SampledSphere

Resources

Events

Careers

Contact

  • Enquire
  • Services
    • Our labs are your labs

      Sample storage

      • Biobanking Services
      • ICH Stability Storage
      • Photostability Testing
      • Sample Data Storage
      • SampledSphere™

      Sample Management

      • Sample Lifecycle Management
      • Sample Data Management
      • Program Management

      Multiomics

      • Analytical Sample Processing
        • Extraction
        • Blood Fractionation
        • Normalization
        • Sample Processing Quality Control
        • Aliquoting
      • Sequencing
        • Whole-Genome Sequencing
        • Whole Exome Sequencing
        • Targeted Sequencing
        • Sanger Sequencing
        • RNA Sequencing
        • Methylation Sequencing
        • Protein Biomarker Discovery
      • Microarrays
        • Genotyping Arrays
        • Transcriptome Profiling Arrays
        • Methylation Profiling
      • PCR
        • Droplet Digital PCR
        • qPCR
      • Bioinformatics
        • Bioinformatics Analysis
        • Bioinformatics Custom Reporting

      Cellular Services

      • Cell Sample Processing
        • PBMC Isolation
        • Lymphoblastoid cell lines (LCL) Generation & Expansion
        • Fibroblast Generation and Expansion
      • iPSC Services
        • iPSC Reprogramming
        • iPSC Gene Editing
        • iPSC Expansion
        • Neural Progenitor Cell (NPC) differentiation
        • iPSC Quality Control
      • Histology
      • Cell Line Repositories

      Kitting & Logistics

      • Custom Clinical Kitting
      • Sample Logistics
      • Technical Services
      • Validation Services
  • Technology
    • Partner with Sampled and move forward, faster

      Illumina
      Olink
      whole genome sequencing pacbio

      Learn about Service Provision at Sampled

      Our partnerships enable us to provide our clients with access to technology immediately, without the initial overheads and complexities of setting up their own labs. 

      John DelliSanti

      Chief Executive Officer

  • Applications
    • Supporting a wide range of applications:

      Oncology

      Genetic Disorders

      Neurodegenerative Diseases

      Cardiovascular Diseases

      Infectious Diseases

      Autoimmune Diseases

      Metabolic Disorders

      Inflammation

      Substance Abuse

      Our commitment to supporting a wide range of applications, from oncology to substance abuse, underscores our dedication to advancing healthcare and improving patient outcomes across diverse medical challenges.

      View all application areas

      John DelliSanti

      Chief Executive Officer

  • About
    • Learn more about our mission, approach & standards

      About sampled

      Learn more

      Meet the team

      Learn more

      Join the team

      Learn more

      Our Facilities

      Learn more

      Clients Partners

      Learn more
  • Blog
    • News and insights from Sampled and the wider industry

      Sampled Partners with EBiSC to Expand Access to Stem Cell Lines in the US

      April 8, 2025

      Sampled Selected as Genome Characterization Center for the NCI

      March 27, 2025
      Outsourcing freezer storage

      Why Outsourcing -80°C Freezer Storage Could Save Your Lab Money

      January 17, 2025

      Join us on our blog where we share our passion for unraveling the science of precision medicine, offering practical knowledge and applications from over 25 years of experience in analytical and biorepository services.

      View all our blog posts here

      Mike Sheldon

      Senior Director Scientific Affairs

Search
START TYPING AND PRESS ENTER TO SEARCH
  • Enquire
  • Services
    • Sample Storage
    • Sample Management
    • Multiomics
    • Cellular Services
    • Kitting & Logistics
  • Technology
  • Applications
  • About
  • Blog
  • Resources
  • Careers
  • Events
  • Contact
Search
  • Skip to primary navigation
  • Skip to main content
  • Skip to footer

Overcoming challenges in high-throughput biomarker discovery through Olink® Explore workflow

October 4, 2023 admin

Table of Contents

  • Challenges in proteomics
  • A new method of studying protein interactions
  • A new approach to biomarker discovery
    • Explore HT workflow
    • Explore 3072 workflow
  • Overcoming the challenges in high-throughput biomarker discovery
  • Outsourcing biomarker discovery to Sampled

Challenges in proteomics

In the past several decades researchers have had to rely on mass spectrometry-based techniques to quantify and identify the proteins involved in their samples. These techniques were low throughput however and often required difficult protocol optimizations and time-consuming data analysis pipelines. While useful, these techniques were inadequately slow and required a lot of “hands on” time from researchers. It wouldn’t be long before a new approach to studying proteomics was discovered, using protein chips or microarrays researchers were able to facilitate large-scale, high-throughput proteomic studies. Despite aiding in the advancement of the field, analyzing the data and delineating protein concentrations and interactions from large-scale datasets remained challenging.

A new method of studying protein interactions

Olink’s Proximity Extension Assay (PEA) technology is a new method of quantifying and identifying proteins of interest in complex samples such as blood serum or plasma. Olink platforms such as the Explore HT® and Explore 3072® uses PCR amplification of DNA tags unique to each target protein in proportion to the abundance of the target proteins in the sample: First, two antibodies that carry complementary oligonucleotides (acting as unique barcodes for each antibody) bind to different parts of the target protein must be brought close to each other on the target protein (see Figure 1).

biomarker discovery

When successful PCR amplification of a DNA tag for the antibody target protein occurs, quantitative PCR reports it as a proxy for the abundance of the target protein (see Figure 2). 

biomarker discovery with olink proteomics


Finally, a short-read Next Generation Sequencing (NGS) platform is used to measure the abundance of the target protein by measuring the proportion of the DNA tags present after PCR (see Figure 3).

protein biomarker discovery

With this novel approach to biomarker discovery, researchers are now able to utilize Olink’s HT and 3072 kits in combination with liquid handling and short read sequencing platforms to identify/quantify low abundance proteins with high specificity and accuracy in serum or plasma samples.

A new approach to biomarker discovery

The first step in the workflow involves selecting either the Olink HT or 3072 kit to measure over 5300+ proteins or 3000 proteins, respectively, across 10 orders of magnitude in protein concentrations. Here, Olink’s industry-leading specificity is founded on PEA technology (me, which generates signals only when two matched oligonucleotide-tagged antibodies bind to their intended target protein and generate a correctly hybridized DNA template for readout, eliminating false positives and ensuring data accuracy.

Explore HT workflow

  • Sample Preparation & Dilution using liquid handling platforms such as those manufactured by Hamilton and the Mosquito/Dragonfly platforms by SPT Labtech
  • Sample incubation prior to PCR step with the Mosquito liquid handling platform
  • PCR sets up with Mosquito and Dragonfly, and PCR pooling steps using Sciclone G3 NGSx liquid handling platforms.
  • A manual library purification step along with Quality Control
  • The NGS libraries are then sequenced on Illumina’s NovaSeq 6000 short read sequencing platform
  • Data analysis of results using Olink’s proprietary analysis software. Automation reduces manual steps, while excluding data points that don’t meet criteria before normalization. Moreover, the software effectively identifies the underlying causes of any issues, pinpointing technical and human errors.
    • Olink Pre-Process software ngs2counts
    • Olink NPX Explore HT Software

Explore 3072 workflow

  • Sample Preparation & Dilution using liquid handling platforms such as those manufactured by Hamilton and the Mosquito/Dragonfly platforms by SPT Labtech
  • Incubation preparation with the Mosquito platform
  • PCR 1 sets up with Dragonfly, PCR 1 pooling and PCR 2 sets up, pooling steps with Sciclone G3 NGSx platforms
  • Manual Library Purification steps along with Quality Control
  • The NGS libraries are then sequenced on Illumina’s NovaSeq 6000 short read sequencing platform
  • Data analysis of results using Olink’s proprietary analysis software. Automation reduces manual steps, while excluding data points that don’t meet criteria before normalization. Moreover, the software effectively identifies the underlying causes of any issues, pinpointing technical and human errors.
    • Olink Pre-Process software ngs2counts
    • Olink NPX Explore Software

Overcoming the challenges in high-throughput biomarker discovery

Olink’s Explore HT and 3072 kits are just one part of the biomarker discovery process, as shown in the workflow above, liquid handling platforms such as SPT Labtech’s Dragonfly instruments are also necessary in order to accurately add dilutant and PCR master mix. Briefly, the Dragonfly platform harnesses innovative positive displacement technology to enable accurate and repeatable nanoliter to milliliter dispensing, every time to ensure accuracy and repeatability. While the Mosquito dilutes samples and adds assay reagents for both Olink kits. The Mosquito also utilizes positive displacement pipetting solutions and combines this with the power of miniaturization and automation to reduce costs, improve productivity, and maximize research output.

Once the PCR step has concluded and the NGS libraries are prepared, the library can be sequenced using Illumina’s NovaSeq 6000 platform. The NovaSeq 6000 is a powerful sequencer that can generate massive amounts of short-read sequencing data in a short period of time. The sequencing data is processed using bioinformatics tools to align the reads to a reference genome, identify single-nucleotide polymorphisms (SNPs) and quantify gene expression levels.

Finally, trained experts are then able to take the raw data taken from the NovaSeq 6000 platform and normalize it using Olink’s proprietary software to yield “Normalized protein expression” values or NPX.

In conclusion, the Olink Explore HT/3072 kits, SPT Labtech liquid handling along with Hamilton and  Sciclone G3 NGSx platforms and Illumina’s NovaSeq 6000 platform provide a comprehensive workflow for high-throughput biomarker discovery. This workflow enables researchers to quickly and accurately identify potential biomarkers that can be used for diagnostic or therapeutic purposes. However, purchasing, maintaining, and training staff to run these platforms is highly expensive and time consuming.

Outsourcing biomarker discovery to Sampled

There is an alternative to purchasing these platforms and kits. Outsourcing your samples for high throughput biomarker discovery to Sampled allows researchers to save on capital expenditure since you no longer need to invest in platforms, consumables, and reagents for each step in this workflow outlines above. Furthermore, outsourcing removes the need to train staff on new platforms and time-consuming optimization steps required for each step of the workflow. Our trained experts have been trained by each of these manufacturers allowing us to provide industry-leading turnaround time and accuracy.

Speak to one of our experts today to learn more about how our Protein Biomarker Discovery workflow can accelerate your research.

Filed Under: Uncategorized

Footer

Sampled logo

Sampled
30 Knightsbridge Road
Building 3, Piscataway, NJ 08854
U.S.A

Tel:  +1-732-273-0699

Latest news

  • Sampled Partners with EBiSC to Expand Access to Stem Cell Lines in the US April 8, 2025
  • Sampled Selected as Genome Characterization Center for the NCI March 27, 2025
  • Why Outsourcing -80°C Freezer Storage Could Save Your Lab Money January 17, 2025

Keep up to date

Connect with us on Linkedin

Sign up for our newsletter

Search site

Copyright © 2025 Sampled.com | Legal | Privacy policy | Cookies | Web build by...

Infinity BiologiX LLC, Roylance Stability Storage Limited and Roylance Scientific Limited are doing business as Sampled.

Speak to an expert

Tell us about your requirements and you will be contacted by our staff for personalized assistance

Speak to an expert

Tell us about your requirements and you will be contacted by our staff for personalized assistance

Sign up for our newsletter

Enquiry form

Search sampled.com

Free sample pack

Fill out the form below to receive a sample kitting pack with packaging examples and more information. 

Learn more about our kitting services