Collaborative Genomics Center (CGC) 

 


The Collaborative Genomics Center at the Vaccine & Gene Therapy Institute of Florida (VGTI Florida®) provides consultative research services that include whole genome microarray analysis using the Illumina® iScan platform, sequencing-based assays using the Illumina® Hi-Seq 2500 Sequencing System for sequencing genomic DNA, mRNA, microRNA, or ChiP, and gene validation using the high-throughput Applied Biosystem’s OpenArray® or Fluidigm’s BioMark system. The CGC consists of an 8-member genomics team and an 8-member bioinformatics team.
 
View the interactive
VGTI Florida
Collaborative Genomics Center (CGC) Brochure.




 
Download the VGTI Florida
Collaborative Genomics Center (CGC) Brochure.



 

The Center currently consists of two cores:
the Genomics Core and the Bioinformatics Core

 
Our objectives:
 
  • To provide an SOP-driven sample acquisition, genomic analysis, bioinformatic reporting, and data management framework to assist researchers with their genomics needs and reporting.
  • To support researchers throughout the experimental design, sample collection, genomic processing and data analysis processes.
  • To provide advanced bioinformatic tools in the functional analysis of transcriptional signatures.
  • To develop data integration methods that will allow collaborating groups to benchmark their vaccine/pathogenesis/therapeutic experiments against existing signatures of protection, also with links to publically available datasets.


 

 
Microarray Platform

Illumina® Whole Genome Expression Bead Chips

SOP-driven complete assay includes sample banking, total RNA isolation, 1-cycle or 2-cycle (small sample) amplification, labeling, hybridization, scanning, QC, and standard bioinformatics report.

Capability to profile low number of cells, tissues, or small volumes of blood.

Semi-automated standard bioinformatics report includes raw data, QC, annotation, preprocessing, contrasts, unsupervised analysis, and differential gene analysis.


Microarray Assay Codes:
 
GEN01 Microarray Illumina® WG BeadChip, complete 1-cycle assay: includes sample banking, total RNA isolation, 1-cycle amplification, labeling, hybridization, scanning, QC and standard bioinformatic report.

GEN02 Microarray Illumina® WG BeadChip, complete 1-cycle assay: includes sample banking, total RNA isolation, 1-cycle amplification, labeling, hybridization, scanning, QC and standard bioinformatic report, plus senior project and biological design consultation.

GEN10 Bioinformatics Advanced Reporting: A standard bioinformatics report includes raw data, QC, annotation, preprocessing, contrasts, unsupervised analysis, and differential gene analysis. Advanced reports include gene set enrichment, pathways, functional genomics, modeling and publication quality figure generation.


Next Gen Sequencing Platform

Illumina® Hi-Seq 2500 Sequencing System Platform
  • DNA-seq, mRNA-seq (multiplexed), miRNA-seq, non-coding RNA seq
  • Novel techniques allow for small input sample material (50ng allows for >90% coverage of sequence complexity roughly equivalent to 5,000 cells)
  • Digital gene expression
  • Novel transcript and isoform discovery

Sequencing Assay Design

Due to the highly flexible Illumina® Hi-Seq 2500 Sequencing System platform and the ever-expanding options for Next Generation Sequencing, a direct consultation with the CGC and the Investigator is needed before final study design and pricing estimates can be determined.


Laboratory Automation

SOP integrated Beckman Biomek® FXp platform improves workflow speed and quality control

High Throughput qPCR Validation Platforms

OpenArray® Real-Time System is used for array-based, high throughput qPCR validation of microarray results (e.g. 100 genes in one run). Custom themed arrays designed in house are available (e.g. IFN signaling genes, transcriptome, Inflammasome).

We will work with you to determine the best approach and strategy for implementing next generation sequencing into your specific research program.


Nanofluidics: Fluidigm Biomark Platform

The Biomark HD system consists of a microfluidics based platform that allows for the use of nanoliter scaled reactions. This system allows for a wide array of sample sources and applications including digital PCR, real time PCR, targeted sequencing, SNP analysis and can support single cell applications. The 96x96 format allows for flexibility in assay design and application, including our custom immunology panels.


Bioinformatics

The CGC bioinformatics team has produced standardized and semi-automated bioinformatic technologies designed to analyze and summarize genomic data from multiple platforms and at the capacities necessary for our workload (5000+ transcriptomic assays/year).
  • Standard bioinformatic reports can be generated on small (12 arrays/1 flow cell) to large projects (100’s of samples) in a matter of hours.
  • Advanced bioinformatics reporting is available on an hourly basis that includes gene set enrichment, pathways, functional genomics, modeling, and publication ready output.

We are dedicated to our overall aim to build novel assay and functional genomics analysis capacity by adapting genomic and bioinformatic analysis tools to research being done by our collaborators and our customers.
 
 
Contact Information:

VGTI Florida Collaborative Genomics Center
Vaccine & Gene Therapy Institute of Florida
9801 SW Discovery Way
Port Saint Lucie, FL  34987
Phone: (772) 345-5673
 
Director:
Mark Cameron, Ph.D.
Vaccine & Gene Therapy Institute of Florida
9801 SW Discovery Way
Port Saint Lucie, FL  34987
Phone: (772) 345-5673
Email: 

 
Genomics Coordinator:
Li Pan
Email:
Project Coordinator:
Stephanie Richards
Email: 
 
Bioinformatic Core Manager:
Peter Wilkinson
Phone: (772) 345-5711
Email: 



 
Research Assistants:
Andrew Smith - MS
Petra Stafova - Ph.D.
Michael Cartwright - BS
Navnita Dutta - MS
John Pyles - MS
 
Bioinformaticians:
Ali Filali - Ph.D.
Slim Fourati - Ph.D.
Amit Sabnis - Ph.D.
Aarthi Talla - MS
Courtney Steel - BS
Khader Ghneim - MS
     
















 

 

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