Cryopreservation of Taconic strains

To avoid Genetic Drift, Taconic has embryos cryopreserved from strains and stocks that it provides. Taconic refreshes all inbred stocks every 5 years or 10 generations whichever comes first.

Taconic Production Harmonization

Inbred Production: 

• Taconic has only one Foundation Colony that provides breeders to all subsequent colonies and including all global partners. This is a way to assure that all animals produced by Taconic and its partners are genetically harmonized.

Outbred Stocks: 

• All outbred stocks originate from a nucleus stock and are bred following Poiley's outbred breeding scheme.

Genetic Testing Program

Taconic's Genetic Monitoring Program uses molecular genetic technologies to verify genetic identity, monitor genetic background, detect genetic contamination, and assess genetic stability of mouse and rat colonies.

For mice, genetic background monitoring is primarily performed using a single nucleotide polymorphism (SNP) panel. This differentiates commonly used inbred strains and substrains and supports applications such as genetic background characterization, contamination detection, and speed congenic backcross programs.

For rats, genetic background monitoring is performed using a multiplexed amplicon panel targeting a collection of SNPs to ensure genetic background consistency and verify continued conformity to the established colony profile.

This approach assesses genetic background composition, genetic diversity, heterozygosity, and potential genetic drift across rat colonies.

In addition to background monitoring, Taconic uses targeted genotyping assays, including TaqMan PCR, qPCR, endpoint PCR, and array based methods, to verify spontaneous mutations, engineered alleles, transgenes, and zygosity. For selected models, phenotypic assays such as flow cytometry may be used as supplemental verification that the expected biological trait or protein expression is present.

Inbred strains:

1. Foundation Colonies:
   All foundation colonies are genetically characterized prior to release into production. Mouse foundation colonies are characterized using SNP panels, while rat foundation colonies are characterized using amplicon sequencing panel. Genetic profiles are reviewed against historical colony records and expected strain profiles to confirm genetic identity and background integrity.
   
   
2. Genetic Monitoring Program: 
   A routine genetic monitoring program evaluates a defined subset of breeders to verify genetic quality and colony integrity. Monitoring is designed to detect genetic contamination, unexpected genetic drift, and loss of strain fidelity.
   
   For mice, SNP analysis is used as the primary monitoring platform. Additional genotyping assays may be incorporated when differentiation between closely related substrains or phenotypically similar strains is required, particularly in locations where contamination risk exists.
    
   For rats, multiplexed amplicon sequencing panel is used to monitor genetic background consistency and verify continued conformity to the established colony profile.
   
   
3. Genotyping: 
   In addition to genetic background monitoring, inbred strains carrying spontaneous, engineered, or targeted mutations are routinely genotyped to verify the presence of the expected allele. When appropriate, zygosity is also confirmed to ensure colony integrity and breeding accuracy.

Outbred stocks:

1. Genetic Monitoring Program: 
   All outbred stocks undergo routine genetic monitoring at least annually, or more frequently when colony risk assessments indicate increased monitoring is warranted.
   
   Mouse colonies are evaluated using SNP based genetic monitoring panels and rat colonies are evaluated using multiplexed amplicon sequencing panel. These analyses assess genetic diversity metrics including heterozygosity, allele frequency distributions, and inbreeding coefficients. Results are compared with established colony baselines to verify that genetic diversity is maintained and that colonies remain representative of the intended stock.
   
   This monitoring program is designed to detect loss of genetic diversity, excessive in breeding, unintended genetic shifts, and contamination events. Results are used to guide colony management decisions, including genetic refreshment from cryopreserved material when necessary.
   
   
2. Genotyping:
   For outbred stocks carrying spontaneous, engineered, or selected mutations, targeted genotyping assays are used to verify the presence of the expected allele. Additional testing may be performed when required to support colony management, breeding decisions, or customer requirements.

Genetically Engineered Models

Bringing a New GEM into Taconic: When a new model is brought to Taconic for commercial distribution, all genetic documentation is verified:

• Genetic background: SNP profile characterization
  
• Generation number: Historical information of matings including backcrosses and intracrosses
• Type of genetic modification: Targeted mutagenesis, CRISPR/CAS 9 modifications and Random Insertion
• Adverse phenotypes: History of adverse phenotypes
• Other characteristics

Colony Breeding: During barrier production the model is mated using the most efficient mating format in order to comply with the 3 Rs (Replacement, Reduction and Refinement) Genotyping and Genetic Background Testing

• All GEM models commercially available have a defined SNP profile in order to characterize the genetic background of the model.
  
• Genotyping, includes testing for the mutation, determination of zygosity for the mutation and in some cases the presence of the functional transgene.

Genetic Audits

All colonies maintained at Taconic are subject to periodic genetic audits. The audit process has two levels: operational level auditing and data monitoring. In operational auditing, inventories will be audited. The data monitoring involves project-specific clinical, genetic and breeding data collection and subsequent analysis by scientists in Taconic’s Genetics Department.    

Genetic Monitoring Reports

For each commercial colony the frequency and number of samples tested is dependent on the risk of genetic integrity break at each location. Colonies with no risk for a break in genetic integrity are tested at least yearly.  Colonies at highest risk are tested monthly.