[Lilug] Unrelated Question

[Josef 'Jeff' Sipek]

I realize my reply is somewhat late, but I thought I'd share my thoughts
anyway.

On Mon, Mar 13, 2017 at 22:06:35 -0400, Robert Wilkens wrote:
> On this mailing list a few months ago (??) there was discussion of DNA and
> Crispr and all that.
> 
> I finally got curious enough to buy a DNA test kit, but i didn't do
> anything with it yet (didn't get it yet).  Thanks to this list i learned
> there are places you can upload your raw DNA data file to for analysis, one
> i found was something called promethease i think.
> 
> In the 'sample results' (again, i don't have mine yet) -- one single result
> (gene) found showed a likelihood for autism, schizophrenia, and chronic
> sinusitis, and i deal - daily - with some level of all three.  I am
> expecting a similar genetic result in that department.  I am curious if i
> am right.

My mom got curious about the ancestry aspect of it last year, and I couldn't
help but try to read up on it.  I looked at two or three websites, which I'm
not going to name to avoid advertising for them (and I'd have to look them
up again anyway to get the names right).  Since the services were very
similar, I'll just lump them into a simple "they".

The thing that I found intriguing about some of the DNA ancestry sites was
that they let you download the "raw" data.  (The interpreted data is of the
form "you are 35% eastern European, 27% western, ..." and therefore a cute
curiosity, but otherwise totally useless if you or your family has *ever*
moved.  I could see how it could be useful for someone who didn't know that
some ancestor was from a different continent.)  Anyway, raw data...  If you
dig deep enough into the FAQs, you can find out what sort of sequencing they
do.  They'll say things like "we use blah-blah DNA testing, which samples
750k locations."  If you do a bit of reading up on DNA and then do a bit of
math, you realize that what they are really saying is "of the 3 billion
base pairs in your DNA, we look at less than 1 million, so we ignore 99.9%".
While I am certain that this sort of sampling is perfectly fine for very
course grained classification (e.g., which continent are you from?), I
expect it to be mostly useless if you want to do any serious research.

When reading up on this, I had an unfair advantage - a friend of mine has
spend some time working with DNA sequencing researchers so he was able to
dumb down some of the explanations to my level.  He concluded our
conversation with this gem: "I would heartily recommend against such
screening".

(He also pointed out that there is a problem that no one in genetics likes
to talk about - the missing heritability problem [1].  I don't even pretend
to understand it, but as far as I know the gist of it is - using DNA is a
questionable way to answer questions like "how intelligent/something are
you?", but it is ok for matching up DNA substrings against geotagged
substrings for genealogy reasons.)

There apparently are some new developments with DNA sequencing
and genotyping, but it is all "lab grade" stuff.


As other's have pointed out, there is certainly a privacy issue.  One of the
pay-for features is actually "willful privacy violation" of sorts - they try
to figure out family relationships between the DNA samples they received.
And if you pay them, you can see the results.  This can be very useful for
finding long lost relatives, but at the same time it encroaches onto
people's privacy in some ways.

Ultimately, do whatever makes you happy.  Chances are that even such a
limited sampling of ones DNA can provide days of entertainment to amateurs
like us.

Jeff.

[1] https://en.wikipedia.org/wiki/Missing_heritability_problem

> I think someone mentioned some kind of "open source" DNA analysis?  If
> there is can you mention what it was called?  I will then put it 2-3 months
> ahead on my calendar to then remind me to find and try it once i have
> results, hopefully something compatible with ancestry's file format (? is
> it different?).
> 
> I am OK to run software comptaible with Linux, Android, or Windows.
> 
> -Rob
> 
> 
> 
> ---
> Sent from Tablet

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