
Analyzing my DNA - richardburton
http://blog.alexmaccaw.com/analyzing-my-dna
======
tstactplsignore
>"What's interesting is that the older the species, the more the chromosomes,
or at least this is the trend. "

This isn't true: there's no such trend (Fruit flies have 8 chromosomes), and
the sentence belies an important misunderstanding of taxonomy. Also, plants
tend to have high chromosome counts because of
[polyploidy](<http://en.wikipedia.org/wiki/Polyploid>).

Additionally, the author seems to be latching onto some odd victorian-era
esque ideas about biology here. There are several fern species which are
younger than humans, and several salamander species, and thousands of other
extant species. Modern fern species aren't "older" than humans simply because
they had distant cousins in the fossil record who were, on the face,
morphologically similar.

Evolution is a bush, not a ladder, and it doesn't make sense to say that any
one of the end nodes (extant species) is "older" than any other unless you are
talking about the very fuzzy barrier of speciation at which the majority of
the pre-species' population could not breed with the population it was
diverging from.

------
karpathy
For anyone interested, 23andme is also starting to sequence exomes (the
important parts of the protein coding regions) for $999, which can potentially
provide much more interesting information than simply looking at SNPs. But
from the website, it looks like they are still in closed beta:
<https://www.23andme.com/exome/>

However, there are several blog posts describing the types of results and
analysis the exome enables. For example,
[http://jchoigt.wordpress.com/2012/07/02/a-first-look-at-
my-e...](http://jchoigt.wordpress.com/2012/07/02/a-first-look-at-my-exome-
variants-from-23andme/) and <http://blog.goldenhelix.com/?p=1282> but more can
be found on Google.

~~~
mbreese
I thought they started this in late 2011 and stopped the program a few months
later. Has anyone been part of the program since then?

~~~
gabeiscoding
Nope. It was a Pilot and they are not sure about doing more exomes.

From my last chat with Brian Naughton (their lead informatics guy) about this,
it sounds like they are planning on doing more sequencing in the future. But
it could be whole genome and it may be geared more towards research (your
selected based on your phenotype) than open to any customer.

------
tokenadult
One of the most interesting things I've learned about human genetics by
joining a local "journal club" including several researchers who are members
of the Behavior Genetics Association is just how little is certain about
genetic influences on any human trait of interest. The review article Johnson,
W. (2010). Understanding the Genetics of Intelligence: Can Height Help? Can
Corn Oil?. Current Directions in Psychological Science, 19(3), 177-182

[http://apsychoserver.psych.arizona.edu/JJBAReprints/PSYC621/...](http://apsychoserver.psych.arizona.edu/JJBAReprints/PSYC621/Johnson%20Current%20Directions%20Psych%20Science%202010%20\(G%20and%20E%20in%20IQ\).pdf)

looks at some famous genetic experiments to show how little is explained by
gene frequencies even in thoroughly studied populations defined by artificial
selection.

"Together, however, the developmental natures of GCA and height, the likely
influences of gene-environment correlations and interactions on their
developmental processes, and the potential for genetic background and
environmental circumstances to release previously unexpressed genetic
variation suggest that very different combinations of genes may produce
identical IQs or heights or levels of any other psychological trait. And the
same genes may produce very different IQs and heights against different
genetic backgrounds and in different environmental circumstances. This would
be especially the case if height and GCA and other psychological traits are
only single facets of multifaceted traits actually under more systematic
genetic regulation, such as overall body size and balance between processing
capacity and stimulus reactivity. Genetic influences on individual differences
in psychological characteristics are real and important but are unlikely to be
straightforward and deterministic. We will understand them best through
investigation of their manifestation in biological and social developmental
processes."

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brenfrow
It should be called Y-chromosomal Noah, since he and his sons would all trace
through one mans genetics. And well there was genetics from four different
women on the Arc... So the Eve makes sense.

------
hingisundhorsa
"certain European populations have a mutation that causes lactase to be
produced throughout their lives". Lactase persistence is interesting. There
has been selection pressure for persistence in Northern European (eg: about
98% of Irish people have lactase persistence) populations but not in Southern
Europe (under 40% in Italy) and one might even say "almost selection against"
in Asia (under 10% in China). Apparently, the gene first evolved in the Near
East, possibly tied to first domestication of the auroch and then spread
radially from there into Europe. Convergent evolution, ie: lactase persistence
using different genes, also came about in the Bantu population in Sub-saharan
Africa which enabled this population to spread further south and overtake San
populations (bushmen). Perhaps this is the same selection pressure in action.

------
Gmo
Well, that's a bit late, but if you want an easy tool to have extra
information about your 23andMe analysis, you can also use this :
<http://my.promethease.com>

More info about what it can do here :
<http://www.snpedia.com/index.php/Promethease>

SNPedia can also be of interest to anyone here, it is a wiki centralizing
information about all known human SNPs (including literature references)

Disclaimer: One of the person running this is my colleague.

------
hfsktr
Are insurance companies doing this yet? I imagine a Gattaca-like future when I
hear of this kind of stuff. Not that I fear it but I don't trust any company
or government to do the right thing with the information...

I am curious how accurate it all turns out to be (it is noted that percentages
play a role). I have only basic understanding of the math and biology so I am
probably making tons of assumptions but from the post:

"One way of investigating this, is by studying identical twins. Since they
have the exact same DNA, any differences between the two can be attributed to
environmental factors."

I have identical twin sisters (from a fraternal twin father even, born on the
same birthday...the odds). To me they look nothing alike but to outsiders sure
maybe.

The points I am curious about:

1a. Doesn't DNA mutate? Even if twins start with identical DNA it could mutate
from any number of environmental variables couldn't it?

1b. Couldn't it only mutate in just one, making them have different DNA in the
end?

Like I said basic understanding. Does 23andme give a 'layman' introduction to
any of this stuff? One of the other comments says it makes you read some stuff
before getting certain results but is it the kind of stuff that 'normal'
people can understand without having to read another book of references?

Sorry about the long post; stopping now.

~~~
gizmo686
>1a. Doesn't DNA mutate? Even if twins start with identical DNA it could
mutate from any number of environmental variables couldn't it?

Human DNA does not mutate that often (If I recall correctly, the average human
can expect to see ~230 mutations in their nuclear DNA in their lifetime, this
includes that parts of DNA that we believe do nothing) What is far more common
is related to epigenetics. Attached to DNA are various promoters and demoters
that control how much a given gene is expressed. These can and do change based
on envirement.

What is also far more common is a mutation in the mitochondrial DNA. However,
the only thing mitochondria does for us is to help break down sugars, so
mutations in mtDNA are not that significant.

~~~
hfsktr
So essentially even when it does mutate the chances that something important
is overwritten is fairly low.

Does anyone know of an online resource that explains this kind of stuff in
easy to digest format? Something like a ELI5 for DNA/Cells.

~~~
Slickarango
MITx is offering a bio course [1]

[1]<https://www.edx.org/courses/MITx/7.00x/2013_Spring/about>

edit: After re-reading I understand this is really not what you are looking
fore, but i'm going to leave it here anyway

------
Semaphor
Always wanted to try that, but with $80 shipping costs for Germany that's just
a little bit too much.

~~~
davej
Yeah, it's a bit hefty to ship it outside US/Canada. Remember the price
includes shipping it to you and shipping it back to 23andMe. DHL will also
collect the package from your door (at no extra cost) when you're finished.

If you know a friend/relative (or two) who is also interested then you can
order more than one kit and save a little on shipping.

I decided to pay the $80 to get it shipped to Ireland. I sent off my saliva
sample a couple of weeks and I'm currently awaiting the results.

------
ecolak
23AndMe doesn't tell you much about your DNA actually, they can only tell you
some things about already known variations. If you really wanna know
everything about your DNA, you should look at whole genome sequencing (WGS).
WGS is usually done by companies like Illumina and analysis can be done by a
company like Bina Technologies. The whole field is getting more and more data
and analytics driven so there's lots of opportunities for software engineers
and data scientists. Check out <http://www.binatechnologies.com/vision> to get
a better idea of the field.

------
bjornsing
> _A single change in a base pair can dramatically alter the protein created,
> and easily account for the differences between our two species [human and
> chimpanzee that is]._

Not to be picky, but I seriously doubt that. ;)

~~~
JunkDNA
While he's seriously incorrect, it _is_ however worth remembering that a
caterpillar's DNA bases don't change at all when it becomes a butterfly. It's
all about _the degree_ those proteins get expressed, in what ratios, and
(crucially) _when_ that makes an organism. Sort of like if I give you the
ingredients to a recipe:

bread cheese ham egg

You could scramble the egg, put it with the ham and cheese and put it all
between bread and have a sandwich. Or you could coat the bread with the egg
and throw into a frying pan and make a Monte Cristo. Both sandwiches, but
pretty different.

As computer types we want to believe that DNA sequence is an analog to
computer code. It's not a perfect analogy. There is the currently very hot
field of research into epigenetics which is looking into the chemical
decorations on DNA that make parts active and inactive at certain points in
time. These are heritable, but unlike the sequence, are routinely and
intentionally altered by cells in your body (often in response to
environmental stimuli). So the environment can make temporary changes that get
passed onto offspring, potentially affecting early stages of development. The
thing is, development is crucial and not all processes are reversible (e.g.
the lens in the eye only gets made once). So what long term effect do these
changes have? Nobody has the foggiest idea yet.

~~~
kaliblack
Great information. You increased my knowledge and my appetite.

I'd say that the computer code analogy is how most people understand DNA: a
set of constants with values. This is how DNA is generally portrayed.

------
inovator
23andme also has upgraded their website but still in beta mode. You guys can
opt in for it here <https://www.23andme.com/you/beta_optin/>

------
malay
If you want to dig into the million SNP raw data from 23andMe any further than
what is presented on the website, Jeff Hammerbacher and Konrad Karczewsk
taught a Skillshare on doing your own personal genome analysis with Python and
various other tools.

Slides here: <http://www.slideshare.net/jhammerb/20130206skillshare>

Github repo here: <https://github.com/hammer/personal-genome-analysis>

------
pagliara
I'm awaiting my 23andme results right now. I'm very excited for my results and
this post has inspired me to learn more about the science and research that
has enabled us to learn so much about ourselves from our genes.

My friend recently got their results back and I was really impressed with how
well 23andMe presents the data to you. They do a really good job explaining
what the data means. In fact, in some sections, 23andme will only tell you
your results after reading through the informational material they provide.

------
2321sdadas
Hmm, I imagine that this is a complete scam. Or am I too skeptic? Where is the
proof that this is 100% legit and not some mumbo-jumbo psyche stuff?

~~~
leocassarani
Definitely too skeptical. Every piece of research that 23andme uses to
interpret your genetic data is backed by a wealth of citations and studies.
Each "discovery" is rated on a confidence scale from 1 to 4, with experimental
research being a 1 and undisputed, established research being a 4.

Nothing's stopping you from downloading your own genetic data as a text file
and performing the same types of analysis yourself.

Also, Occam's razor.

------
inovator
For $99 you can get DNA analyzing; that is a cheapest price you can find
anywhere imo. However, their service is extremely slow. You are looking at
about 6-8 weeks until you get to see your result. I guess they are trying to
offset the expenses. Nevertheless, it's a great service to find out your roots
and health problems.

~~~
anonfunction
That doesn't even seem extremely slow to me. My gram buys crap from china on
tv that takes 6-8 weeks. Maybe it's because I know little to none about the
subject, but how long should it really take?

~~~
mbreese
Ideally, it would be about a week of processing time (probably a little less).
But, I assume they have a limited number of machines and a backlog. And they
probably batch everything to make it as cost-effective as possible. At $99
they are running very close to cost.

------
deanje
I recently did this also, heres the process in pictures:
[http://deanjerkovich.com/2013/01/20/getting-my-genome-
sequen...](http://deanjerkovich.com/2013/01/20/getting-my-genome-sequenced/)

please excuse the technical inaccuracies - this was prior to me going on an
adventure of learning exactly what this involved.

------
kkwok
Having studied the techniques used to analyze DNA, I wish 23andme would send
you your raw data. Nevertheless still awesome and crazy to see your own DNA
being analyzed.

~~~
patdennis
You have access to your raw data through 23andme. At least I do. It's a text
file (sitting in a Truecrypt partition, in my case).

~~~
kkwok
My apologies. 23andme does provide the raw data from the genotyping. What I
think I meant to say was I wish they could do sequencing and give that data.
Obviously I understand it's prohibitively costly though.

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anonfunction
"My DNA is 2.9% neanderthal, which puts me in the top 91% of 23andme's members
(not sure what conclusions to draw from that!)."

Checkmate, evolution deniers.

~~~
DanBC
When has science of fact ever got in the way of someone who denies evolution?

These are the kind of people who put saddles on dinosaurs and have "Creation
Museums" (<http://creationmuseum.org/>)

------
CleanedStar
"Studies have shown that identical twins who grow up in separate families have
an IQ correlation of 0.74, while adoptive siblings have no more similar IQ
than strangers."

First off the bat, such studies are obviously social science, not science.

Secondly - there is this idea that one can boil entire brains down to one
number like a CRC or checksum - the IQ number. Then you can rank them in order
I suppose. It is obviously a ludicrous endeavor on reflection. It's like the
Douglas Adams joke that the answer to life, the universe and everything is 42.
When science actually makes progress on the brain, I'm sure biologists of the
future will look on IQ like we look on phrenology.

Thirdly, these social science studies of twins mentioned were done by Thomas
J. Bouchard, Jr. He's someone who writes op-eds for the Wall Street Journal -
I guess Nature and Science are too full and his work crowded into there.

The second edition of the Mismeasure of Man by Stephen Jay Gould is a good
book on this topic.

There was a hysterical conservative reaction to Gould's book just as there was
a hysterical progressive reaction to the Bell Curve. Which shows this is
really a political debate, not a scientific one. This is a political debate
going back about 10,000 years, really. I am skeptical of any social scientific
study that proposes it has found all the answers.

~~~
icelancer
>Secondly - there is this idea that one can boil entire brains down to one
number like a CRC or checksum - the IQ number. Then you can rank them in order
I suppose. It is obviously a ludicrous endeavor on reflection.

Nothing of that diatribe is reflected in the statistic you just quoted.
Pointing out a correlation between IQ doesn't necessarily mean IQ is some
perfect heuristic to weed out the proles.

