New term proposal: `lib_concentration`

[nbroomand]

New term details This term will be for the MInAS project's proposed ancient extension.

Term name - Library Concentration
Structured comment name - lib_concentration
Definition - Concentration of library in copies per µl, as inferred by qPCR. 
Expected value - integer
Value syntax - {integer}
Example - 123000000
Preferred unit - copies/µl
Package(s) - ancient

Additional context

[nbroomand]

Why is the "lib_concentration" in copies/µL as inferred by qPCR? I would think the more common way to report would be in ng/µL? I think this should also include a note about how it was measured (ie nanodrop, qubit, etc) since the way it was measured makes a huge difference. Also I'm assuming this is for already indexed libraries but it doesn't specifically note that, so I feel like clarifying that might be helpful!

[Kelzor]

I think Nasreen's question raises two points. Does this term only apply to non-indexed/pre-PCR libraries? If so that should be clarified.

I think the copies/µL could be kept. You can convert ng/µL to copies/µL as long as you have a fragment length estimate. qPCR assays also assume an avg fragment length, whatever the length of the standard constructs are, so both methods have a built-in assumption. The benefit of qPCR besides higher precision (although I think this depends on your machine and how well it's maintained) is that the minimum threshold of quantification is much lower. I rely heavily on qubit due to low costs and ease of use.

[jfy133]

Copying from the internal discussion too:

I'm not a wet lab person, so we will need someone else to verify, but when I did my labwork during my masters, we only used nanodrop etc for modern DNA. It often wasn't sensitive enough for low biomass ancient DNA libraries, for which we used a tape station, which is more accurate as you measure the actual DNA molecules. I don't know if this is standard or not though... Also nanodrops are sensitive to non-DNA contamination, so that could make it difficult too. For us at least it's not indexed libraries but rather adapter ligated libraries (before amplification) because that should reflect roughly the amount of original DNA in the sample.