Get number of mutations in CDR3 region

[Blowfish82]

Dear Team,

I want to know the number of mutations per clonotype in the CDR3 region of my IGH data.
Is there a way to see the number of mutations in one of the export formats?
I usually work with the tables resulting from command "exportClones".

Your reply would be extremely helpful.

[PoslavskySV]

Hi,

could you elaborate in more detail. Do you mean the number of mutations in germline parts of CDR3 region?

[Blowfish82]

Thank you for your fast response,

Yes, you are right, I mean the germline part. Let´s look at the Vgene,
I think the colum "vBestIdentityPercent" in the exportClones format reflects a length normalized mutation rate to the best aligned vGene.
If I also want to know, how many (absolute, not percentage) mutations were detected in the V-part of the sequence (not as percentage), in which column should I look for it?

Many thanks!

[Blowfish82]

I think I got the solution.
In the "exportClones" Table, there is a column called "allVAlignments".
There all VHits and their alignment statistics are listet. It has a pattern as follows, segmented by "|":

60|304|325|0|244|SA180TSA194GSA209GSA213TSG242CSG254CSC260TST261ASG275ASC293TSG297ASA299G|1052.0

The last entry is the aligment score (here it is 1052), and the second last shows all mutations (e.g. substitutions etc.) and at which positions they occur.
So If I count all numbers between letters (grep"[A-Z][0-9]") then I get the number of mutations (its 12 mutations in this case).

Think my problem is solved.
Have a nice day.

[PoslavskySV]

Hi,

You are right! vBestIdentityPercent reflects the number of mutations normalized by the length of V part of clonotype assembling feature (i.e. if you assemble clones by CDR3 that is GermlineVCDR3Part, if assembling feature is VDJRegion than it is VRegion).

For the number of mutations you are also right. You can check this doc for the details about encoding.

Also, we'll add the number of mutations in export in upcoming release - thank you for reporting!

[amikelov]

I also would like to mention the possibility to calculate the number of mutations in CDR3 for the clonotypes which are part of lineage trees - for them we are able to reconstruct germline CDR3 sequences with N-nucleotides and so can describe mutations even in these regions.
Take a look at our guide for BCR lineage tracing, you might find it helpful:
https://docs.milaboratories.com/mixcr/guides/b-cell-lineages-webinar/