The messiest part of Omics? Dealing with all the different sample types
The good, the bad, the...uhhh: Everything you ever wanted to know about all the different Omics sample types!
But first, what's a 'sample type?'
It just refers to the source material being tested!
For molecular testing, this is usually a body fluid or something that came in contact with a body fluid!
Blood tubes:
When you think of a sample type you probably immediately envision a standard blood tube.
In 'the industry' we call these vacutainers (because there's a vacuum behind the seal that sucks the blood in…slurp!).
There's also lots of pretty colored tubes.
The one we like best for genetics is the lavender tube (purple top) because it's a tube that isn't full of potential inhibitors that might interfere with down-stream sample prep.
Yellow tops (ACD) and green tops (heparin) are also usually acceptable although heparin can be carried over as an interfering substance with some nucleic acid extraction methods (especially filter columns).
Streck tubes and PAXgene tubes are also pretty common for cell free DNA collection (non invasive screening) or applications that test RNA.
Saliva:
Spit tubes became really popular in genetic testing because of direct to consumer ancestry products!
Saliva is terrible in lots of ways, though.
It can be contaminated with all sorts of things found in the oral cavity.
Like, whatever was eaten last along with the bacteria that live inside your mouth.
Saliva samples can also be very viscous depending on the individual.
This makes them challenging to open without contaminating everything nearby but it also can make them very hard to pipette accurately!
Swabs:
Oral, anal, vaginal, nasal…basically any surface or orifice that can host an infectious agent or secrete something is a potential candidate for swabbing.
These come in two flavors, dry swabs (not ideal) or liquid stabilized (way better sample quality!).
For pediatric patients there are also now 'lollipops' to trick kids into thinking they're getting a treat when they're actually giving you a cheek swab!
Urine:
This one is a staple of the diagnostics industry, mainly for 'occupational testing' which is a euphemism for drug testing, but there are genetic screening applications that use urine too.
Some bladder and prostate cancer tests use urine as a sample type along with a number of PCR tests that use it to detect urinary tract infections.
One fun fact is that in occupational testing labs, the accessioners (scan samples in *beep*) note the 'aroma' of the sample.
You know, just in case it's actually apple juice.
💩💩💩:
At home collected fecal samples for microbiome or cancer screening are undoubtedly the worst.
They're like a box of chocolates, 'you never know what you're gonna get.'
Is it a bulk sample?
Did the patient follow the instructions?
Are there remnants on…everything?
But, before you try to answer ANY of those questions, make sure you have gloves on...
Brian Krueger