<p>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.</p>
<p>With MiXCR we have specific presets that allow analyse 10x data in one single line command:</p>
<pre><code>mixcr analyze 10x-5gex-full-length \
 --species hsa \
 sample_R1.fastq.gz \
 sample_R2.fastq.gz \
 sample_result
</code></pre>
<p>Also feel free to check out our documentation portal:</p>
<p><a href="https://docs.milaboratories.com/mixcr/reference/overview-built-in-presets/#10x" rel="nofollow noreferrer">https://docs.milaboratories.com/mixcr/reference/overview-built-in-presets/#10x</a></p>

CC BY-SA 4.0
2023-01-24T16:16:04.313Z
2023-01-26T16:27:11.983Z
2023-01-26T16:27:11.983Z
Mark Izraelson
<p>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 <code>TRAC</code> from <code>TRBC1</code> and so forth.</p>
<p>However, in most cases researchers are interested in clonotypes (combinations of variable regions) and these you can only obtain by using the <a href="https://support.10xgenomics.com/single-cell-vdj" rel="nofollow noreferrer">dedicated TCR or BCR kits</a> 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</p>
<p>The human TCR loci can be found for example at <a href="https://www.genenames.org/data/genegroup/#!/group/370" rel="nofollow noreferrer">HUGO</a>. 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)</p>
<p>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 <a href="https://www.genenames.org/data/genegroup/#!/group/886" rel="nofollow noreferrer">heavy chains</a> 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.</p>

CC BY-SA 4.0
2021-08-05T15:13:07.020Z
Thank you I got a question, in this data base I could not find anything corresponding to TCRVδ2 , you think in which part I can find this gene?
Mahta Mira
CC BY-SA 4.0
2021-08-06T07:21:23.747Z
The nomenclature used by immunologists may not match the official gene names (which are in HUGO). The TCR gamma variable genes are named TRGV followed by a number. Problems with different names for the same gene / protein are all over the place and you will sometimes have to search several data bases (HUGO, UniProt, Entrez ... ) or the literature for an answer
PPK
CC BY-SA 4.0
2021-08-04T11:52:06.397Z
2021-08-05T11:04:37.700Z
2021-08-05T11:04:37.700Z
PPK
<p>I need idea, intuition, suggestion please</p>
<p>I have <code>10X scRNA-seq</code> of <code>PBMC (multiome's 3' poly-A capture)</code>, can I capture <code>TCR/BCR</code> from my scRNA-seq or I need <code>TCRseq</code> ? 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</p>

<scrnaseq><seurat><10x-genomics>
TCR-seq or scRNA-seq
# TCR-seq or scRNA-seq

(Asked by: username_0 on 2021-08-03)

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

**Tags:** scrnaseq, seurat, 10x-genomics

---

## 2 answers

### Answer by username_2 on 2021-08-04. Score: 5 | Accepted answer

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](https://support.10xgenomics.com/single-cell-vdj) 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](https://www.genenames.org/data/genegroup/#!/group/370). 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](https://www.genenames.org/data/genegroup/#!/group/886) 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.

> **Comments:**
> **username_0**: Thank you I got a question, in this data base I could not find anything corresponding to TCRVδ2 , you think in which part I can find this gene?  
> **username_2**: The nomenclature used by immunologists may not match the official gene names (which are in HUGO). The TCR gamma variable genes are named TRGV followed by a number. Problems with different names for the same gene / protein are all over the place and you will sometimes have to search several data bases (HUGO, UniProt, Entrez ... ) or the literature for an answer  

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### Answer by username_1 on 2023-01-24. Score: 2

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


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