Who Should Use This Core And Why

Comparison of a conventional qRT-PCR vs. high throughput lab platform

For a study having 96 samples and 96 gene expression assays requiring 96x96=9,216 PCR reactions: This equals one 96 x 96 well plate in the core. By conventional PCR, the cost for Master Mix for 96 plates would be ~100 mL ($7,000) and would take 24-48 business days. This same study using Dynamic Arrays and the BioMark platform is completed in 3 hours and the master mix volume is 400 µl ($40.00).

Cost Effective Cutoff Point for Sample and Assay Numbers

Dynamic Arrays are an excellent platform for studies requiring larger numbers of samples vs. targets. However, this platform may not be appropriate for studies with only a few samples and/or assays. A standard cutoff point (cost-wise) is 15 samples vs. 15 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 PCR methods. Also, as numbers of samples and/or assays increase the more cost effective PCR data point or sample. For miRNA, the data obtained is significantly more reproducible and accurate as compared to microarrays (CVs of 4% vs. 20-40%).

Examples of Previous and Continuing Studies

 

  1. The SABRe in CVD Initiative; Project 4 in this study consists of 7,000 samples for profiling 754 miRNA assays 4.

  2. Relation of platelet and leukocyte inflammatory transcripts to body mass index in the Framingham heart study. 5. This study consists of 2,250 FHS participants and over 500 mRNA expression analyses.

  3. Relationship between Markers of Platelet Activation and Inflammation with Disease Activity in Wegener's Granulomatosis (J Rheumatol 2011 Jun; 38 (6):1048-1054). Total 563 plasma/serum samples were analyzed for 7 different ELISA assays using the robotic system.

  4. Animal studies. Multiple studies needing many gene expression assays but only having small amounts of tissue or few cells; i.e. murine vein gene expression studies, murine platelet/monocyte/cerebral tissue studies.

  5. 450 human fat tissues samples analyzed for 96 gene expression values.

  6. Human platelets and PBMCs analyzed for 36 gene expression assays.

  7. http://www.framinghamheartstudy.org/participants/news.html

  8. http://www.ncbi.nlm.nih.gov/pubmed/20606121

  9. http://www.ncbi.nlm.nih.gov/pubmed/21411717

 

CONTACT US
Co-Director:

Kahraman Tanriverdi, PhD
Phone: 508-856-6962
kahraman.tanriverdi@umassmed.edu
www.umassmed.edu/htcore