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exseitanist

How To Determine Hla-Dq* ?

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I just joined this site, 6 months after my celiac diagnosis.  Thank you for talking about this disease!

 

23andme lists several SNPs associated with my risk of celiac disease, but none of their descriptions mention HLA-DQ2 or HLA-DQ8.  Even looking up those SNPs in snpedia.com only showed HLA-DQA1.

 

I read that -DQ2 or -DQ8 are almost always found in celiac patients.  If 23andme doesn't list either of those variants for my genetic profile, does that mean that I don't have either of them?  Or is there a knowledge gap I need to fill?

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That place has had some issues.  They seem to look for genes with associations (apparently not all proven) and go with statistics.  

 

 

"we still do not have any assurance that the firm has analytically or clinically validated the PGS for its intended uses, which have expanded from the uses that the firm identified in its submissions."

 

http://www.fda.gov/ICECI/EnforcementActions/WarningLetters/2013/ucm376296.htm

 

 

http://money.cnn.com/2013/11/25/technology/fda-23andme/index.html

 

 

Read the company's info carefully to see what the issues might be.

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That place has had some issues.  They seem to look for genes with associations (apparently not all proven) and go with statistics.  

 

 

"we still do not have any assurance that the firm has analytically or clinically validated the PGS for its intended uses, which have expanded from the uses that the firm identified in its submissions."

 

http://www.fda.gov/ICECI/EnforcementActions/WarningLetters/2013/ucm376296.htm

 

 

http://money.cnn.com/2013/11/25/technology/fda-23andme/index.html

 

 

Read the company's info carefully to see what the issues might be.

I see, thanks.  Are there low-cost genetic tests that would highlight the gene variants associated with celiac disease?  It's purely curiosity at this time since I had my diagnosis via biopsy.

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I had my doctor order them thru Quest years after I was officially diagnosed.   There are several places that do it.  To my surprise, my insurance paid for it without a peep!  Just proving, that when it comes to Celiac Disease, they haven't a clue.    :o

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In my 23andMe technical report for celiac for gene HLA-DQA1 they have SNP rs2187668 and say "We only report data on one subtype of HLA-DQ2. Of all the risky HLA-DQ subtypes, this subtype, called HLA-DQ2.5, is most often associated with Celiac Disease".

Someone recently had a very nice post explaining how these are all related. DQA1 and DQ2.5 are not two choices for the same gene but I don't understand it enough to explain more!

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Hi there,

 

Here are two really good links (particularly the second one) that may help explain 23andme's weird reporting system as it relates to the more common DQ type nomenclature: 

 

http://snpedia.com/index.php/Celiac_Disease

 

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386975/#!po=53.1250 – This is actually a study. Very informative and interesting if you choose to read through the whole thing. However, if you skip to page 10 and click on table 3, you'll find a list of the celiac related DQ types, their SNP tags as well as risk alleles. I'm not sure if 23andme is still testing for all of these SNP tags, but the DQ2.2, DQ2.5 and DQ8 tags still work for me (my chip is from last September/October). I suggest referencing the first link for DQ2.2, because I think they've since updated one of the tags.

 

As others have said, 23andme only looks for DQ2.5 when establishing celiac disease risk, however they are also reporting on a few other SNP's (from different chromosomes or different parts of chromosomes, so non HLA-DQ types) that may be associated with celiac. Their studies and any they cite on these other genes/risk factors have yet to be validated. 

 

Best wishes,

Ninja :)

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I had my doctor order them thru Quest years after I was officially diagnosed.   There are several places that do it.  To my surprise, my insurance paid for it without a peep!  Just proving, that when it comes to Celiac Disease, they haven't a clue.    :o

Nice that they covered it for you, I'll have to ask at my next doctor visit unless I decide that my 23andme snp data is sufficient for me.

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Hi there,

 

Here are two really good links (particularly the second one) that may help explain 23andme's weird reporting system as it relates to the more common DQ type nomenclature: 

 

http://snpedia.com/index.php/Celiac_Disease

 

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386975/#!po=53.1250 – This is actually a study. Very informative and interesting if you choose to read through the whole thing. However, if you skip to page 10 and click on table 3, you'll find a list of the celiac related DQ types, their SNP tags as well as risk alleles. I'm not sure if 23andme is still testing for all of these SNP tags, but the DQ2.2, DQ2.5 and DQ8 tags still work for me (my chip is from last September/October). I suggest referencing the first link for DQ2.2, because I think they've since updated one of the tags.

 

As others have said, 23andme only looks for DQ2.5 when establishing celiac disease risk, however they are also reporting on a few other SNP's (from different chromosomes or different parts of chromosomes, so non HLA-DQ types) that may be associated with celiac. Their studies and any they cite on these other genes/risk factors have yet to be validated. 

 

Best wishes,

Ninja :)

This is great information, particularly table 3 you referenced.  That helped me understand that my DQ type is DQ2.5 since I have a T on s2187668.

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does not everyone have rs4713586? I am very confused as to what this is actually saying. I have DQ8 but what is it will DQ2? You have to have those alleles? in that order exactly on those SNPs? I am trying to find rs4713586 but It does not exist on my file. I am confused, I thought these SNPs were just position on the genome not something else. 

can someone clear my confusion?

 

 

Also how do these genes work? because  the DQ8 is said to be involved in nasal polyps as well, and I have nasal polyps. I am currently trying to figure out if I have celiacs, pretty sure I do. If the gene active for nasal polyps does that mean it is active for celiacs too?

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