At @ucdavis @bonesandbugs says she is focusing on “Sequencing the dead” in honor of Halloweenpic.twitter.com/ehI0Te1pPc
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At @ucdavis @bonesandbugs says she is focusing on “Sequencing the dead” in honor of Halloweenpic.twitter.com/ehI0Te1pPc
Now Introducing ancient DNA work by taking about work of Allen Wilson at @UCBerkeley
And @bonesandbugs caveats amcient DNA work by saying you cannot get DNA from dinosaur fossils because “they are rocks”
Discussing what makes DNA degrade - UV irradiation, water / freeze thaw, microbes
Showing some results from looking at the damage / quality of ancient DNA samples
Nice visual - if you imagine regular DNA is long streamers - ancient DNA is like the confetti that comes from this - not immediately but after the parade ...
Discussing the 1st work on using next gen sequencing to look at ancient DNA samples - eg Poinar et al. 2006 and Green et al. 2006
Over the years they have come up with entertaining ways to engage students and others to do ancient DNA work
Refined approaches to make the work very very very very clean - to reduce risk of modern DNA mixing with ancient DNA samples
Oldest DNA they have sequenced so far was from a horse bone - about 700,000 years old - got about 1x coverage
Also going some protein work (e.g., of ancient rhino teeth)
They get a LOT of requests from people who want help with doing some analysis - some pretty crazy - they have a box in the lab they refer to as “Letters from Mars”
This comes back to the story she started out with today - a family in SF had a coffin discovered during a dig in their yard - and no agencies wanted jurisdiction over it - so they contacted Elissa Davey who runs a project called “Gardeb of Innocence”
Elissa Davey brought together a team to try and figure out who the young girl was in the coffin from the yard
They then dug through records and found this house was on the grounds of an old cemetery for which the graves were supposed to have been moved but which some apparently were not
Then the team sent a small piece of hair to @bonesandbugs and colleagues but without a root - and despite common perception - you can get some DNA (very little) from hair even without root
Now discussing a DNA library prep method they have developed to deal with ancient DNA - where every small bit of DNA is critical - so need more efficient methods for small amounts of DNA
And as an aside @bonesandbugs just told people waiting in the back to come into the room “Don’t be scared. I’m just dead. It is not contagious. As far as we know”
Back to the DNA isolation / library approach - one key thing was to use a method that did not require cutting at a uracil in DNA b/c ancient DNA has a lot of uracil after cytosine deamination
They did a modification which used forked adapters not circular ones to avoid the uracil cutting - now discussing other ancient DNA library approaches too (including “BEST” method and ss2.0 method)
They made use of some of the strategies from these different methods to come up with a new method they call “The Santa Cruz method” or something call it “Seriously?” Which she will explain later apparently
A qPCR assay shows that the methods using single stranded DNA work the best in efficiency
Shameless plug - spun off company Claret Bio to do this (and says she is highly conflicted here since it came from her lab partly) and she is on the SAB and their method is called SRSLY (thus the seriously comment earlier)
Hair is really good for this kind of work because you can clean outside to remove contaminants and then go after DNA on inside - and they can do this with very very small amounts of DNA (eg 100 pg)
One key thing - the DNA in hair is really really fragmented and this is why people thought you could not get DNA out of hair - because the assays being used only worked if the DNA was not so fragmented
Solution - stop using the STR PCR methods and other approaches that only work with larger DNA pieces if you want to assay DNA in hair
Ok now back to the girl in the coffin - they were able to do DNA analysis of hair samples and got information about her mitochondrial profile and SNPs in nuclear genome
So instead of the normal human DNA forensics they used SNP genotype based approaches - mentioning 23 and me, Ancestry and FamilyTree DNA SNP approaches (they use some overlapping SNPs but not completely overlapping)
Challenge - hair DNA is not great and they do not get full coverage of possible SNPs - and then they use a variation of an approach called Imputation to build model of some missing SNPs
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