Help vetting HLA-DQ typing provider

[John1]

My doctor said it is not available to them so I am looking for a private company to get it done.

I found "Intolerances & Sensitivities DNA Test" advertised by a well known pharmacy in the country I live.

Quote

What's analysed in our food sensitivities test

Gluten intolerance

rs2187668
rs2395182
rs4639334
rs4713586
rs7454108
rs7775228

Does this look right, are they testing for the correct genes, are there any that are missing?

I am not good with biology and really do not have a clue when it comes to this kind of stuff. I do know that HLA-DQ typing is not a diagnosis, I would like the test as a chance to exclude it as a possibility.

Any wisdom would be greatly appreciated!

[Wends]

I’ve done quite a bit of research reading and the science is ongoing, there’s new genes associated with Coeliac being discovered. It may come down to genetic ancestry as recently HLADQ7 is a new one that is not tested for in the standard test. This may account for the less than 1% of coeliacs without DQ2 or DQ8 high risk alleles. It’s true most Northern European Coeliacs (90%) have the HLADQ2, and HLADQ8 (9%). Its fascinating research and it just reinforces the gold standard of a biopsy in diagnosis at present in the absence of the standard DQ2 and 8 typing as the less than 1% may be missed. 

According to this company, these are the full susceptible genes presently known and tested for in the extended test. They do the standard test of the 2 markers (same as NHS hospital testing, I’ve had this done) most common high risk genes, HLADQ2 and HLADQ8.

16 markers in addition to the standard ones.

DQA1*01, DQA1*02:01, DQA1*03, DQA1*05, DQA1*06, DQB1*02, DQB1*03:01, DQB1*03:02,
DQB1*03:03, DQB1*03:04, DQB1*03:05, DQB1*04, DRB1*03, DRB1*04, DRB1*07, DRB1*11

Hope that’s helpful!

[Wends]

Hi John1.

My first reply was moderated because I mentioned a different company that test to the one you asked about. Not sure why. I’m newbie on here too! Anyway. And the one I was referring to is what lead me to research and read recent papers on Pubmed on the HLADQ7 allele, which is rarer. I’m awaiting results.

The markers are quoted from a different company, not the one you refer to (just so the first reply makes sense).

I only understand the celiac disease gene typing as referenced. And how the NHS hospital reported it. Sorry don’t know enough on how that relates to the genes beginning with rs… you list.

Hopefully you get some more replies on this one.

 

[Scott Adams]

At this point all celiac disease markers haven't yet been discovered, so no genetic test could completely rule out celiac disease, although you might be 98%+ sure that you don't carry the genes if you tested negative. As for non-celiac gluten sensitivity, the research on this is just beginning, and as far as I know there may not yet be genetic markers identified for it, and they currently don't have an agreed upon way to diagnose it, other than with an elimination diet. 

[John1]

On 8/11/2024 at 8:31 PM, Wends said:

Hi John1.

My first reply was moderated because I mentioned a different company that test to the one you asked about. Not sure why. I’m newbie on here too! Anyway. And the one I was referring to is what lead me to research and read recent papers on Pubmed on the HLADQ7 allele, which is rarer. I’m awaiting results.

The markers are quoted from a different company, not the one you refer to (just so the first reply makes sense).

I only understand the celiac disease gene typing as referenced. And how the NHS hospital reported it. Sorry don’t know enough on how that relates to the genes beginning with rs… you list.

Hopefully you get some more replies on this one.

 

Thanks for your sharing what you've learned so far, you have definitely gone deeper into the biological side of things than I have.

I emailed the company I'm looking into and they told me that they check for the following HLA alleles.

• HLA-DQA1
• HLA-DQB1
• HLA-DQ7
• HLA-DQB1
• HLA-DQ 2.2
• HLA-DQ 2.2

Any incite as to whether this is above or below what the average HLA typing checks for would very helpful.

On 8/12/2024 at 5:53 PM, Scott Adams said:

At this point all celiac disease markers haven't yet been discovered, so no genetic test could completely rule out celiac disease, although you might be 98%+ sure that you don't carry the genes if you tested negative. As for non-celiac gluten sensitivity, the research on this is just beginning, and as far as I know there may not yet be genetic markers identified for it, and they currently don't have an agreed upon way to diagnose it, other than with an elimination diet. 

Thanks for confirming!

I don't have a very strong suspicion of Celiac, I'm leaning more towards a fructan sensitivity at the moment as I have been reacting to certain fructan foods.

I know that HLA typing isn't a diagnosis, or even an absolute disqualifier, although having a completely negative result would definitely give me the extra confidence I need to attempt the gluten challenge, knowing that it's much more than likely not doing damage. Obviously if my symptoms don't go away even with small amounts I will have to ask my doctor for a referral.

[Wends]

23 hours ago, John1 said:

Thanks for your sharing what you've learned so far, you have definitely gone deeper into the biological side of things than I have.

I emailed the company I'm looking into and they told me that they check for the following HLA alleles.

• HLA-DQA1
• HLA-DQB1
• HLA-DQ7
• HLA-DQB1
• HLA-DQ 2.2
• HLA-DQ 2.2

Any incite as to whether this is above or below what the average HLA typing checks for would very helpful.

Hi John,

yes they are the alleles currently known that are associated with risk of Coeliac disease. So a useful test to know your susceptibility, including the newer DQ7 rarer allele.

I’m personally interested in the newer HLA-DQ7, as wasn’t tested for that on the NHS; they test for the standard High Risk alleles - HLA-DQA1, HLA-DQB1 (DQ2.5 and DQ8, and the DQ2.2 which is technically half and lower risk than having two copies. I’m not a geneticist but that was my understanding of reading scientific papers on it. The higher risk is HLA-DQ2.5, followed by DQ8 alleles - as reported in Europe and the US. Hope that makes sense. I’m still learning about this myself and just starting to get my head round it so to speak. I was never satisfied with the unconfirmed diagnosis of less than 1% risk of it being coeliac disease when I was so ill on a gluten containing diet and gluten challenge. I have a science and research background and love reading journals so started to look into it. It’s quoted from a European review study that 0.7% of biopsy diagnosed coeliacs disease patients do not have the DQ2 and DQ8 high risk alleles. In an Italian study the newer DQ7 quoted to be associated in patients not having the standard alleles. In addition the DQ7 is associated with milk protein sensitivity. (Research shows about 50% of coeliacs react to milk the same as gluten. I’m waiting for more research to be done on that one!).

Good luck and hope you get answers you are looking for.

[cameo674]

So those rs numbers tell researchers where the dbSNP is located in a Genome so that other reasearchers or an AI system can look in that specific spot for that Snip of information.  You can look those rs # s by pasting the numbers after rs into the lookup on this page https://www.ncbi.nlm.nih.gov/snp/ right under the Blue header bar at the top of the webpage.  Since you are not a researcher, I do not know how this will help you though.