In a previous post I discussed a roadmap toward ubiquitous metagenomic sequencing for diagnostics. The ultimate goal is that sequencing a sample (and detecting known and unknown pathogens) should be as simple and cheap as qPCR. If you’re interested in the sequencing side of this take a look at the
Yes I think it could be. About 60% of the sample seems to be rRNA. So it partly depends if it’s cheaper to put the additional cost in the prep or the sequencing.
For a proof of concept I would tend to put it on the sequencing then better characterize the whole process, before deciding how to proceed.
I'm curious, working with environmental (soil, water etc) samples I encountered samples whose content was even over 90% rRNA. In the swabs, is most of the rRNA you encountered is human? and if so do you think incorporating a human rRNA depletion to the prep would be easier then a e.g. general use case sort of pull-down probe?
Interesting and educational read!
Do you think rRNA depletion could be incorporated somehow?
Yes I think it could be. About 60% of the sample seems to be rRNA. So it partly depends if it’s cheaper to put the additional cost in the prep or the sequencing.
For a proof of concept I would tend to put it on the sequencing then better characterize the whole process, before deciding how to proceed.
Thank you for the answer Nava!
I'm curious, working with environmental (soil, water etc) samples I encountered samples whose content was even over 90% rRNA. In the swabs, is most of the rRNA you encountered is human? and if so do you think incorporating a human rRNA depletion to the prep would be easier then a e.g. general use case sort of pull-down probe?
Yes, mostly human it seems this paper provides some numbers: https://www.medrxiv.org/content/10.1101/2022.05.12.22274799v1.full-text