Why this Core?

At the VUMC High-Throughput Biomarker Core Laboratory, we specialize in delivering cost-effective, high-throughput gene expression, complete miRNA, SNP genotyping, and proteomic analyses. We achieve this through a combination of gold standard RT-qPCR and sequencing methods, leveraging custom Integrated Fluidic Circuit (IFC) technology from Standard BioTools and the Illumina NextSeq 2000 Instrument.

Our RT-qPCR analysis is conducted on IFC chips (Dynamic Arrays) utilizing Liquid Handling Robots, including Mosquito LV and Dragonfly Discovery by SPTlabtech, Hamilton Star by Hamilton, F.A.S.T. by Formulatrix, epMotion 5075tc by Eppendorf, Janus Automated Workstation by Perkin Elmer, and Viaflo384 by Integra Biosciences. This approach significantly reduces time and experimental costs, allowing us to complete tens of thousands of reactions with minimal pipetting steps and smaller reagent volumes.

 Benefits of utilizing the high-throughput BioMark HD Real-Time PCR System:

• Quick Turnaround Times: Experience rapid processing and analysis of samples.
• Highly Cost-Effective Cutoff Points: Optimize costs efficiently based on sample and assay numbers.

Example Study: For a study with 96 samples and 96 gene expression assays, requiring a total of 9,216 PCR reactions (without PCR replicates), this equates to using just one Dynamic Array 96.96 in our core lab. In contrast, conventional PCR for this study would necessitate 96 96-well PCR plates or 24 384-well PCR plates. The cost for Master Mix for either 96 or 384 PCR plates would be approximately 100 mL ($7,000), and it would take 24-48 business days to complete. However, utilizing Dynamic Arrays and the BioMark platform in our core lab, the same study is completed in just 3 hours, using a master mix volume of 400 µl (costing approximately $50.00).

Cutoff Point: Dynamic Arrays are ideal for studies requiring a large number of samples compared to a large number of targets (genes, miRNAs, or genotyping). A typical cutoff point (cost-wise) is 20 samples vs. 20 targets/assays. If a study involves more than 20 samples and 20 assays, the overall cost is lower (and much faster) compared to conventional qPCR methods. Moreover, as the number of samples and/or assays increases, each PCR data point or sample becomes more cost-effective. This platform eliminates the need to pipette individual components for each sample-target, resulting in more reproducible and accurate data. For miRNA studies, the obtained data is significantly more reproducible and accurate compared to microarrays (CVs of 4% vs. 20-40%).

Olink Proteomics - Protein Quantification by qPCR: Our platform allows us to run Proximity Extension Assays (PEA) from Olink, enabling relative and absolute quantification of proteins through qPCR analysis. We can quantify 5, 21, 48 or 96 proteins from 40 to 88 samples at a time (using only 1 µl of the sample) plus 8 controls simultaneously with just 1-hour hands-on time. There are 2 Target 48 panels (one human and one mouse), 15 Target 96 panels (14 human and one mouse, each containing 92 unique proteins & 4 controls) to choose from. Samples can include body fluids such as plasma, serum, tissue or cell lysates, etc.

Olink Proteomics - Protein Quantification by Next Generation Sequencing: Our platform also enables Proximity Extension Assays (PEA) from Olink for relative quantification of proteins through sequencing analysis. We can quantify up to 5,416 proteins from 172 samples (using only 2 µl of the sample) plus 10 controls simultaneously within 2 days with Explore HT. Again, the samples can include body fluids such as plasma, serum, tissue and cell lysates, etc.

For more information about other sample types, please contact us at htbiomarkercore@vumc.org.

miRNA Profiling: Given that the number of miRNAs (200-300) is smaller than the number of genes (2,000-8,000) in each tissue, running a miRNA profiling study with high-throughput qPCR is very achievable. Hundreds of samples can be profiled for several hundreds of miRNAs in a single day using the gold standard RT-qPCR method on our high-throughput platform.

By utilizing the VUMC High-Throughput Biomarker Core Laboratory, you will save both time and money while obtaining high-quality data from expert hands. For more information, please reach out to us at htbiomarkercore@vumc.org.