Genetic Testing Program
Taconic currently uses Single Nucleotide Polymorphisms (SNPs) and genotyping in its Genetic Monitoring Program, to monitor genetic background. More specifically, the program uses the Illumina platform and has developed several SNP Panels for Genetic Monitoring of rats and mice, including a 2050 SNP Panel that differentiates among the most used inbred strains, a 257 SNP Panel that differentiates among C57BL/6NTac, C57BL/6J and C57BL/6JBomTac substrains, and a rat SNP Panel with over 750 SNP markers that can be used for speed congenic backcrosses in addition to strain background characterization. Taconic also uses genotyping through Taqman PCR, qPCR or chip base analysis PCR, and in some cases phenotyping data (Flow Cytometry Analysis) to verify that the pertinent protein is made.
- Foundation Colonies: All Foundation colonies are characterized with SNP Panels: 2050 SNP Panel for mice and 759 SNP Panel for rats. The SNP profile obtained is compared and verified with the line's historical information.
- Genetic Monitoring Program: A genetic monitoring program tests a subset of breeders to verify genetic quality. This testing is performed on a monthly basis and it is reported on our website. The SNP Panel used for this is a customized panel analyzed by PCR-based screening of specific SNP and mutation markers that distinguishes among all the genetic backgrounds for which a contamination risk exists at the location. In addition, inbred strains are assessed using the 2050 Illumina SNP panel on a yearly basis.
- Genotyping: In addition to genetic background monitoring, if an inbred strain carries a spontaneous mutation (e.g. Ptprc) the mutation's presence is verified. In many cases the zygosity of the mutation is also monitored.
- Genetic Monitoring Program: All of Taconic's outbred stocks are tested at least once a year or if there is genetic risk more often. Genetic monitoring SNP Panels for mice and rats (98 SNPs for mice, 96 SNPs for rats) are used to monitor the level of heterozygosity, allele frequencies and inbreeding coefficient of all the SNPs within the different colonies and ensure those parameters are consistent for the various colonies of each outbred line. This monitoring is designed to detect and limit inbreeding of the colony and signal the need to refresh from cryopreserved material.
- Genotyping: In addition to genetic background monitoring if the outbred stock carries a spontaneous mutation, its presence is verified.