Question: Very basic - Understanding the nomenclature of +G/-A
0
gravatar for dave
4.7 years ago by
dave0
United States
dave0 wrote:

I understand how alleles are written on SNPedia, such as:

(A;A)    0    normal
(A;G)    2.1    1.32 x risk of rheumatoid arthritis.
(G;G)    2.2    >1.32 x risk of rheumatoid arthritis

However, when searching on the web I often found things written in this manner that I do not understand:

FOLR3 rs7925545 +G/-A reduced folate carrier

From this last description, does anyone know how to read (a) what's the normal or most common, (b) what the +C and -A indicate?  For example, on that one I am AA.  Does that make me more likely to be a reduced folate carrier or more likely?

I don't know if the +G/-A is about orientation or probability.  

It would be wonderful if someone could explain this to me so that when I see things written in the "+G/-A" format I know how to read that on dbSNP and so on.

Thanks!
Dave

 

snp • 971 views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by dave0

Sorry, I do not know what you mean by "add a G and remove an A".  Do you mean that the predicted trait is more common if you have a G or lack an A?  So the normal would be AA and AG or GA would be the less common variants?  As you can see, I do not see how it's supposed to be read.

How do I translate "+G/-A" into the SNPedia format?  That's all I'm asking.  Perhaps information is lost or it's not as complete, and that's fine, but any assistance in helping me to just get past that hump would be helpful.  Thanks!

 

ADD REPLYlink written 4.7 years ago by dave0

"Add a G and remove an A" means literally what's written and has absolutely nothing to do with any trait or other phenotypic information. This is purely genotype information.

Regarding SNPedia, I have no clue what its format is, but here's the entry there.

ADD REPLYlink written 4.7 years ago by Devon Ryan91k

Ah, sorry.  Software engineer.  2 years of college biology, so I know what an allele is and what dominant means and what ATG and C stand for, but not much more.

What I'm looking for is when confronted with the +G/-A nomenclature and looking at an rsXXXXXX pair of my own, how to read it.  If it's written in the "FOLR3 rs7925545 +G/-A reduced folate carrier" format, and I'm GG, what that implies in terms of probability (which is not stated or known for my example, but you get the idea I hope).

So dumb it down a notch or two, I'll get it :-)

ADD REPLYlink written 4.7 years ago by dave0

Ah, no worries. In this case, the +G/-A only tells you part of what you want to know. This position is either heterzygous (a single G) or homozygous (2 Gs) at that position. More information isn't specified. So if you want to know relative risk, then it's at least 1.32 fold increased for rheumatoid arthritis (that would make an absolute risk of at least 2.32%...assuming all else is equal).

ADD REPLYlink written 4.7 years ago by Devon Ryan91k
0
gravatar for Devon Ryan
4.7 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

+G/-A just means "add a G and remove an A". It's not a standard nomenclature, which is something like chr11:g.72134495A>G.

ADD COMMENTlink written 4.7 years ago by Devon Ryan91k

Well, absent the context of or result of or implication of "add a G and remove an A", I'll stick to truck driving, as it helps me not at all.  I put "very basic" in the title for a reason, and knowing that it's equivalent to "chr11:g.72134495A>G" might as well be from Microsoft support.

ADD REPLYlink written 4.7 years ago by dave0

Ah, I had assumed that you were a biologist, in which case that should have made sense. Otherwise, it might be helpful to know what sort of work/education you have such that answers can be tailored into a more accessible form.

ADD REPLYlink written 4.7 years ago by Devon Ryan91k
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