Minimal Strain Sets Explaining All Diagnostic Classes (Number of Markers Explained):
Solution 1: 129S6/SvEvTac and C57BL/6J and C57BL/6NRj
C57BL/6J: 169 / 177 (95.5%)
129S6/SvEvTac: 4 / 40 (10.0%)
C57BL/6NRj: 6 / 38 (15.8%)
Strain Reproducibility
Strain Reproducibility Samples: QR7176, DN8844
Inbreeding Level: 88.0%
Y Chromosome: Host
Congenicity Level: 87.5%
Donor Contribution in Linked Interval: 0.0Mb
The genome of this strain is not reproducible because there are regions that are still segregating (at least 12.0%) at the strain level.
The estimation of contribution of primary and secondary background depends on the number of samples genotyped.
The impact of this on the published phenotype(s) is unknown.
Substrain Reproducibility
79.9% of the genome is distinguishable between two substrains contributing to the primary background. Of this:
Level of inbreeding: 83.5%
C57BL/6J Contributes: 91.7%
C57BL/6NRj Contributes: 8.3%
The genome of this strain is not reproducible because there are regions that are still segregating (16.5%) at the substrain level.
The estimation of contribution of substrains depends on the number of samples genotyped.
The impact of this on the published phenotype(s) is unknown.
Ideogram 1 Ideogram 2
Notes
Genetic QC analysis (GQC) was performed on representative samples from the donor submission and provides a baseline reference. Regardless of the material ordered (live mice, sperm, embryos, resuscitated animals), the provided material is guaranteed to contain the primary genetic alteration of interest; however, the composition of the genetic background may vary (See Reproducibility sections of the report for details). The impact of genetic background on previously reported phenotypes has not been evaluated.
GQC analysis was done on two XY samples, QR7176 and DN8844, at the time of importation and the conclusions are consistent in all samples. The results of the analysis are congruent with the SDS and DN8844 is the representative sample selected for the report. The primary (host) background is C57BL/6. There is positive evidence of C57BL/6J and C57BL/6N substrains. The secondary background is 129S6 (no mention of this is found in the SDS). There is evidence of a third background, consistent with complex genetics possibly from CD-1 (donor) as indicated in the submission and the SDS as the donor strain. CD-1 is not included in our consensus since it is outbred (represented by gray, unknown). The mitochondrial genome is consistent with at least one backcross to a female from the C57BL/6 background. The Y chromosome is consistent with at least one backcross to a male from the C57BL/6J background. The Cre construct is detected in both samples. The genome of the MMRRC_010588-UNC strain is 88.1 % inbred at the strain level. At least 11.9% of the genome is segregating for the 129S6 and CD1 backgrounds. The level of inbreeding estimated by MiniMUGA is inconsistent with the number of backcross generations reported in the SDS. After ten generations the expected level of inbreeding is >0.955. 21.3% of the genome is segregating for the two substrains (C57BL/6J and C57BL/6N) that contribute to the primary (host) background. The contribution of C57BL/6J is 85.8%, the contribution of C57BL/6N is 7.1%.
The estimated inbreeding, congenicity, and the relative strain/substrain contribution depend on the number of samples genotyped. The genomes of strains that are not fully inbred are not completely reproducible.
Special Considerations
Based on this report, a request has been made to update the strain name from B6J.Cg-Tg(Tagln-cre)1Jomm/Mmnc to B6.Cg-Tg(Tagln-cre)1Jomm/Mmnc (1/19/23).
WARNINGS
This sample likely has more than 2 genetic backgrounds (unexplained regions and/or fractured ideogram). The strain selected for secondary background may be incorrect. The estimation of the contribution of primary and secondary background are likely incorrect. This can potentially be addressed with input from the user.