Deep Sequencing of BCR Heavy Chain Repertoires in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome, 2025, Ryback et al

[hotblack]

It appears there’s tools to infer a subject‘s genotype from fastq data (https://tigger.readthedocs.io/en/stable/#core-abilities).

If we can get to this and combine it with other expression ratio data then maybe it will allow us to see if those in the mild/moderate group simply have higher IGHV3-30 due to a genetic predisposition. As opposed to it being the result of some sort of dynamic immune response. I think. In theory…

Maybe those more familiar with these tools can confirm? Maybe it’s already been done and I missed it. I need to reread the paper tbh

I don’t really know what is possible here. But equally am unencumbered by the knowledge of what is not possible

So am hoping to have a prod around anyway in the coming weeks for the enjoyment of learning something.

 

[DMissa]

Intriguing! Is that the current evidence in the literature or is this based on your own unpublished data?

Literature, DecodeME and discussions with people in the field who have a critical eye

 

[audrey_ryback]

It appears there’s tools to infer a subject‘s genotype from fastq data (https://tigger.readthedocs.io/en/stable/#core-abilities).

If we can get to this and combine it with other expression ratio data then maybe it will allow us to see if those in the mild/moderate group simply have higher IGHV3-30 due to a genetic predisposition. As opposed to it being the result of some sort of dynamic immune response. I think. In theory…

Maybe those more familiar with these tools can confirm? Maybe it’s already been done and I missed it. I need to reread the paper tbh

I don’t really know what is possible here. But equally am unencumbered by the knowledge of what is not possible

So am hoping to have a prod around anyway in the coming weeks for the enjoyment of learning something.

Hi @hotblack , I just thought I'd pipe up here in case it is useful: The fastq files in this dataset do not contain genotype information about the individual beyond their rearranged BCRs (because the library prep enriches specifically for BCR transcripts). What Tigger does is infer germline VDJ alleles for a given individual, and whether an individual has a novel allele (rather than a point mutation introduced by SHM) in a gene segment.

I did run Tigger on this dataset as part of my PhD, but I didn't see anything that I thought was particularly striking (see Table). The percent of the repertoire that changed allele call post genotyping was generally very low, and there were very few novel alleles - none in the ME/CFSmm group.

Some V genes are more/less commonly used in the naive B cell repertoire, but I'm not sure if this bias occurs at the level of individual alleles (but there may well be some alleles that are particularly favourable or unfavourable to produce productive rearrangements).

 

[jnmaciuch]

If we can get to this and combine it with other expression ratio data then maybe it will allow us to see if those in the mild/moderate group simply have higher IGHV3-30 due to a genetic predisposition. As opposed to it being the result of some sort of dynamic immune response. I think. In theory…

Maybe those more familiar with these tools can confirm? Maybe it’s already been done and I missed it. I need to reread the paper tbh

Unfortunately that won’t really tell you anything about the specific types of genetic mutations that increase expression of some genes. It’s a tool to help with initial alignment of reads in the protein-coding sequences. If you wanted to find out point blank whether there’s a specific germline mutation higher in ME/CFS than controls (unconnected to the slight V gene skewing here) that’s probably something that would require a much bigger sample size to answer definitively

This data type is quite limited to answer questions beyond the specific ones that the authors set out to answer.

[edit: whoops, cross-posted with @audrey_ryback ]

 

[hotblack]

Thank you so much @jnmaciuch and @audrey_ryback that’s incredibly useful and kind of you both to spend the time explaining.

I’ve been going back through the paper today and how tailored the design is to the particular questions really comes through. As well as how much is covered. It’s nice to understand a bit more about the ideas in it than a year or so ago too!

I’m going to carry on looking at these tools anyway as they seem interesting and I’m learning bits about them and the biology. I’ll be perhaps less bothered if I get stuck though. And if there’s anything either of you think may be interesting for me to look at please do let me know.