The genotyping unit at the Biomedical Sciences Research Center "Alexander Fleming", is a newly established unit, started operating at the beginning of 2008. Its aim is to provide scientists with genotyping services based on SNP detection.
The facility’s infrastructure includes a pyrosequencing genetic analyser (PyroMark ID MA) capable of quick and efficient SNP analysis of as many as 480 samples per day, in addition to all the necessary equipment for a more conventional microsatellite genotypic analysis. We offer customised services for better design, optimisation and validation of genotypic assays, according to the individual’s needs.
Scientific coordinator: Dr Eleni Douni
Scientific operator: Vangelis Rinotas
• Speed congenics
Traditional backcrossing requires a minimum of 10 generations, up to three years to complete, and uses five times the number of animals. In contrast, the Speed Congenics program requires a maximum of five generations where candidate breeders are genotyped at each generation and those with highest percentage of the desired strain are selected to father the next generation.
The unit provides genetic testing services using a combination of both microsatellite and single nucleotide polymorphism (SNP) panels for characterizing and selecting breeders in a wide variety of inbred mouse strains subsequently used for the generation of congenic animals.
• Mouse whole genome scanning
The unit offers microsatellite and SNP based Genome Scanning Services for gene identification projects, based on linkage analysis, offering coverage for a number of mouse strains (i.e. C57BL6, DBA2J, CBA, 129S6, 129P2), as well as bioinformatic analysis using suitable mouse genetic software.
• Genetic quality control monitoring
Whole genome scanning (rapid or more detailed) for routine strain background monitoring, or in case of suspected contamination error, is a quick, inexpensive and reliable method compared to physical, immunological and biochemical assays, traditionally used for genetic quality assessment.
• ES cell line purity verification
In addition to mouse strain purity verification, the facility provides genetic screening of ES cell lines used for gene targeting experiments.
• Transgene copy number validation
Quick, easy to perform, custom made assay designs for accurate identification of transgene copy number integration. Up to six copies can be successfully quantified.
• Microbial / viral detection
The unit offers detection screening assays for numerous bacterial and viral contaminants of animal house colonies.
• Mutation screening
The unit can provide custom made assays for a wide range of known mutations associated with disease, such as single point mutations, insertions/deletions and sequence amplifications.
• Customized mutation screening assays
Biotage, the manufacturing company of the genetic analyzer PyroMark ID, offers in its database more than 1,000 customized assays for routine clinical screening diagnostics. Examples of these include screening for cancer mutations and CpG methylation in hMLH1, p16, K-ras and B-raf, screening for other disease associated genes such as APOE, HFE, MTHFR, UBE3A and OCA2 associated with Angelman / Prader Willi syndrome.
The unit offers population screening for a number of validated polymorphisms with pharmacogenetic implications, associated with positive or negative responses to therapeutic agents.
• CpG methylation status quantification
PyroMark ID provides highly reproducible quantification of methylation frequencies in individual consecutive CpG sites, enabling accurate measurement of even small changes in methylation levels that are associated with deregulation of gene expression and tumorigenesis.
• Microbial / viral detection and resistance assessment
The unit can offer screening assays for identifying numerous bacterial and viral agents as well as detecting genetic mutations that confer resistance to antibiotics and anti-viral drugs.