At the VUMC High-Throughput Biomarker Core Laboratory we provide cost-effective high throughput and rapid gene expression, complete miRNA, SNP genotyping and proteomic analyses by using gold standard RT-qPCR and sequencing methods with the combination of custom Integrated Fluidic Circuit technology from Standard BioTools and Illumina NextSeq 2000 Instrument.
We are performing the RT-qPCR analysis on IFC chips (Dynamic Arrays) using Liquid Handling Robots (Mosquito LV and Dragonfly Discovery by SPTlabtech, epMotion 5075tc by Eppendorf, Janus Automated Workstation from by Perkin Elmer, Viaflo384 by Integra Biosciences), which significantly saves time and experimental costs (i.e., completing tens of thousands of reactions with minimal pipetting steps and much smaller volumes of reagents).
Benefits of using high-throughput BioMark HD Real-Time PCR System:
- Quick turnaround times
- Highly cost-effective cutoff points for sample and assay numbers
Example Study: For a study having 96 samples and 96 gene expression assays requiring 96x96 = 9,216 PCR reactions (without any PCR replicates): This equals only one Dynamic Array 96.96 in our core lab. By conventional PCR, this study requires 96 of 96 well PCR plates or 24 of 384 well PCR Plates . The cost for Master Mix for 96 or 384 PCR plates would be ~100 mL ($7,000) and would take 24-48 business days to complete this study. By using our core same study by using Dynamic Arrays and the BioMark platform is completed in 3 hours and the master mix volume is 400 µl (~$50.00).
Cutoff Point: Dynamic Arrays are an excellent platform for studies requiring large numbers of samples vs. large numbers of targets (genes, miRNAs, or genotyping). However, this platform may not be appropriate for studies with only a few samples and/or targets. A standard cutoff point (cost-wise) is 20 samples vs. 20 targets/assays. If a study has more than 20 samples and 20 assays, the overall cost of a study using this platform is cheaper (and much faster) as compared to conventional qPCR methods.
Also, as number of samples and/or assays increase the more cost-effective PCR data point or sample. This platform does not require pipetting individual component of qPCR reaction for each sample-target. Thus, no pipetting equals no pipetting errors which means more reproducible data. For miRNA studies, the data obtained is significantly more reproducible and accurate as compared to microarrays (CVs of 4% vs. 20-40%).
Proteomics: Protein by qPCR: This platform allows us to run Proximity Extension Assays (PEA) from Olink, which is simply relative and absolute quantification of proteins by qPCR analysis. We can quantify 92 proteins from 88 samples (1 µl sample only) plus 8 controls simultaneously only with 1-hour hands on time. There are 15 panels (92 proteins in each panel) to choose from for human and 1 panel for mouse. Samples can be body fluids such as plasma, serum or tissue samples, cell lysates etc.
Proteomics: Protein by Next Generation Sequencing: This platform allows us to run Proximity Extension Assays (PEA) from Olink, which is simply relative quantification of proteins by Sequencing analysis. We can quantify up to 3,072 proteins from 88 samples (3 µl sample only) plus 8 controls simultaneously only 2 days. Samples can be body fluids such as plasma, serum or tissue samples, cell lysates etc.
Please contact us at htbiomarkercore@vumc.org for more information about other sample types.
miRNA Profiling: Since numbers of miRNAs (200-300) are smaller than genes (2,000-8,000) in each tissue running a miRNA profiling study with high-throughput qPCR is very doable. Hundreds of samples can be profiled for several hundreds of miRNAs in a single day by using gold standard RT-qPCR method on our high-throughput platform.
By utilizing the VUMC High-Throughput Biomarker Core Laboratory, you will be able to save both time and money and get high quality data from expert hands.
Please contact us for more information at htbiomarkercore@vumc.org