Vermont Integrative Genomics Resource - VIGR
The Vermont Integrative Genomics Resource (VIGR) is an overarching umbrella encompassing four distinct shared resource facility arms:
- DNA Analysis: The University of Vermont Cancer Center DNA Analysis Facility provides an array of fast, affordable, user-friendly DNA/RNA analysis services to the members of the University of Vermont Cancer Center, the University of Vermont research community and outside Institutions. Primary services offered for a fee include DNA Sanger sequencing, real-time quantitative PCR, DNA fragment analysis, SNP detection, nucleic acid extraction, image analysis, analytical flow cytometry, and support for absorbance, chemiluminescence, and fluorescence assays.
- Microarray: The Microarray Facility utilizes the Affymetrix GeneChip system to support global gene expression profiling using the standard 3’ arrays, miRNA, gene and exon arrays. The facility also provides supports for DNA idenfitification, quantification, and profiling for DNA studies using the DNA mapping (SNP), Promoter, Phylochip, and custom arrays.
- Massively Parallel Sequencing Facilities: The University of Vermont Cancer Center/College of Medicine Massively Parallel Sequencing Facility provides genome-scale next generation DNA sequencing. This facility employs the use of the massively paralleled sequencing (MPS) technology on the Illumina HiSeq 1500 system which is a sequencing by synthesis approach (SBS). Next generation sequencing (also known as deep sequencing or high throughput sequencing) enables researchers to sequence as much as an entire human or mouse genome with greater than 50 fold coverage. A single run on the Illumina HiSeq 1000 can generate over 350 billion bases of DNA/RNA.
- Bioinformatics Shared Resource: The primary source for bioinformatics support for members on campus, and offers services related to genomic sequencing, epigenetic modification, or expression. This core enables investigators to navigate large complicated data sets and summarize those data into publishable inferences.
How to Access Services
VIGR is now using iLab Solutions for all service requests and distribution of data.
To get started, you must register for an account:
- Navigate to the core page.
- In the upper-right-hand corner of the screen, select sign up.
- Complete the registration form on the sign-up page.
- Receive a “welcome” email from iLab (typically within one business day) with login credentials
and basic instructions.
We have developed a number of “How to” Manuals to help with some basic functions:
The Common Equipment Room is located in HSRF 307 and allows 24/7 access to a variety of user driven equipment for trained investigators. Equipment includes:
- Imaging equipment including: Bio-Rad Pharos FX PLUS, Bio-Rad Personal FX, and Versa Doc 4000 MP
- BioTek Synergy H4 Multi-plate reader
- NanoDrop Spectrophotometer
UVM Cancer Center Member Benefits: Cancer Qualified Research Subsidies
Membership in the UVMCC gives qualified researchers access to UVMCC subsidies in the Vermont Integrative Genomics Cancer Resource (VIGR). This includes:
- 50% subsidy for DNA facility services
- 15% subsidy on library preparation with the Massively Parallel Sequencing (MPS) facility
- 15% subsidy on microarray hybridization and scanning in the Microarray facility (MA)
- 15% subsidy on bioinformatics analysis with the Bioinformatics Shared Resource (BSR)
Note: Dedicated funds for each service arm are not unlimited. Subsidies apply until annual budgeted funds are expended.
Receipt of the subsidy requires UVMCC membership (see “For UVM Cancer Center Members
) and prior
approval of a project by the UVMCC administration (contact Kate.Webster@uvm.edu
A list of Cancer Qualified Research criteria is given below:
All Research Supported by the NCI with the following prefixes:R00, R01, R03, R15, R18, R21, R24, R25, R33, R37, R41, R42, R43, R44, R55, R56, P01, P50 sub-projects, P20, SC1, SC2, U01, U10, U19, U54, U56 and N01 research contracts and peer-reviewed, funded subcontracts of Center Members participating in collaborative research. (Note: Shared resources of multi-component grants are not eligible for inclusion)
- Cancer-related Research Supported by Other NIH Institutes (same prefixes as above) and Funding Organizations (i.e. ACS (Nat’l), NSF, EPA, VA (Central Office), AICR, NIOSH, FDA, AHRQ, AACR, amFR, CIRM, CPRIT, CDC, FAMRI, FBRP, MRA, MMRF, NYSTEM, CBCRP, TRDRP, DoD Breast, Ovarian, Prostrate Cancer Program, Susan G. Komen, Leukemia and Lymphoma Society, Breast Cancer Foundation, Cancer Research Foundation Of America, & Howard Hughes Medical Foundation).
- Unfunded Clinical Research Studies approved by the NCI’s Cancer Therapeutics Evaluation Program (CTEP) or the UVMCC Protocol Review Committee.
- UVMCC/CCSG or UVMCC approved Pilot Project Awards
Any cancer-related projects that fall outside the above criteria will require review by the UVMCC Executive Leadership team. Proposals that do not meet the Cancer Qualified Research criteria listed above should be submitted to the Executive Leadership of the UVMCC (Gary.Stein@uvm.edu, Kate.Webster@uvm.edu).
Receiving the Cancer-Subsidy when placing a request in iLab:
Once your project has been approved to receive the subsidy, the staff at VIGR will be notified. When you first place a service request in iLab to VIGR, you will see the full cost of the request displayed. The staff will review the request and confirm that it should receive the subsidy. At that time, the cost will be adjusted with the appropriate subsidy and you will see the actual cost to your grant for the work to be done.
Note: Services rendered prior to project approval will be charged the full amount and changes to the billing will not be retroactive.
Citing The Vermont Integrative Genomics Resource DNA Facility
Please remember to cite the University of Vermont Cancer Center-Larner College of Medicine Vermont Integrative Genomics Resource DNA Facility in your abstracts and publications. These citations demonstrate to the NCI and other funding organizations (as well as the UVM administration) the importance of this facility to UVM researchers and thereby encourage their continued support.
We try to keep a current list of all publications that cite the facility, so please let us know when your papers are published!
Citing The DNA, Microarray, and Massively Parallel Sequencing Facilities
Please remember to cite the University of Vermont Cancer Center-Larner College of Medicine DNA and/or Microarray (if used after July 1, 2017) and/or Massively Parallel Sequencing Facilities in your abstracts and publications:
- "The automated DNA sequencing (or other molecular analyses, i.e. rtQPCR, Molecular Imaging, etc.) was performed in Vermont Integrative Genomics Resource DNA Facility and was supported by University of Vermont Cancer Center, Lake Champlain Cancer Research Organization, and the UVM Larner College of Medicine."
- The target preparation and array hybridization was performed in the Vermont Integrative Genomics Resource Microarray Facility and was supported by the University of Vermont Cancer Center, Lake Champlain Cancer Research Organization, UVM College of Agriculture and Life Sciences, and the UVM Larner College of Medicine."
- "The next-generation sequencing was performed in the Vermont Integrative Genomics Resource Massively Parallel Sequencing Facility and was supported by the University of Vermont Cancer Center, Lake Champlain Cancer Research Organization, UVM College of Agriculture and Life Sciences, and the UVM Larner College of Medicine."
Citing the Bioinformatics Shared Resource
Please remember to cite the University of Vermont Cancer Center-Larner College of Medicine Bioinformatics Shared Resource in your abstracts and publications:
"Sequencing analysis and other bioinformatics services were provided by the Vermont Integrative Genomics Resource DNA Facility and supported by the University of Vermont Cancer Center, Lake Champlain Cancer Research Organization, and the UVM Larner College of Medicine."
Citing the Vermont Genetics Network Microarray Facility (for arrays made prior to July 1, 2017)
The National Institute of General Medical Sciences of the NIH, which funds the Vermont Genetics Network (VGN), requires that we acknowledge them as the source of funding that supports your work whenever you publish papers, chapters, abstracts or otherwise present your work if you have accessed services in a VGN Core. Please acknowledge the VGN grant by number and cite the specific VGN Core(s) at the University of Vermont in all publications and grant applications if you are using data or tools generated in a VGN Core. Please send us the PDF file of your publications and let us know if the grant is awarded.
Below is an example of how you must cite the VGN grant and specific core(s) used:
Research reported in this (publication, release) was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103449. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH.