For a targeted sequencing project I would like to include the switch regions of the IGH locus targeted by the class switch recombination. The regions are not "officially" annotated for hg38, and I only found vague hints in the literature (for example: Article Non-coding Class Switch Recombination-Related Transcription ...
). I also tried to identy AGCT, GAGCT, and GGGGT-rich regions in the hg38 assembly myself, see the attached image.This looks ok, but if anybody has another source for the regions, I would be very happy indeed. Thank you very much,
Fabian
Hey Fabian Knörr , I have the same question here. Did you find a solution ?
Best,
Davide
Hi Davide, not really an „official“ answer, but I checked for sequence characteristics in the regions and selected the areas. I could share the script and the final coordinates I selected, if that would be of help!
Fabian
Hey, Fabian
yes, thx. That would be helpful. It seems IgH locus is better resolved in chm13 - (The T2T-CHM13 reference genome has more accurate sequences for immunoglobulin genes than GRCh38 | bioRxiv) - maybe we may want to try this on chm13 as well.
Also, are the regions you found any different from those in table 2 here?
Frontiers | Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses (frontiersin.org)
Hey Davide, sorry for my late reply. Yes, I also looked at this publication and used some of their coordinates directly (see table).
I also did a search for motifs in the area (AGCT, GAGCT, GGGGT).
Finally, as I was designing an enrichment panel for sequencing, I was not able to include all regions due to low probe perfomance.
Not sure if this is of any help, I could provide you with the R script, if you are interested.
- Badges
- Science topic