DNA Analysis Facility
The DNA Analysis Facility at the University of Vermont Cancer Center provides a wide array of efficient, user friendly, and affordable DNA analysis services to members of the University of Vermont Cancer Center, the University of Vermont research community, and outside institutions. Services provided for a fee include DNA Sequencing, RT-qPCR, DNA fragment Analysis, nucleic acid extraction, image analysis, SNP detection, human cell line authentication and projects on demand.
The facility provides a variety of important benefits free of charge to our users including experimental design consultation, data analysis and trouble shooting. Our annual Open House is a popular day long event highlighting our services and new technologies. The facility hosts a monthly Cancer Research and Technology Seminar series, presents software and instrumentation tutorials with the goal to educate and support our users, and showcase new services. A computer workstation area is adjacent to the main lab and has freeware and purchased programs available for user driven data analysis with full support from nearby facility staff.
- Automated DNA Sequencing
- Cycle sequence reactions
- Sequence runs
- Fragment Analysis.
- Genotyping, haplotyping, microsatellite markers
- T-RFLP, AFLP
- Human and Mouse Cell Line Authentication
- Includes DNA extraction and microsatellite analysis
- Real time qPCR
- Quantitative PCR (absolute or relative)
- Allelic Discrimination Assays
- SNP Detection (low or high-throughput)
- RNA and DNA extractions
- Nucleic Acid and Protein Quantification
- Molecular Imaging
- Consultation and Troubleshooting
- Computer workstation with DNA analysis software
- ABI Prism 3100-Avant Genetic Analyzer (4 capillary)
- ABI Prism 3130xl Genetic Analyzer (16 capillary)
- ABI Prism 7900HT Sequence Detection System (Real-time qPCR)
- AB 7500 Fast Real-time PCR System
- BioRad Personal Molecular Imager FX
- BioRad PharosFX Molecular Imager FX (with external Laser)
- BioRad Versa Doc 4000 MP
- BioTek Synergy H4 Hybrid Reader
- DNA Engine 96-well gradient Thermal Cycler (2)
- NanoDrop (2)
The software accessible to users includes: GeneMapper, Sequencher, Chromas, Edit View, BioEdit, Quantity One, Primer Express, Primer Select, and Dissociation Curve software.
Criteria and Process for the University of Vermont Cancer Center Member Subsidized Rates:
Guidelines updated 5/8/2014
Cancer Research Projects conducted by approved members that meet specific criteria are eligible to receive a 50% subsidy for all services in the DNA Analysis Facility arm of the Advanced Genome Technologies Core. For information regarding the University of Vermont Cancer Center membership or to confirm the status of your membership please visit the University of Vermont Cancer Center website – “For Members”.
A list of Cancer Qualified Research criteria is given below. If your project meets the criteria for Cancer Qualifying Research, you can contact Tim Hunter, Director of AGTC directly to set-up services.
If a project falls outside of the criteria listed below, prior approval is required by the University of Vermont Cancer Center Executive Leadership (Gary Stein, Claire Verschraegen, and Kate Webster).
Projects are NOT automatically cancer qualified by the nature of their funding agency. All projects require that the PI make a request by email to either Tim Hunter or the University of Vermont Cancer Center Leadership for “cancer qualifying” determination. All projects require review and approval PRIOR to submitting work to the DNA Analysis Facility.
Cancer Qualified Research includes:
- 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 Research Foundation (BCRF), 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 University of Vermont Cancer Center Protocol Review Committee.
- The University of Vermont Cancer Center or the University of Vermont Cancer Center /LCCRO approved Awards (e.g. the University of Vermont Cancer Center /LCCRO Pilot Project Awards, Program Awards, etc.)
Any cancer-related projects that fall outside the above criteria will require review by the University of Vermont Cancer Center Executive Leadership team. Proposals that do not meet the Cancer Qualified Research criteria listed above should be submitted to the Executive Leadership of the University of Vermont Cancer Center (Gary Stein, Claire Verschraegen, and Kate Webster).
Receiving the Cancer-Subsidy when placing a request in iLab:
Once your Grant has been approved to receive the subsidy, the staff at the DNA Analysis Facility will be notified. When you first place a service request in iLab to the DNA Analysis Facility, 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 lowered by 50% and you will see the actual cost to your grant for the work to be done. If you use a grant prior to getting it approved you will be charged the full amount and changes to the billing will NOT be retroactive, so be sure to have your grant reviewed prior to sample submission.
Citing the Advanced Genome Technologies Core (DNA Analysis and Massively Parallel Sequencing Core Arms)
Please remember to cite the University of Vermont Cancer Center Advanced Genome Technologies Core 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 as when your papers are published.
For Cancer Qualifying projects that were completed prior to Nov. 30, 2008:
- "The automated DNA sequencing (or other molecular analyses, i.e. rtQ-PCR, Molecular Imaging, etc.) was performed in the University of Vermont Cancer Center DNA Analysis Facility and was supported in part by grant P30CA22435 from the NCI. The views expressed are those of the author and do not represent the views of the NCI."
For Cancer Qualifying projects that were completed after Nov. 30, 2008:
- "The automated DNA sequencing (or other molecular analyses, i.e. rtQPCR, Molecular Imaging, etc.) was performed in the University of Vermont Cancer Center Advanced Genome Technologies Core and was supported by the University of Vermont Cancer Center, Lake Champlain Cancer Research Organization, and the University of Vermont College of Medicine."
For other users, state that DNA sequencing (or other molecular analysis) was performed in the University of Vermont Cancer Center Advanced Genome Technologies Core.
Links of Interest