first draft for autism markers

[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.

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:

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.

Comments

[mellowtigger]

Ok, so it looks like it is a matter of "translation" then. Cytosine and thymine are expected at this location, according to the SNPedia entry, but you and I have guanine and adenine instead. Left/right confusion. But if all of our other addresses are appropriately labeled, then why would these two particular entries be different in the SNPedia? *frustration*