This is another search capability of MGI. It allows researchers to ask how inbred mouse strains differ from each other at the molecular level by enabling queries of SNP data for 88 strains of mice obtained from NCBI's dbSNP resource (Build 142) [35, 36]. Users can query by gene, proximity to gene, and strain and results can be sorted by dbSNP Function Classes or by Strain, and drag columns to reposition strains of interest [37].
Figure 2.2 The Mouse Models of Human Cancer Database (MMHC), formerly Mouse Tumor Biology Database (MTB). Data on frequency and types of cancer in inbred strains and following manipulation (genetically or chemically), photomicrographs, and references are available on this website.
Source: Images were retrieved from the Mouse Models of Human Cancer Database (MMHC, formerly MTB), Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, Maine. World Wide Web (URL: http://tumor.informatics.jax.org) (April 2020).
Sanger Mouse SNP Database (https://www.sanger.ac.uk/sanger/Mouse_SnpViewer/rel‐1505)
This is similar to the MGI SNP database but provides specific annotation on a more limited number of inbred strains. This resource has sequence data on 36 inbred strains representing strains most commonly used in biomedical research today to those with great genetic diversity [38, 39]. The strains were sequenced and annotated, and base changes, relative to the C57BL/6J reference strain as well as predicted effect of changes are listed. This information can be useful when one suspects a molecular difference in a gene in an inbred strain with a specific lesion associated with a known genetic mutation. One example came from the observation of ectopic mineralization in several inbred mouse strains in an aging study that resembled, to various degrees, lesions observed in B6.Cg‐Abcc6tm1Jfk (ATP‐binding cassette, sub‐family C [CFTR/MRP], member 6) null mice, a mouse model for human pseudoxanthoma elasticum (PXE) [40]. Four strains were found to have the same SNP in the Abcc6 gene that was predicted to have a major effect and later confirmed to function as a hypomorphic mutation (Table 2.2) [41–43].
While often assumed that the reference strain (C57BL/6J) is wild type for the gene under investigation, it may actually be the abnormal gene in the reference strain. An example is alcohol dehydrogenase 7 (Adh7, formerly called Adh4, that is no longer listed in the Sanger SNP database). As shown in Table 2.3, there are two SNPs predicted to be missense mutations with significant effects [44]. However, the strains listed (129, C3H/HeJ, DBA/2J, and KK/HlJ) are actually wild type and the C57BL/6J (reference strain) and C57BL/6NJ are the hypomorphic mutant strains. This change partially explains alopecia and dermatitis that is a strain specific phenotype in most B6 substrains [45].
Table 2.2 SNP comparison between inbred strains for the Abcc6 gene. A search of the Sanger Mouse SNP database (17 January 2020) revealed a single base difference predicted to be a missense mutation (yellow) that has a predicted significant effect (*). Note that not all of the 129 substrains carry this allele.
| Gene | Chromosome | Position | dbSNP | Reference | 129P2/OlaHsd | 129S1/SvlmJ | 129S5SvEvBrd | C3H/HeJ | C57BL/6NJ | DBA/2J | KK/HiJ |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Abcc6 | 7 | 45,979,026 | rs32751584 | T | C | C | C | C | ‐ | C | C |
| Abcc6 | 7 | 45,979,027 | rs32751586 | G | ‐ | A | A | A | ‐ | A | A |
| Abcc6 | 7 | 45,979,329 | rs52492784 | T | C | C | C | C | ‐ | C | C |
| Abcc6 | 7 | 45,979,332 | rs255648560 | C | T | ‐ | ‐ | ‐ | ‐ | ‐ | ‐ |
| Abcc6 | 7 | 45,979,342 | rs52081041 | T | C | C | C | C | ‐ | C | C |
| Abcc6 | 7 | 45,979,350 | rs52476049 | T | C | C | C | C | ‐ | C | C |
| Abcc6 | 7 | 45,979,428 | rs32751588 | T | C | C | C | C | ‐ | C | c |
| Abcc6 | 7 | 45,979,479 | rs226776926 |
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