Genetics to the rescue!

7 May

It’s somewhere between pet peeve, best compliment, and favorite inside-the-lab joke when someone says “do the genetics”.  As in “hey we found this piece of fur/tissue/excreta out in the field, could you do the genetics on it?” or “we want to know XYZ, couldn’t you just do the genetics and tell us?”

Who is that masked lab geek?

Of course I want to just swoop down like some sort of laboratory super hero – cape swirling around the tops of my knee-high boots, hands propped powerfully on my magical pipetter tool belt – and declare, “Never fear, I shall DO THE GENETICS!”  My battle cry would probably be “Multiplex!” or something geeky yet powerful.

In fact, my genetic super hero alter ego was recently called forth her biosafety-level-2 phone booth to do the genetics for a Department of Natural Resources in distress.

Chronic wasting disease was recently detected in a deer from northern Wisconsin – that’s almost 200 miles further north than anyone was expecting to see a case of this disease that, until now, had remained primarily localized in southern Wisconsin and northern Illinois.  This disease has been a constant concern for the DNR, a consternation for hunters, and a cost of many state dollars.  Needless to say, an entirely new outbreak was a bit disconcerting.  Questions were raised, speculations were rampant.  How did a diseased deer show up so far from the hot zone?  Was there a conspiracy?  Was someone illegally transporting deer?  Were captive deer farms leaking disease on to the landscape?  Was it just all a big bungled mistake?

Couldn’t someone just do the genetics and find out…Never fear!

As it turns out – Yes! – genetic analysis is extremely useful for answering some of these forensic investigation-type questions – Does this diseased lymph node match this dead deer?  Did this sick deer come from Northern Wisconsin or someplace else?  Is this deer the type that lingers longer with disease or succumbs faster?  Collaborating with the DNR and the Wisconsin Veterinary Diagnostic Lab, we got a sample of the lymph node that had tested positive.  Since we had already spent years building up a genetic database of deer across the state, it would be relatively easy to place the lymph node sample as a member of the northern, southern or other populations.  And the answer to that question made today’s news.

And what sort of science news geek would I be if I didn’t give some back story to the science news with me in it!

A few more details –

From the article:  “…The state Department of Natural Resources said Monday that a lymph node from the female deer came from tissue with the same genetic makeup as other northern Wisconsin deer…”

How it works:  This was based on a genetic assignment test.  Basically, we use genetic data to determine where an individual came from – we sample lots of deer from several potential source populations, calculate the frequency of many different genetic characteristics (in this case alleles at 15 microsatellite markers in the deer DNA), look at the genetic characteristics of our mystery deer, and determine which of the source populations is most likely to contain an animal with those characteristics.   It goes like this:

How a genetic assignment test works

From the article:  “…The genetic finding, the DNR says, means the deer did not inexplicably find its way from known disease areas in the southern part of the state….”

 True – the Shell Lake area was far enough away from the current CWD zone that the deer populations are genetically pretty different.  We could pretty confidently say that the mystery lymph node came from a northern deer – not a deer translocated or migrated from the southern population.

From the article:  “…it also confirmed that the agency didn’t mix up results at some point, somehow producing a positive test with a deer from southern Wisconsin….”

 Well, sorta – so far we’ve just determined that the lymph node came from the north, we’re still waiting on analysis from a forensics lab to confirm that the lymph node is an exact match to the remains of the dead deer in question.  But since we know the lymph node didn’t come from a mislabeled deer from the southern disease zone, the DNR can probably breath a little easier while we await the final confirmation.

From the article:  “…Also, because genetic testing showed it came from the wild deer population, “there is probably little reason to think that she originated from a game farm,”…”

True, but… – we haven’t actually done any tests to rule out connections to game farms.  But since the deer was such a good match to the wild population, we’d likely find that game farm populations were A) quite different from local wild deer in which case we could confirm our CWD+ deer was a wild one, or B) quite similar to the local wild population making it hard to tell which side of the fence a deer came from.  Either way, we can’t rule out wild, so why blame a game farm?

So there’s a little more background to the science behind the news story.  The practical upshot –

Doing the genetics = cool!

Science writing = tricky!  So many details to cover within a word limit!

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