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I need idea, intuition, suggestion please
I have 10X scRNA-seq of PBMC (multiome's 3' poly-A capture), can I capture TCR/BCR from my scRNA-seq or I need TCRseq ? I googled and likely TCR and BCR immune profiling require 5' transcript capture and the V(D)J variable sequence is on the 5' end of the gene. So the 3' capture typically yields the C constant region of TCR and BCR transcripts. can you help me please? Thank you
The 3' gene expression protocol will capture TCR and BCR mRNAs but this may not be very helpful to you. As you already mentioned only the 3' end will be sequenced, which are the constant regions. With this data you may potentially be able to discriminate TRAC from TRBC1 and so forth.
However, in most cases researchers are interested in clonotypes (combinations of variable regions) and these you can only obtain by using the dedicated TCR or BCR kits from 10X. They contain specific sets of primers for these genes to cover the whole TCR or BCR gene body and not only the 3' end. This way you can see the different clonotypes in your population
The human TCR loci can be found for example at HUGO. The last gene at each locus is the constant and is identified by a C at the end. TRAC = T cell receptor alpha constant (I did not use the correct naming convention in the original answer, sorry)
B-cell receptors basically are membrane bound immunoglobins (IG). Therefore you will likely find the constant regions of the heavy chain in your data. The different heavy chains are what identifies the IG. For example IGHA1 is the heavy chain of an alpha IG. If the secreted and membrane bound form of the IGs is always the same per B-cell, unfortunately, is beyond my knowledge of B-cells.
According to our experience 3’ sequencing does not produce enough data to recover TCR and BCR repertoire. But we have some experience recovering repertoires from non enriched 5’ 10x RNA-Seq GEX data.
With MiXCR we have specific presets that allow analyse 10x data in one single line command:
mixcr analyze 10x-5gex-full-length \
--species hsa \
sample_R1.fastq.gz \
sample_R2.fastq.gz \
sample_result
Also feel free to check out our documentation portal:
https://docs.milaboratories.com/mixcr/reference/overview-built-in-presets/#10x
