first draft for autism markers
2009-Mar-24, Tuesday 09:47 pm![[personal profile]](https://www.dreamwidth.org/img/silk/identity/user.png)
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.
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:
I still have more references to check. There are so many autism markers! More to say in the second draft later, I guess.
gene | address | normal | autism risk | me | reference |
MET | rs1858830 | GG | CC x 2.27, CG x 1.67 | CC | PubMed |
ADRB2 | rs1042714 | CC | GG x 1.33 - 1.60 (or even twice that) | GG | PubMed |
GABRB2 | rs2617503 | CC or TT | CT x ? | CT | ScienceDirect |
APC | rs1804197 | AA | CC x ? | CC | PubMed |
NPAS2 | rs1811399 | ? | C (unspecified heterozygous risk) | AC | Nature |
EN2 | rs1861973 | ? | C (unspecified heterozygous risk) | CT | Nature |
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:
- bad gene chip results (disappointing),
- contamination (also disappointing),
- brand new mutation (exciting!), or
- a data mixup in how the SNP addresses are reported (confusing)?
I still have more references to check. There are so many autism markers! More to say in the second draft later, I guess.
no subject
Date: 2009-Mar-25, Wednesday 03:37 am (UTC)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.
no subject
Date: 2009-Mar-25, Wednesday 03:59 am (UTC)no subject
Date: 2009-Mar-25, Wednesday 04:04 am (UTC)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. :)
no subject
Date: 2009-Mar-25, Wednesday 04:20 am (UTC)rs1042714: CC normal
I had quite a few normal results too. I did not cross-reference all of those links, though, to add them to the table. Maybe on a 3rd or 4th draft of this table. :)
rs2617503: CC normal
rs1804197: CC risk?
The article summaries did not specify the risk level associated with the rogue nucleotide. If I could buy the articles, it probably has that detail in it.
rs1811399: AC ? matches yours.
rs1861973: CC ? you got CT.
The article here mentioned only the "C" allelle, so I'm sure that your CC result would qualify. I'm just not sure if my own "CT" conveys any risk or not. Again, more information in these article summaries would help a lot!
rs2710102
rs1322784
What were your results here? We can suspect translation problems if your results are also "out of line" with expected values.
Promethease program
No, I didn't have any luck getting the most recent program to run on my Vista 64-bit system at home. I did get the older version to work, but I still had to manually select a new output directory for my results file. It would not write to the default directory, for unknown reasons.
no subject
Date: 2009-Mar-25, Wednesday 12:17 pm (UTC)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
no subject
Date: 2009-Mar-25, Wednesday 01:37 pm (UTC)no subject
Date: 2009-Mar-25, Wednesday 08:09 pm (UTC)