calc_genoprob for CC's

[Richard Baker]

We have several established cell lines from CC mice along with their miniMUGA genotypes for QC to verify strain. Assuming I set up the cross correctly (risib8?), will qtl2 calc_genoprob yield valid results? Is there a ready source to obtain the crossinfo matrix? I've been unable to find a cross reference between the original CC designations and the current strain nomenclature. 

[Dan Gatti]

Hi Richard,

 

You can get genoprobs for the CC strains at MegaMUGA resolution from UNC at: https://csbio.unc.edu/CCstatus/index.py?run=FounderProbs . You’d have to do some data wrangling to get them into qtl2 genoprobs format.  UNC puts the homozygotes first and qtl2 may expect the genotypes to be sorted by founder code name (i.e. AA, AB, AC, etc.). You’d also have to split the data up into a list with one 3D array per chromosome.

 

Or you could use the MiniMUGA genotypes. Your question about getting the breeding funnel order may be better answered by someone at UNC (http://csbio.unc.edu/CCstatus/index.py?run=contact). But using the MegaMUGA probs might be the easiest way to go.

 

Dan

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[Karl Broman]

There’s CC data in R/qtl2 format at https://github.com/rqtl/qtl2data/tree/main/CC

The miniMUGA genotypes will be useful for verifying strain identity, but I don’t think they’ll be sufficiently dense to be sufficient on their own.

Could you say more about the nomenclature change?

karl

[Richard Radcliffe]

Gonna jump in here with something that is somewhat related. There are several CC strains (8 I think?) that that do not have genotype data in a useable format at this time. Based on subtle encouragement from Karl,  I've written some R code that uses haplotype data found at https://csbio.unc.edu/CCstatus/CCGenomes/CCGenomes and Karl's founder genotypes to generate qtl2-friendly genotypes for these CC strains. I'm sure the code is a little clunky (I'm barely even a novice R user), but it seems to work pretty well with the one strain that I tested for which genotype data are available (CC001). I plan on testing a few more strains to make sure it's all good -- just haven't gotten to it yet.  

Assuming it works as it's supposed to, there's still the problem with the crossinfo data for these strains. 

-Richard

[Daniel A Skelly]

Hi Richard,

Piggybacking on Dan's helpful e-mail, I believe you can obtain the funnel codes for many CC strains in a file that Karl prepared and can be found here https://github.com/rqtl/qtl2data/blob/main/CC/cc_crossinfo.csv. If you need additional funnel codes you might turn to Table S1 of https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6505143/.

Best wishes,

Dan

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[Richard Baker]

Thank you all for the advice and for pointing me to the available resources, especially Table S1 of Shorter et al. I completely missed that one. [Karl, the nomenclature change I mentioned was, e.g., UncM4363_NYGC --> CC001. I had found the funnel codes in an earlier publication, not Shorter et al.]

To be clear, the plan would be to treat the samples as unknowns and use the miniMUGA genotypes to verify CC strain identity for QC purposes.