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| 215-214-1696 Cynthia.Spittle@fccc.edu |
The Genotyping Core provides a centralized resource for the human and mouse genotyping needs of investigators at Fox Chase Cancer Center (FCCC). These services are necessary to support the pre-clinical and population studies that are designed to identify genetic biomarkers and signatures that may be associated with cancer risk, disease progression or drug efficacy and toxicity. Cost-effective genotyping services are also beneficial to investigators who utilize knock-out or transgenic strains of mice in their research. Services and instrumentation are available for polymorphism, mutation and CpG methylation analysis. New services are developed and offered based on the latest advances in genotyping and biomarker research and the changing needs of FCCC investigators.
Function
The Genotyping Core provides cost-effective genotyping services to laboratory investigators, clinicians, epidemiologists and behavioral researchers who wish to perform pre-clinical or population-based studies. The staff is available for consultation regarding current testing and product information as well as appropriate sample collection, storage, and handling.
Single nucleotide polymorphisms (SNPs) and other forms of germline and somatic genetic variation (STR’s, copy number, mutation) are the focus of intense research due to their possible role in predicting disease susceptibility, prognosis and therapeutic response. The Genotyping Core is equipped with a PSQ96 System (Biotage), an ABI7900 Sequence Detection System and a CEQ8800 for the analysis of targeted sequences of DNA. The facility can provide expertise in the development and analysis of polymorphism panels that include genes that are of highest interest in cancer prevention and treatment, i.e., DNA repair, Phase I and Phase II detoxification, immunoregulation and viral clearance, steroidogenesis, cell cycle regulation, and drug metabolism. Hotspot mutation assays have been developed for K-ras, N-ras and B-raf.
In addition to gene mutations, epigenetic alterations, such as CpG methylation, contribute to molecular signatures. The CPBGF offers quantitative analysis of CpG methylation by pyrosequencing or real-time fluorescent PCR. Pre-designed and optimized assays are available for several common gene promoter regions that are hypermethylated in multiple types of cancer (i.e., p16, MGMT, hMLH1). Global methylation status can also be assessed in the human and mouse genome utilizing assays targeting LINE-1 and B1 repetitive elements, respectively. We have developed a panel of methylation assays to characterize colorectal tumors with the CpG island methylator phenotype (CIMP Panel). Custom assay development is also available to meet an investigator’s specific research needs.
Variations in class I and class II human leukocyte antigens may contribute to an individual’s susceptibility to virus-related cancers of the cervix (HPV) and liver (HCV/HBV). PCR-based assays are available for the typing of HLA markers of interest. Genotyping methods are also available for the analysis of genetic variation and subtypes of HPV and HBV.
The Genotyping Core also provides mouse genotyping services for investigators who maintain and use colonies of transgenic and knock-out mice in their research. General colony maintenance and the selection of appropriate animals for experimentation require the accurate and rapid genotyping of littermates. DNA is extracted from tail or toe clippings and analyzed using PCR-based protocols. Assistance in the development and/or optimization of new genotyping protocols is provided as needed.Description
The Genotyping Core occupies approximately 600 sq. ft. on the second floor of the Cancer Prevention Pavilion. Laboratory equipment includes the PSQ96MA, CEQ8800, ABI7900, an Eppendorf MasterCycler Gradient Thermal Cycler, an MJ Research PTC-225 Tetrad Thermal Cycler and a BioRad Dyad Thermal Cycler. A Baker SterilGuard II hood is dedicated exclusively to the preparation of PCR reactions. An Eppendorf 5075VAC System is used for automated DNA extractions from tissues and cells. General laboraory equipment includes horizontal electrophoresis apparatus for DNA analysis, a Corning pH meter (model 340), refrigerator and freezers (-20®C and -80®C) for reagent and specimen storage, non-circulating water bath, and dry block incubators. Equipment rooms are located across the hall and provide access to a UV box and an Alpha Imaging System for gel documentation and a Baker SterilGuard II hood dedicated to biohazard sample handling.