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Joined: Apr 2013
Posts: 372
Fifth_Degree_AS_Kicker
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jroc,

Promethease did have the similar type data. My 45 days has expired but I did download all of the data. While active, you could export/view results in different formats and bar graphs was one of them.

DavidP -- I'm curious how your results came out on Promethease for the Crohn's. The following were my results (sorry I have NO idea how to clean up the columns):


Name Repute Summary
rs6601764(C;T) Bad 1.16x increased risk of developing Crohn's disease
rs9469220(A;G) Bad 1.1x risk of Crohn's disease
rs10883365(A;G) Bad 1.2x increased risk for developing Crohn's disease
rs13361189(C;T) Bad 1.3x increased risk for Crohn's disease
rs4958847(A;G) Bad 1.3x increased risk for Crohn's disease
rs7807268(C;G) Bad 1.3x risk for Crohn's disease
rs2241880(C;T) Bad 1.4x increased risk for Crohn's disease in Caucasians
rs2201841(C;T) Bad 1.5x increased risk for Crohn's disease; 2x increased risk for Graves' disease
rs1000113(C;T) Bad 1.5x risk of Crohn's disease
rs9858542(A;A) Bad 1.8x risk
rs6908425(C;C) Bad 1.95x increased risk of developing Crohn's disease
rs6596075(C;C) Bad 2x risk of Crohn's disease
rs11229030(C;C) Bad higher odds of Crohn's disease
rs12567232(A;G) Bad Increased risk for Crohn's Disease
rs2631367(C;C) Bad Increased risk for Crohn's Disease
rs11209026(G;G) Bad Normal, but higher risk for certain autoimmune diseases.
rs12037606(G;G) Good Normal risk of developing Crohn's disease
rs3814570(C;C) Good Normal risk of developing Crohn's disease
rs11465770(C;C) normal Crohn's Disease risk

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Magical_AS_Kicker
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Originally Posted By SimplySouthern

Promethease did have the similar type data. My 45 days has expired but I did download all of the data. While active, you could export/view results in different formats and bar graphs was one of them.

Thanks, that's cool. I just took a look at the promethease website and the site and the reports have changed a lot since when I did it back in 2013. Looks much more professional now and they integrate with the 23andMe through their API so you don't have to manually upload. I might have to drop another $5 on a new report.

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Fifth_Degree_AS_Kicker
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DavidP, (or anyone else that recalls it)

I recently ran across an article that was written in very layman's terms that suggested those with emphasis of bad repute for ERAP1 were more likely affected with Axial involvement whereas if the bad repute was stronger on the Il23R side, it most likely affected peripheral areas (I know you touched on that above but there was another article that went more into it).

I'm hoping with your expertise of research you may have crossed paths with such an article. I'm terrible about reading something of interest and not printing it and then can't find it to reference it.

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Hi Simply Southern,
Its hard to know what to make of Crohns Disease SNPs.
Of the ones you listed I had 8 for which CD risk was normal and 8 with slightly raised risk of CD.
Of the total of 149 CD SNPs I had 99 - Not set; 23 of Good Repute and 27 of Bad Repute.
Of the CD SNPs of Bad Repute the most interesting were those at the NOD2 locus on chromosome 16 since the NOD2 locus is considered to represent one of the strongest genetic risk factors for Crohns Disease.
They were
rs2066843 (T;T) 4.1X risk of CD
rs17221417 (G;G) 1.9X risk of CD and
rs2076756 (G;G) 1.7X risk of CD.

I don't think there are any articles which put a simple hypothesis ERAP1 bad repute SNPs -> axial disease Vs IL23R bad repute SNPs -> peripheral diseae.

You might have been thinking of this article - which is quite dated now.
http://www.sciencecodex.com/major_geneti..._treatment_hope

Understandably, most of the AS cohorts in genetic studies have in the past enrolled probably mainly classic AS cases - and very few more atypical cases - like those with an undifferientiaed spondyloarthropthy.

Recently the focus has been on IL23 and IL23R because of the discovery of a population of entheseal-resident IL23R+ T cells. It is speculated that other unique IL23R+ T cells might populate the skin, the gut, and the eyes.


Dx Oct 2006 B27+ undifferentiated spondlyarthropathy (uSpA) with mild sebhorrhoeic dermatitis and mild Inflammatory Bowel Disease (IBD) controlled by NSD since 2007.
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Fifth_Degree_AS_Kicker
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That is in fact the article I was thinking of. I had viewed it a week or so ago and for some reason moved on and could not recall where I had seen it, naturally wanting to recall it thereafter.

Thanks for stopping my insanity of searching!

I have NOT been diagnosed with Crohns or IBD but have IBS and Diverticular Disease. My Mom has suffered with Diverticulitis for years and has a strong bout of it a few times a year. For the prevention, she takes nothing but an antibiotic which in time, heads it off. I do use Miralax daily when tends to limit my IBS to a moderate occurrence. I honestly believe that has been of great help. Anyway, I've wondered if there isn't something beyond that going on -- for both my Mom and I, but as yet, no suggestion of CD.

As for the Il23R focus, skin issues have never been a concern however as a child, I had frequent conjunctivitis (a couple times as an adult) and frequent soreness/redness and dry eye. I went to a Ophthalmologist and nothing was found but had no outbreaks so he said it could be but saw no damage. I have wondered if Lazik could have masked previous damage...no clue as the procedure is out of my realm of knowledge. So many avenues of research!

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ERAP1 is known to be highly polymorphic with at least 70 nsSNPs, although the majority are rare. Considering the more common SNPs, at least 15 SNPs in ERAP1 are known to be associated with AS. Until recently it was not known whether they acted independently or as disease associated haplotypes. Recent studies have shown the latter, that SNPs occur as distinct haplotypes (hereafter called allotypes) in the human population and that these allotypes encode functionally distinct ERAP1 molecules. Using a range of substrates researchers have demonstrated that each allotype has a trend bias toward ‘normal’, ‘hypofunctional’ or ‘hyperfunctional’ ERAP1.
The prevalence of specific ERAP1 allotypes is different in AS cases and healthy controls, although, at this stage the exact frequency of each allotype has not yet been accurately established for the general population or for AS cohorts. Each person has a pair of ERAP1 allotypes (one from each parent) and each of the chromosomal copies of ERAP1 are co-dominantly expressed. Most healthy controls have at least one ‘normal’ ERAP1 allotype compared with AS patients, who in general have two ‘hypoactive’ allotypes (and sometimes hyperactive allotypes). The disease associated ERAP1 allotype combinations have a reduced ability to generate peptides for presentation at the cell surface by MHC class I molecules, including HLA-B27. Hence, an ERAP1 pair composed of a ‘normal’ and a ‘hypoactive’ allotype will still produce sufficient peptide ligands, and of sufficient quality, as to allow for the normal biochemical functioning of HLA-B27.
Increased disease risk is potentially manifested in two ways. Firstly, aberrant ERAP1 activity, either hypo-functional of hyper-functional, might result in increased misfolding of HLAB-27 in the ER and the generation of B27 homodimers and an unfolded protein response; and secondly, aberrant ERAP1 activity might generate unstable peptide ligands and result in elevated cell surface B27 homodimers which could activate NK cells (through KIR3DL2 engagement) and/or Th17cells.

I have presented here only a simplified summary of a paper entitled “Functionally distinct ERAP1 allotype combinations distinguish individuals with Ankylosing Spondylitis” by Reeves, Colebatch-Bourn, Elliot, Edwards and James – 2014.
Regards to all – David.

http://www.pnas.org/content/111/49/17594.short


Dx Oct 2006 B27+ undifferentiated spondlyarthropathy (uSpA) with mild sebhorrhoeic dermatitis and mild Inflammatory Bowel Disease (IBD) controlled by NSD since 2007.
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Hi jroc and Simply Southern,

If you fit our 23andme ERAP1 data to the table in the above paper we should be able to guess what allotypes we have.

The five main SNP's in 23and me are rs2287987 (M349V); rs30187 (K528R); rs10050860 (D575N); rs17482078 (R725Q) and rs27944 (Q730E)
It's pretty simple for me and Simply Southern - we have two of the normal functioning *002 allotypes, that is amino acids MKDRQ for both our ERAP1 versions.

jroc on the other hand has one and possibly two hypofunctional alleles.


Dx Oct 2006 B27+ undifferentiated spondlyarthropathy (uSpA) with mild sebhorrhoeic dermatitis and mild Inflammatory Bowel Disease (IBD) controlled by NSD since 2007.
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Magical_AS_Kicker
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Hi David

That sounds interesting. How do I plug my data into the table to figure out my allotype - were you meaning this table? - http://www.pnas.org/content/111/49/17594/T1.expansion.html

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Hi jroc,

Yeh, that's the table I was refering to.

http://www.jimmunol.org/content/191/1/35/T1.expansion.html

This table is from an earlier paper by the same authors.
The equivalent DNA bases that are reported in 23andme or Promethease are in lower case.

Let us know what you get.

Regards David


Dx Oct 2006 B27+ undifferentiated spondlyarthropathy (uSpA) with mild sebhorrhoeic dermatitis and mild Inflammatory Bowel Disease (IBD) controlled by NSD since 2007.
Joined: Apr 2013
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Fifth_Degree_AS_Kicker
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Call me dumb, call me tired.....I am totally lost. I have opened both links and see no where to enter data. What am I missing??

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