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#512196 - 08/22/15 06:05 AM DNA Promethease Report and IL23R and ERAP1
SimplySouthern Offline
Fifth_Degree_AS_Kicker

Registered: 04/21/13
Posts: 372
Loc: South Carolina -- USA
Has anyone used Promethease to analyse DNA results in the determination of the IL23R and ERAP1 status?

I recently got my results and uploaded them to Promethease. I'm still trying to decipher the results but of the genes known to be associated with AS, I fall into the BAD Repute of IL23R across the board however GOOD in all 4 of the ERAP1 results.

Under rs7743761, the results show 20x increased risk of Ankylosing Spondylitis however the gene this falls under this SNP (I believe they call it) is DHFRP2 and shows diseases associated with DHFRP2 include systemic lupus erythematosus (per genecards.org) but no mention of AS on that site (nor have I seen DHFRP2 anywhere in relationship to AS).

Does anyone have light they could shed on understanding this and how (or if) it has relevance to the diagnosis of Spondylitis.

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#512198 - 08/22/15 08:05 AM Re: DNA Promethease Report and IL23R and ERAP1 [Re: ]
SimplySouthern Offline
Fifth_Degree_AS_Kicker

Registered: 04/21/13
Posts: 372
Loc: South Carolina -- USA
www.23andme.com

I ordered the kit and when the raw data was available, I uploaded it to Promethease which gave me the SNPs and Allele and genotype.

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#512199 - 08/22/15 08:12 AM Re: DNA Promethease Report and IL23R and ERAP1 [Re: ]
SimplySouthern Offline
Fifth_Degree_AS_Kicker

Registered: 04/21/13
Posts: 372
Loc: South Carolina -- USA
For instance, I am showing a bad repute for SNP rs7743761(A;A) which is defined as:

20x increased risk of Ankylosing Spondylitis. Greatly increased odds (but still only about 2%) of this disease. But age of onset is usually between 15 and 25, so if you are older than that, there's not much need for worry. Ankylosing Spondylitis is a rare autoimmune disease that causes inflammation of the spine and joints. Based on preliminary research.

This is attached to a gene by the name of DHFRP2 which I had never heard of.

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#512200 - 08/22/15 09:55 AM Re: DNA Promethease Report and IL23R and ERAP1 [Re: SimplySouthern]
jroc Offline
Magical_AS_Kicker

Registered: 10/30/08
Posts: 757
Loc: New Zealand
I ran my snp data through Promethease a couple of years ago.

I've got the 4.6x risk allele for that SNP - http://www.snpedia.com/index.php/Special:FormEdit/Genotype/rs7743761(A;C)

For the ERAP1 related ones I've got 2 higher risk, 3 lower risk.
For the IL23R related ones, I've got 3 higher, 3 normal risk.

I posted some other info at the time here - http://www.kickas.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=496250#Post496250

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#512206 - 08/22/15 03:16 PM Re: DNA Promethease Report and IL23R and ERAP1 [Re: jroc]
SimplySouthern Offline
Fifth_Degree_AS_Kicker

Registered: 04/21/13
Posts: 372
Loc: South Carolina -- USA
So would you say since both of the subset genes were identified in your profile (and mine) that it further confirms the diagnosis of AS (as per the pubmed below)?

http://www.ncbi.nlm.nih.gov/pubmed/18525349

I'm not sure if I'm reading it right to assume having the presence of the two substantiates the diagnosis or what. A little mixed with the findings and conclusion. I know I read somewhere that the two were linked directly to AS.

Under the IL23R my results were:

rs10889677(A;C) -- 1.5x increased risk for certain autoimmune diseases; 2x increased risk for Graves disease
rs11209026(G;G) -- Normal, but higher risk for certain autoimmune diseases.
rs1004819(C;T) -- 1.5x risk
rs11209032(A;G) -- 1.3x higher risk for spondylitis
rs1495965(A;G) -- 1.2x higher risk for spondylitis
rs1343151(C;C) -- normal risk
rs11465804(T;T) -- normal risk

Under ERAP1:

rs10050860(C;T) -- 0.71x lower risk for Ankylosing Spondylitis.
rs30187(C;C) -- Normal low risk (0.1%) for ankylosing spondylitis.
rs17482078(C;T) -- 0.76x lower risk for spondylitis
rs2287987(C;T) -- 0.71x lower risk for spondylitis
rs27434(G;G)
rs27044(C;C) -- normal risk


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#512207 - 08/22/15 03:31 PM Re: DNA Promethease Report and IL23R and ERAP1 [Re: jroc]
SimplySouthern Offline
Fifth_Degree_AS_Kicker

Registered: 04/21/13
Posts: 372
Loc: South Carolina -- USA

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#512209 - 08/22/15 08:18 PM Re: DNA Promethease Report and IL23R and ERAP1 [Re: SimplySouthern]
DavidP Offline
Master_Sergeant_AS_Kicker

Registered: 09/24/07
Posts: 607
Loc: Sale, Victoria, Australia
Hi Simply Southern
Over the years I've tried to stay updated with the latest findings regarding AS.

It might be worth contacting the makers of 'Promethase' and asking them to confirm whether or not rs7743761 which apparently corresponds to DHFRP2 (dihydrofolate reductase psi-2) is really associated with increased risk of AS.

Clearly most of the disease risk for AS currently lies within the HLA B27 gene (and to a much lesser extent HLA B40 B51 B47 and B13), followed next by ERAP1 (formerly ARTS1) then IL23R and then a string of lesser known and possibly less important genes such as CMP2 (Capillary Morphogenesis Protein 2).

Also worth noting is that the increased risk of AS of say x20 of one version of an SNP over the other version is only x20 specific to that particular SNP within that gene.

In the absence of at risk versions of HLA B27, ERAP1 and /or IL23R then the risk of AS associated with lower ranking genetic factors such as CMP2 or (presumably DHFRP2) is probably inconsequential.
_________________________
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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#512212 - 08/23/15 02:11 AM Re: DNA Promethease Report and IL23R and ERAP1 [Re: SimplySouthern]
jroc Offline
Magical_AS_Kicker

Registered: 10/30/08
Posts: 757
Loc: New Zealand
I think David is right. Because the general chance of AS is so low, and the relative risk factors for most of the SNPs reported for AS in Promethease are between 0.7 - 1.5, I don't think they would be of any diagnostic value.

However the 20x relative risk rs7743761(A;A) allele could be an exception since it's a high odds ratio and only a very small percentage of people have that allele - looks like about 2% of Europeans from the Promethease graph.

These are the two studies that are linked to as references in Promethease for that SNP:
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224997/
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680141/

The first one mentions rs7743761 but I couldn't find any mention of a 20x odds ratio or see anything like that in the tables or figures. The second one doesn't seem to mention rs7743761 at all. So perhaps Promethease made an error in their reporting on that SNP.


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#512213 - 08/23/15 04:45 AM Re: DNA Promethease Report and IL23R and ERAP1 [Re: jroc]
SimplySouthern Offline
Fifth_Degree_AS_Kicker

Registered: 04/21/13
Posts: 372
Loc: South Carolina -- USA
I was diagnosed in 1986 after a Nuclear Bone Scan, HLA-B27+ and a Myelogram (and years of back and hip pain) but never kept my records.

At the time, there was no one closely knowledgeable of AS in the area and because I wasn't the worst case scenario (extreme AS case with fusion), I was dismissed by a Rheumy within even looking at any films, reports or blood work. He told me I was wasting his time that anyone with AS would be completely hunched over and unable to straighten up because they were fused. He told me to never come back as he had patients in real need.

Needless to say, I was so humiliated that @%LL would have frozen over before I went through that again so I walked away and refused to see another one but, a lot of things happened since but I've been more focused on those than AS. I'm -.02 on SLE, Bilateral Peroneal Neuropathy, 4 thoracic fractures last year, and so on.....any way....with all that somewhat stabilized, I moved to get closer to family and without established history, I've been told there is no urgency to get in with a Rheumy so I'm in an 8 month wait....for a November appointment. By then, next appointment I will be changing insurances....again. I don't like the closest one taking my insurance is 76 miles away....I could understand if I was in a remote area but....not the case.

Any how, what I find very interesting is the HLA-B27 is not on the report results but under HLA-B there were three (unevaluated) SNPs:

rs2523608(T;T)
rs1058026(T;T)
rs2596439(T;T)

It seems like I have a lot of SNPs for Lupus, Rheumatoid Arthritis, Multiple sclerosis, Crohn's disease, and overall Bad Reputes for Autoimmune conditions.

Overall it seems without clear fusion, variables are so many that a diagnosis can be explained away.


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#512215 - 08/23/15 06:34 AM Re: DNA Promethease Report and IL23R and ERAP1 [Re: ]
SimplySouthern Offline
Fifth_Degree_AS_Kicker

Registered: 04/21/13
Posts: 372
Loc: South Carolina -- USA
Basically treatment. As of right now, all that is pending (last verbal comment in 2014 from the one visit I had with a Rheumy was she was furious that years had passed without any prevention).

Personally I don't care if I have it or not but unless there is some type of reason to suggest treatment, I've been dismissed.


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