, Metabolon’s Global Untargeted Metabolomics panel and Seer’s Proteograph Assay and nanoparticle workflow was used.

Results

By profiling the entire molecular landscape of CLN3 disease, including low abundant protein signatures, over 3400 analytes, 769 metabolites and 2634 proteins, were identified, giving rise to four novel biomarkers into the pathogenic timeline of the disease, including the presymptomatic disease state.

Working with Seer has transformed our multi-omics biomarker discovery initiatives. Seer’s Proteograph is allowing us to generate unbiased, quantitative data for over 3000 pig plasma proteins, enabling us to find new biomarker signatures of slow-progressing diseases like CLN3 Batten disease in animal models.
— Jon Brudvig, Ph.D., Assistant Professor of Pediatrics, Pediatrics and Rare Diseases Group, Sanford Research

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Empower Your Own Research with Seer Technology

Each case study explored here underscores the transformative power of Seer’s Proteograph™ technology in unraveling complex biological mysteries — imagine what it can do for your research.

To explore the full potential of your projects and advance your scientific journey, reach out to our experts at Seer. Let’s collaborate to push the boundaries of proteomics and empower your research with precision and innovation. Contact us today to unlock new dimensions in your scientific endeavors.