Full VDJ reconstruction from lymphoma RNAseq

[katharina.imkeller]

Hi everyone,

I am trying to reconstruct full heavy and light VDJ sequences from lymphoma samples (bulk). Normally it should not be very clonal, so most of the reads should derive from the same sequence. TruSeq RNA sample preparation v2, 75bp single end reads.

I tried different pipelines with MiXCR, but I never get more than half of FWR3 and complete CDR3.

Has anyone ever tried this? I am unsure whether it’s even possible to get a longer assembly, but I also don’t see a reason why the information should not be contained in my reads.
Or is it maybe worth trying one of the single-cell reconstruction tools?

Many thanks,
Katharina

[amit.upadhyay]

Hi Katharina,

We were able to get the chains from a lymphoma sample using BALDR (that we developed). However, recovering the entire chains may depend on your particular sample. You can try some of the single cells tools like Bracer, VDJPuzzle2 as well.

[zqd13]

bulk sequencing VDJFasta works well.

@amit.upadhyay

e were able to get the chains from a lymphoma sample using BALDR (that we developed). However, recovering the entire chains may depend on your particular sample. You can try some of the single cells tools like Bracer, VDJPuzzle2 as well.