Minimal Strain Sets Explaining All Diagnostic Classes (Number of Markers Explained):
Solution 1: 129P2/OlaHsd and 129S6/SvEvTac and C57BL/6J and C57BL/6NTac
C57BL/6J: 22 / 156 (14.1%)
C57BL/6NTac: 21 / 30 (70.0%)
129P2/OlaHsd: 1 / 27 (3.7%)
129S6/SvEvTac: 1 / 39 (2.6%)
Solution 2: 129P2/OlaHsd and 129S6/SvEvTac and C57BL/6J and C57BL/6NRj
C57BL/6J: 22 / 156 (14.1%)
C57BL/6NRj: 21 / 30 (70.0%)
129P2/OlaHsd: 1 / 27 (3.7%)
129S6/SvEvTac: 1 / 39 (2.6%)
Solution 3: 129P2/OlaHsd and 129S6/SvEvTac and C57BL/6JRj and C57BL/6NTac
C57BL/6JRj: 22 / 156 (14.1%)
C57BL/6NTac: 21 / 30 (70.0%)
129P2/OlaHsd: 1 / 27 (3.7%)
129S6/SvEvTac: 1 / 39 (2.6%)
Solution 4: 129P2/OlaHsd and 129S6/SvEvTac and C57BL/6JRj and C57BL/6NRj
C57BL/6JRj: 22 / 156 (14.1%)
C57BL/6NRj: 21 / 30 (70.0%)
129P2/OlaHsd: 1 / 27 (3.7%)
129S6/SvEvTac: 1 / 39 (2.6%)
Strain Reproducibility
Strain Reproducibility Samples: UE3333, NZ1329
Inbreeding Level: 98.4%
Y Chromosome: Host
Congenicity Level: 96.5%
Donor Contribution in Linked Interval: 6.2Mb
The genome of this strain is not reproducible because there are regions that are still segregating (at least 1.6%) 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
93.1% of the genome is distinguishable between two substrains contributing to the primary background. Of this:
Level of inbreeding: 95.7%
C57BL/6J Contributes: 15.5%
C57BL/6NTac Contributes: 84.3%
The genome of this strain is not reproducible because there are regions that are still segregating (4.3%) 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 samples UE3333 (XY), NZ1329 (XX) at the time of importation and the conclusions are consistent in all samples. The results of the analysis are congruent with the SDS (see special considerations in report notes) and UE3333 is the representative sample selected for the report. The primary (host) background is C57BL6. There is positive evidence of and C57BL/6J and C57BL/6NTac substrains. The secondary (donor) background is consistent with 129P2, which is indicated in the submission and the SDS as the donor strain. The mitochondrial genome is consistent with both the host and donor background (identical by descent). The Y chromosome are consistent with the C57BL/6J background. The region containing the allele of interest has the expected donor background (129P2). Both sample(s) are homozygous for the donor background at the locus. The Cre construct is detected in both samples. The genome of the MMRRC: 65291 strain is 98.4 % inbred and 96.5% congenic at the strain level. 3.5% of the genome is segregating for the secondary (donor) background. 4.3% of the genome is segregating for the two substrains (C57BL/6J and C57BL/6NTac) that contribute to the primary (host) background. The contribution of C57BL/6J is 15.5%. The contribution of C57BL/6NTac substrain is 84.3%.
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
This sample has more than 2 genetic backgrounds (unexplained regions and/or fractured ideogram) due to the Cg background. Therefore, the estimation of the contribution of primary and secondary background are likely incorrect.
WARNINGS
There is a discrepancy between the diagnostic backgrounds detected ((129P2/OlaHsd and 129S6/SvEvTac and C57BL/6J and C57BL/6NTac) or (129P2/OlaHsd and 129S6/SvEvTac and C57BL/6J and C57BL/6NRj) or (129P2/OlaHsd and 129S6/SvEvTac and C57BL/6JRj and C57BL/6NTac) or (129P2/OlaHsd and 129S6/SvEvTac and C57BL/6JRj and C57BL/6NRj)) and the primary background (C57BL/6J and C57BL/6NTac) and secondary background (129P2/OlaHsd). This is uncommon and should be investigated further.
The presence of a single diagnostic heterozygous call for a single inbred strain should be treated with caution.
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.