mellowtigger: (dna)
[personal profile] mellowtigger
First draft, but I just want to get something "finished" enough to post, because I have other tasks to work on this week and need to try getting this one out of my head for a short while.  Summary:  I have 4 autism markers, 2 uncertain, several normal markers, and many that remain untested or unexplained.

geneaddressnormalautism riskmereference
METrs1858830GGCC x 2.27, CG x 1.67CCPubMed
ADRB2rs1042714
CCGG x 1.33 - 1.60 (or even twice that)GGPubMed
GABRB2rs2617503CC or TTCT x ?CTScienceDirect
APCrs1804197AACC x ?CCPubMed
NPAS2rs1811399?C (unspecified heterozygous risk)ACNature
EN2rs1861973?C (unspecified heterozygous risk)CTNature

For many autism markers, I have the typical dna pattern instead.  There are a lot of markers that are not tested by 23andme.  There are many studies which mention specific SNP addresses but their summaries do not indicate which base pairs were involved (and I can't afford to purchase all of those articles for their details).

Some markers were tested, but I had results not indicated in any expected combination.  For example, I have AA at rs2710102 (CNTNAP2 gene) but expected values according to the article are CC, CT, and TT for Caucasian Europeans.  Similar shenanigans occur at rs1322784 (DISC1 gene).  What these differences are supposed to mean, I have no idea.  Are they:
  1. bad gene chip results (disappointing),
  2. contamination (also disappointing),
  3. brand new mutation (exciting!), or
  4. a data mixup in how the SNP addresses are reported (confusing)?
Apparently there's some kind of left-hand versus right-hand notation involved in naming the "rs#" addresses, so it could easily be a translation problem there.   Some texts, however, were just plain confusing, like rs1861972 and rs1861973 which seem to simultaneously associate for and against autism, unless I'm misreading that somehow.  I didn't get enough sleep last night, so maybe I should try again in a few days with a fresher mind.

I still have more references to check.  There are so many autism markers!  More to say in the second draft later, I guess.

Date: 2009-Mar-25, Wednesday 03:37 am (UTC)
From: [identity profile] maradydd.livejournal.com
This is really fascinating. I admit I'm a little out of my depth here in terms of answering your questions or even shedding much insight, but I am learning as a result of observing your process. Thank you for doing this! Reading these entries is like opening a present. :)

Since you're posting them publicly, would you mind if I passed the URL to your posts with the "gattaca" tag to the DIYbio mailing list? I think other people would also find them instructive, and others may be able to help shed light on things that are confusing about notation or whatever.

I'd like to know more about autism markers, as well. I won't have the money to spring for a 23andMe test anytime soon, but I was diagnosed with Asperger's syndrome in 2004 and am curious what markers I might have.

Date: 2009-Mar-25, Wednesday 04:04 am (UTC)
From: [identity profile] lordalfredhenry.livejournal.com
Cool! I need to review myself.

rs1858830: GG normal
rs1042714: CC normal
rs2617503: CC normal
rs1804197: CC risk?
rs1811399: AC ? matches yours.
rs1861973: CC ? you got CT.

Did you get prometheaseZ to work with what I mentioned on directory structure or was there more work to do involved? That's really interesting. Now I want to do some reading of those articles. :)





Date: 2009-Mar-25, Wednesday 12:17 pm (UTC)
From: [identity profile] lordalfredhenry.livejournal.com
rs2710102: GG
rs1322784: GG

I usually score high on all the delayed speech development SNPs. IIRC, these were some suspect ones. I'm guessing GG is equivalent to CC. (reversed pair) I found more:
http://www3.interscience.wiley.com/journal/112224058/abstract?CRETRY=1&SRETRY=0


http://en.wikipedia.org/wiki/DNA#Base_pairing

Date: 2009-Mar-25, Wednesday 08:09 pm (UTC)
From: [identity profile] khrysso.livejournal.com
This exploration is all so interesting! I feel very lucky to be privy to it.

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