Can mixcr align Homo sapiens IGK JK-KDE gene?

[suntaosimon]

We use multiplex PCR +gDNA to amplify human IGK with V and JK-KDE primers. After we assembled clones we almost got no clone reads.

IGK chains: 706756 (99.94%)

but,

Reads dropped due to the lack of a clone sequence: 706211

as we can see from the log, almost 100% reads were dropped.

So I took a look at the vdjca file use exportAlignmentsPretty, I noticed there is only IGKV genes have been aligned. No any IGKJ genes where aligned.

Then I blast the fastq_R1 file with NCBI and shows the genes in the R1 (3') are Homo sapiens JK-KDE gene for Jk intron-kappa-deleting-element (KDE) , which is what we amplified.

So I guess mixcr dose not support IGK JK-KDE gene alignment?

Thanks.

[PoslavskySV]

Hi,

currently mixcr doesn't support JK-KDE alignment. We already have some requests to support it, so this is in our roadmap. Can't say when we'll implement it, but we will notify you.