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TNF Genes and Gene Terminology

Posted: Sat May 10, 2014 6:43 pm
by circular
"Seventeen studies that investigated the association between 5 TNF-alpha polymorphisms (-850, -308, -863, -238, and -1031) and AD were retrieved and analyzed...Current findings support an association between -850 C>T polymorphism and the risk of developing AD; hence, they strengthen the suggestion of a potential role for anti-TNF therapy to maintain physiologic levels of TNF-alpha."

"We found a significant asssociation of a TNFR2 exon 6 polymorphism with late-onset AD in families with no individuals possessing the APOE E4E4 genotype under a dominant model. We found no significant association of three polymorphisms in the TNFR1 gene to AD. These results provide further evidence for the involvement of TNF in the pathogenesis of AD."


I'm trying to figure out if these studies specifically studied a gene I just found in Promethease that increases TNF: GMAF rs1800629(A;G)

We've got one study talking "TNF polymorphisms 850, 308, 863 blah blah", another talking "TNFR2 exon 6 polymorphism", and Promethease referring to position rs1800629.

Meanwhile, I thought these "rs" identifications referred to positions on a gene that can show variant alleles, but I keep reading things calling rsblahbalh a gene! Getting confused :?

Re: TNF Genes and Gene Terminology

Posted: Sat May 10, 2014 7:13 pm
by circular
This new study ( ... th+News%29) just mentioned in another thread puts it this way:

"the team explored the effect of a variant in the WWC1 gene on age-related changes in memory function. The particular WWC1 variant under investigation has three potential forms -- CC, TT, or CT".

I assume here, but they don't say, that the "variant" is referring to a *position* on the WWC1 gene that can exhibits different alleles/variants: CC, TT, CT. But who am I to correct the scientists at Elsevier? It must be me who's wrong. But in Promethease I have results for three different reblahblahs on the WWC1 gene. The article doesn't state *which* it is talking about.

Could the real genes, variants, positions, alleles, polymorphisms, ghosts please come forward!


Re: TNF Genes and Gene Terminology

Posted: Sat May 10, 2014 7:19 pm
by circular
Okay, I see in Promethease the position number is not the same as the rsblahblah, so perhaps Elsevier is right (haha) and the rsblahblah is the *variant*. Then why, with differing results at each variant, do we have variants of variants?????????????

Re: TNF Genes and Gene Terminology

Posted: Sat May 10, 2014 7:48 pm
by circular
Got it, rsblahblahs are SNPs. But I still think SNPs *have* variants (c,c etc), not *are* variants???

Re: TNF Genes and Gene Terminology

Posted: Sat May 10, 2014 8:11 pm
by SusanJ
Circ, try this explanation.

And make sure to click through the Making SNPs Make Sense "What is a SNP" in the blue box.

Re: TNF Genes and Gene Terminology

Posted: Sun May 11, 2014 6:41 am
by circular
Thanks SusanJ - will check it out!

Re: TNF Genes and Gene Terminology

Posted: Thu May 15, 2014 11:42 am
by Gina99
Thanks Susan. Also liked the epingentics on the site as well.

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