Twins get 'mystifying' DNA ancestry test results (Marketplace) CBC Documentary

[Cabalen sciences]

https://www.youtube.com/watch?v=Isa5c1p6aC0

This segment is on how genome sequencing operates and how DNA sampling is examined. 

[David Murphy]

I'm kinda curious whether people are genuinely shocked by this. (or am I doing the typical mind thing)

discordance of ~2K snps between them  implies fairly crappy chips.

kinda wondering how much pivots on snps that often don't read well.

They probably should calibrate predictions including knocking out SNPs on a level similar to expected concordance and ensure that random knockout doesn't significantly change predictions.

It's possible to do some cool stuff in real research: I've had cases where I've needed to deal with samples from a single village. As part of QC we use PCA to make sure cases cluster with controls  and some samples from a hundred miles down the road that shouldn't have been included in the set given to me stood out like a sore thumbs.

On Sat, Feb 2, 2019 at 1:30 PM Cabalen sciences <ryangav...@gmail.com> wrote:

https://www.youtube.com/watch?v=Isa5c1p6aC0

This segment is on how genome sequencing operates and how DNA sampling is examined. 

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[Nathan McCorkle]

On Fri, Feb 8, 2019, 6:06 AM David Murphy <murphy...@gmail.com wrote:

I'm kinda curious whether people are genuinely shocked by this. (or am I doing the typical mind thing)

My guess is the general public is probably genuinely shocked and surprised. Myself however barely considers the few sets of 23andme data I've got on myself and close family. It was interesting for the first month or so after I got the data and tried running it through promethease, and then I realized we need quite a bit more data (personally and statistically) for anything very interesting (for me) to come out of it.

Most people seem to be looking for ancestry stuff, or hardcore medical revelations. Both of which are quite complicated in most cases, and analysis of which will probably fall short without manual intervention (or AI algorithms which don't exist yet, because the data sampling and quality is still pretty low for the average datasets).

I think on the one hand, it's good for the biotech industry to gain some income from the normal research/medical-only revenue streams, but on the other also a little deceptive marketing.

[qetzal]

Sandwalk has a good post on this. See https://sandwalk.blogspot.com/2019/01/what-happens-when-twins-get-their-dna.html .

Bottom line, identical twins don’t have completely identical DNA. In fact, none of us do. If you could completely sequence two different cells from different parts of your body, there would be differences that accumulated during cell division.

However, if the Sandwalk post is correct, the twin comparison was affected mainly by small errors in the test, not because of the true but rare actual differences between the twins’ DNA.

[David Murphy]

eh, twins typically vary by something like 100 to 200 bases... ish

Those SNP chips only sample 700k out of 3 billion bases so the odds of even one real difference between twins being real are pretty poor.

Though normal individuals vary almost as much as twins within their own tissues, take samples of blood, skin, brain, liver etc from the same individual and you'll get a few dozen real variants between the tissues.

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[Cathal Garvey]

DNA fidelity is highest in germline cells, but all these snake-oil "We just want your DNA and you to sign our privacy and data-sharing agreements, kthx" tests are testing terminal-generation cheek epithelia.

Extremely thinking-emoji face..

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[qetzal]

Well, this paper by Michael Lynch indicates otherwise. https://www.pnas.org/content/107/3/961

Note the fourth paragraph under the heading “Cumulative Burden of Somatic Mutations“ in the Discussion section:

“Assuming 1.5% coding DNA, these somatic rates roughly translate into approximately 100 to 1,000 mutations per nonreplicating diploid cell at the age of maturity and approximately 10^3 to 10^4 per replicating cell.”

I would guess that epithelial cells from a buccal swab or WBCs from blood would both qualify as cells that are derived from a relatively high number of replications, so would likely be in the 1000-10,000 mutations/cell group.

[Cabalen sciences]

https://www.youtube.com/watch?v=P4Y1HM5vaxk

Now an Update on mail in DNA tests is being discussed here.