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Help Figure Out The Dna -- Who'S Right?


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11 replies to this topic

#1 Traveller

 
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Posted 10 January 2010 - 05:36 PM

Earlier this year I took the Enterolab test, and they said my DNA is HLA-DQ 2,2 (Subtype 2,2). Also "although you do not possess the main HLA-DQB1 genes predisposing to celiac sprue...you have two copies of a gene that predisposes to gluten sensitivity:...
HLA-DQB1 Molecular analysis, Allele 1 0202
HLA-DQB1 Molecular analysis, Allele 2 0202

Wanting to find out more about the genetics to help future generations, I asked my doctor to do a another test. He sent a gene sample to Labcorp. They said I was negative for both DQ2 and DQ8.

Fast forward to the latest test, by Prometheus (myceliacid.com). They said I have one DQ2 --> DQA1*0201/DQB1*02.

Can all the labs be correct?

Do different labs have different definitions of DQ2?

Do I have one beta chain with an alpha that is not DQA1*0201?

How can I make sense of these tests?
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Diagnosed 03/09
Gluten-free since 03/09 (and manic about it)
Looking forward to a better life since 03/09

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#2 Jestgar

 
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Posted 10 January 2010 - 05:41 PM

I don't know specifically how they do the tests, but in general, a genotype test produces a dot for each allele. If you have two of the same alleles, the dots are in the same place and it looks like one dot.

If Enterolab didn't QC their data very well, you might have gotten a read on only one of your alleles (the other one didn't work at all) and since the tech (or machine or whatever) only saw one dot, it concluded that you are homozygous at that allele.

As for the other confusing results, the most likely answer is that one of the labs is wrong, or your sample was contaminated. Were they all from blood samples?

It's also possible (but very very unlikely) that you are a mosaic and have some cells that are completely different. (This could happen if you had a fraternal twin in utero and you absorbed your twin - so really rare.)
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"But then, in all honesty, if scientists don't play god, who will?"
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#3 Traveller

 
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Posted 10 January 2010 - 06:14 PM

I don't know specifically how they do the tests, but in general, a genotype test produces a dot for each allele. If you have two of the same alleles, the dots are in the same place and it looks like one dot.

If Enterolab didn't QC their data very well, you might have gotten a read on only one of your alleles (the other one didn't work at all) and since the tech (or machine or whatever) only saw one dot, it concluded that you are homozygous at that allele.

As for the other confusing results, the most likely answer is that one of the labs is wrong, or your sample was contaminated. Were they all from blood samples?

It's also possible (but very very unlikely) that you are a mosaic and have some cells that are completely different. (This could happen if you had a fraternal twin in utero and you absorbed your twin - so really rare.)


Thanks for the helpful response. Here's one other factoid: Prometheus says my daughter is DQ2 homozygous, and Labcorp says my wife has a DQ2....so apparently Prometheus is consistent in saying I have a DQ2. Does that consistency mean I shoudl believe them over Labcorp?

Prometheus was a saliva sample and Labcorp a blood sample....what does that mean for contamination?
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Diagnosed 03/09
Gluten-free since 03/09 (and manic about it)
Looking forward to a better life since 03/09

#4 Jestgar

 
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Posted 11 January 2010 - 04:51 AM

If your daughter is DQ2 homozygous, then you have DQ2 (or she's not your daughter, but you can take that up with your wife ;) ).

A saliva sample could be contaminated if you kissed your wife before you took the sample, and some of her cells got in to your sample, but...then your daughter is DQ2......

You may be one of those people that is difficult to genotype (I don't know why, but some people never give a clear read for some of their loci), in which case the labs could be misreading, rather than throwing out your poor results.

If you feel like being entertained, send a copy of all your results to each of the labs and ask them to explain the discrepancies.
  • 0
"But then, in all honesty, if scientists don't play god, who will?"
- James Watson

My sources are unreliable, but their information is fascinating.
- Ashleigh Brilliant

Leap, and the net will appear.

#5 nora_n

 
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Posted 11 January 2010 - 07:23 AM

traveller, yes, all the labs are right.

Dq2,2 has DQA10201 DQB1 0202 and enterolab and others call it (nickname is the right word) DQ2,2.

Enterolab gets theirs done at hte American Red Cross and they test the beta chain.

Labcorp actually does test both the alpha and beta chains but they do not tell you. Most doctors would get very confused by the full answer.

They only give you a positive answer if they find DQ 2,5 or DQ8 or half a DQ2 gene, the 05* alpha chain.

Now the DQ2,2 will together with the 05* alpha chain of DQ7 make up the trans version of DQ2,5. That is why some labs bother to test for alpha chains or other genes like DQ7.

Prometheus found the DQ2,2 too but I cannot answer why they did not report you have two copies. Prometheus also tests for alpha chains , in order to detect half genes (alpha05* also is a celiac gene)or the trans DQ2,5.
  • 0
gluten-free since may 06 after neg. biopsy symptoms went away and DH symptoms which I had since 03 got gradually better.
daughter officially diagnosed celiac and casein intolerant.
non-DQ2 or DQ8. Maybe DQ1? Updated: Yes, double DQ5
Hypothyroid since 2000, thyroxine first started to work well 06 on a low-carb and gluten-free diet
Lost 20 kg after going gluten-free and weighing 53 kg now. neg. biopsy for DH. Found out afterwards from this forum that it should have been taken during an outbreak but it was taken two weeks after. vitaminD was 57 nmol/l in may08)

#6 Jestgar

 
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Posted 11 January 2010 - 07:46 AM

Nora, this seems ridiculous, not your interpretation, but that labs would use such different nomenclature.

How could it be that one lab specifically says negative for DQ2, and one lab specifically says positive for DQ2 (one allele) and one lab says no, you have two of the same allele?
  • 0
"But then, in all honesty, if scientists don't play god, who will?"
- James Watson

My sources are unreliable, but their information is fascinating.
- Ashleigh Brilliant

Leap, and the net will appear.

#7 nora_n

 
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Posted 11 January 2010 - 01:09 PM

It is becaue of the DQ2,2 which is not considered a celiac gene, but has maybe slightly higher risk,
and DQ2,5 which is considered the celiac gene. In fact, it is the main celiac gene.

Nomenclature: In the old days it was different, so if you run ito old papers they nicknamed DQ genes something with w in it..

DQ is just nicknames.

To confuse more, in medical literature they often also mention DR type.

If you have jsut started reading about DQ and HLA and DQA1 and stuff, then DR is confusing since they mention DR3 and DR4 and DR7 and so on.

But if you study the pages and lists and tables at en.wikipedia.org , HLA DR , HLA DQ and some of the subpages like HLA DQ2 or DQ2, you get the hang of it.

(there are even more DQ2 types...)

nora
  • 0
gluten-free since may 06 after neg. biopsy symptoms went away and DH symptoms which I had since 03 got gradually better.
daughter officially diagnosed celiac and casein intolerant.
non-DQ2 or DQ8. Maybe DQ1? Updated: Yes, double DQ5
Hypothyroid since 2000, thyroxine first started to work well 06 on a low-carb and gluten-free diet
Lost 20 kg after going gluten-free and weighing 53 kg now. neg. biopsy for DH. Found out afterwards from this forum that it should have been taken during an outbreak but it was taken two weeks after. vitaminD was 57 nmol/l in may08)

#8 CSU Grad

 
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Posted 11 January 2010 - 01:31 PM

It is becaue of the DQ2,2 which is not considered a celiac gene, but has maybe slightly higher risk,
and DQ2,5 which is considered the celiac gene. In fact, it is the main celiac gene.

Nomenclature: In the old days it was different, so if you run ito old papers they nicknamed DQ genes something with w in it..

DQ is just nicknames.

To confuse more, in medical literature they often also mention DR type.

If you have jsut started reading about DQ and HLA and DQA1 and stuff, then DR is confusing since they mention DR3 and DR4 and DR7 and so on.

But if you study the pages and lists and tables at en.wikipedia.org , HLA DR , HLA DQ and some of the subpages like HLA DQ2 or DQ2, you get the hang of it.

(there are even more DQ2 types...)

nora




Please do not use Wikipedia as a source of detailed DNA information. Anyone can post anything they want to there, and they do. If you want valid information please use some other source!
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#9 Traveller

 
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Posted 11 January 2010 - 02:34 PM

Thanks to everyone for the helpful information. From my reading, it appears the only issue of concern is whether I have two DQ2, or one....
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Diagnosed 03/09
Gluten-free since 03/09 (and manic about it)
Looking forward to a better life since 03/09

#10 nora_n

 
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Posted 12 January 2010 - 08:17 AM

About DQ and wikipedia, it has been very enlightening.

There are rumors going on about 12-year-olds who write articles at wikipedia.

But if you check who keeps editing pages, you see that there are certain people watching over certain pages. They will revert the pages if anyone posts...just try editing, and see how long it lasts. It will probably only last some hours or a day. And, I heard they stopped the possibility for anyone to edit now. I have not tried it lately.

The main thing with wikipedia that might be annoying for some, is that it is supposed to reflect the current wiev. Now there are lyme wars and some other wars going on, for ecxample there are two equally valid guidelines, but this Tim Vickers and even more certain others keep reverting it to just one view (those who do not believe there is chronic lyme , and who deny antibiotics to chronic lyme patients) but it might be because they thing there is only one view.

With DQ etc, we mostly check the charts because we want to know what the aplha and beta chaisn are, and what the terminology is.
I have noticed they have updated these pages over time, and it does reflect current views.

Several people here do have celiac in spite of negative gene tests, and of course that is too advanced or controversial for wikipedia.
Gluten ataxia, and the DQ1 thing with gluten ataxia is not really accepted by wikipedia either. (I have not checked lately)
  • 0
gluten-free since may 06 after neg. biopsy symptoms went away and DH symptoms which I had since 03 got gradually better.
daughter officially diagnosed celiac and casein intolerant.
non-DQ2 or DQ8. Maybe DQ1? Updated: Yes, double DQ5
Hypothyroid since 2000, thyroxine first started to work well 06 on a low-carb and gluten-free diet
Lost 20 kg after going gluten-free and weighing 53 kg now. neg. biopsy for DH. Found out afterwards from this forum that it should have been taken during an outbreak but it was taken two weeks after. vitaminD was 57 nmol/l in may08)

#11 CSU Grad

 
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Posted 14 January 2010 - 02:21 PM

You, personally, may be happy with Wikipedia, and that is fine. Not sure where you got the "12 year olds" out of my post, because I didn't say that. Age is not a determinate of intelligence!

Some things to note, however:

If you quote Wikipedia as a source on a university paper you will get an "F".

If you attempt to publish a study using Wikipedia as a source, you will be academically blacklisted and never publish again.

Now, why is that? I suppose one could get all conspiracy theory on us and suggest its the academia putting the little guy down, but the truth is that because it is open to edit by anyone and everyone, the data is not reliable.

Statistically, academically, legally speaking data must be reproducible and defensible especially when used in medicine. Wikipedia is neither, and it is very irresponsible to suggest that someone use Wikipedia for information pertaining to their personal health.


About DQ and wikipedia, it has been very enlightening.

There are rumors going on about 12-year-olds who write articles at wikipedia.

But if you check who keeps editing pages, you see that there are certain people watching over certain pages. They will revert the pages if anyone posts...just try editing, and see how long it lasts. It will probably only last some hours or a day. And, I heard they stopped the possibility for anyone to edit now. I have not tried it lately.

The main thing with wikipedia that might be annoying for some, is that it is supposed to reflect the current wiev. Now there are lyme wars and some other wars going on, for ecxample there are two equally valid guidelines, but this Tim Vickers and even more certain others keep reverting it to just one view (those who do not believe there is chronic lyme , and who deny antibiotics to chronic lyme patients) but it might be because they thing there is only one view.

With DQ etc, we mostly check the charts because we want to know what the aplha and beta chaisn are, and what the terminology is.
I have noticed they have updated these pages over time, and it does reflect current views.

Several people here do have celiac in spite of negative gene tests, and of course that is too advanced or controversial for wikipedia.
Gluten ataxia, and the DQ1 thing with gluten ataxia is not really accepted by wikipedia either. (I have not checked lately)


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#12 nora_n

 
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Posted 15 January 2010 - 11:52 AM

I am not writing a science paper, or having exams.
You remind me of one of my teachers who thought that the internet was just full of nonsense and things written by cranks, and she did not realize that most people do sort the information from the internet.
....I once notified a political party in in a country in Europe that a nationwide tv station in another coutry was showing images of a fake website some people had put up depicting them as racists and spreading awful nazi prppaganda. The tv station had to broadcast that they were wrong or mislead for two days in each of their news programs....

I find the charts at wikipedia, in the articles about HLA DQ and HLA DR, very useful as I have not seen any others anywhere, and wipipedia does explain what the alpha and beta chains look like (so that people can understand their test results, which come in various forms.

If I do not agree with something (i have read other things than wikipedia too), I can comment on that whenever I answer someone. I do not take wikipedia too seriously, I do not neccessarily agree with everything.

Do you have anything useful to add? Any other sites? Any textbooks that are better? There are several medical papers online, but they usually do not explain the basics nor have the charts.

Again, I am not writing a paper here, I just need some good explanation to people who want to understand the basics with the HLA DQ and DR terminology. Even doctors and nurses are terrible at that and get it wrong, and wikipedia has proved to be useful here.

If some other useful site turns up, I can add that one too, or recommend that one, but right now I have none.
  • 0
gluten-free since may 06 after neg. biopsy symptoms went away and DH symptoms which I had since 03 got gradually better.
daughter officially diagnosed celiac and casein intolerant.
non-DQ2 or DQ8. Maybe DQ1? Updated: Yes, double DQ5
Hypothyroid since 2000, thyroxine first started to work well 06 on a low-carb and gluten-free diet
Lost 20 kg after going gluten-free and weighing 53 kg now. neg. biopsy for DH. Found out afterwards from this forum that it should have been taken during an outbreak but it was taken two weeks after. vitaminD was 57 nmol/l in may08)




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