T Cell Repertoire Deep Sequencing

Question

[shrutidesai0208]

Currently stuck with finding the #bioinformatics related difference in #DNA sequencing and #RNA sequencing for #tcell repertoire.. Any help will be really appreciated..

[GenoMax]

With most common sequencing technologies one is sequencing DNA (or RNA converted to DNA before sequencing). (Direct RNA sequencing is shown to be possible with nanopore but not practiced widely AFAIK). Are you asking about genome sequencing vs transcript sequencing for t-cell repertoire?

[shrutidesai0208]

For an assay in immunotherapy drug clinical trial, it mentions that deep tcr sequencing is done with RNA sequencing and DNA sequencing both. Considering the given scenario, I want to know if the data analysis steps will be different when dealing with the data from both the assays. I understand the basic information utility of DNA and RNA sequencing, which I would state here: So DNA seq of repertoire will give me the different types of clones that can be present in the sample considering the recombinations in the cell, where as RNA seq will give me the actual clonal heterogeneity in the sample. The issue I have here is, while representing the data from both the assays what difference I have to keep in mind?

[Devon Ryan]

Well, they didn't actually sequence RNA, the made cDNA and sequenced that.

[WouterDeCoster]

Direct RNA sequencing is shown to be possible with nanopore but not practiced widely AFAIK

Yeah it needs to mature a bit, but indeed possible.

[Satyajeet Khare]

Which species? Thymocytes/peripheral? CD4/CD8? Adult/neonatal?

Here is one dataset. Human cord blood peripheral CD4+ T-cells in vitro differentiated RNA-Seq.