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Need Help With Genetics Interpretation


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#1 domesticactivist

 
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Posted 29 October 2011 - 03:36 PM

My kids both had genetic testing done a while ago and I'm revisiting the results. I'm wondering what they imply for my own genetics. We can't afford to have me tested, and I can't do the blood tests since I've been gluten-free for nearly a year.

Bear in mind, the kids have different biological fathers (whose genetic info is inaccessible).

DQA1

SON
DQA1 -
(0505/0509
and
a )0505/0509
or
b ) 0508 rare)

DETECTED: DQA1*0501/0505
homozygous for 0505


DAUGHTER
DQA1 -
(010201/010202/010203 and 0103)
OR
(010204 and 0103)

NOT DETECTED: DQA1*0501/0505

Does this mean that I must possess one copy of DQA1*0501/0505 and then either of the values listed for my daughter?

Would one copy of DQA1*0501/0505 still pose risk regarding gluten?

DQA1*0103 is protective against celiac according to Wiki... and it looks possible that I would have both this and the risk factor. Do they cancel each other out? Or is it about the combination of this gene with whatever the DQB1 is that is more important?



DQB1 -

SON
(030101/030104/0313/0319/0322/0324
and
a ) homo
or
b ) 030103/0316
or
c )0321
)
OR
(030103/0316 and 0321)

NOT DETECTED: DQB1*0201/0202
NOT DETECTED: DQB1*0302

So does this mean that my son does not have DQ2 or 2.2 or 2.5, but does most likely have DQ7.5? (combo of DQA1*0505 and DQB1*0301)?

DAUGHTER
DQB1 -
(
060301 and
a ) 060401/06027/0634
or
b ) 060403
)
OR
(
060401/0627/0634 and
a )0626N
or
b)0628
)
OR
(
060403 and
a )0626N
or
b )0628
)
OR
(0607/0632 and 060802/0621)

NOT DETECTED: DQB1*0201/0202
NOT DETECTED: DQB1*0302

That's a mind-numbing list of possibilities, but all look like 06*, no celiac risk factors at all for my daughter, yes?

By extension, I'm wondering if it follows that my genetics would be:

DQA1*0501/0505
AND
DQA1*0103 OR DQA1*010204 OR DQA1*010201/010202/010203

DQB1
the list is way long here, but I'd be having one of my daughters 06* numbers and one of my son's 03* numbers, yeah?

I'm guessing that when there is the "/" in this case, that indicates that those are all the possibilities for a give allele in light of the testing accuracy. Does it mean something else?

Thanks in advance!
  • 0
Our family is transitioning off the GAPS Intro Diet and into the Full GAPS Diet.
Gluten-Free since November 2010
GAPS Diet since January/February 2011
me - not tested for celiac - currently doing a gluten challenge since 11/26/2011
partner - not tested for celiac
ds - age 11, hospitalized 9/2010, celiac dx by gluten reaction & genetics. No biopsy or blood as we were already gluten-free by the time it was an option.
dd - age 12.5, not celiac, has Tourette's syndome
both kids have now-resolved attention issues.

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#2 Mari

 
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Posted 31 October 2011 - 10:14 PM

This report reminds me of a tissue typing report, a woman had been tested for compatibility for a bone marrow transplant and it seemed she did have one of the main celiac gene DQ B alleles. The DQ B alleles correlate more than 99% with a predisposition to develop celiac disease so for this purpose the results of the DQ A alleles can be ignored. The DQ B *06 alleles are a subgroup of DQ B *01 and some of them confer a risk for developing non-celiac sprue. This is a gluten induced leaky gut syndrome. It appears the neither child has inherited a Main Celiac Gene (DQ2 or DQ8) but there are rare combinations of some of the other DQ B alleles that put the person at risk.
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DQ6/DQ8
HLA-DQ B allele 1 *0602: HLA-DQ B allele 2 *0302
Gluten free and Cow Dairy free since 2006

#3 Skylark

 
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Posted 02 November 2011 - 07:39 PM

OK. The genes separated by slashes are similar enough that the PCR test cannot tell them apart. Your son does have two copies of A1*0505 or something very similar, so you also have a copy.

The 030101, 0321, and, 030103, and 030104 are all DQ7 (B1*0301) variants. (reference is http://onlinelibrary...08.01070.x/full) I can't figure out the others but they will be similar since the PCR cannot tell them apart. In caucasian Americans DQ7 is inherited with A1*0505 97% of the time because DQA1 and DQB1 are in strong linkage disequilibrium. He is very likely double DQ7.5, or something very close. It's not surprising that gluten made him so sick.

Your daughter is some "flavor" of DQ6. Given US population frequencies she is most likely 0102/0604 on one chromosome and 0103/0603 on the other. (DQ6.3 and DQ6.4)

That was handy of your kids to get totally different genes AND be close to homozygous. :lol: You are probably DQ7.5 on one chromosome and DQ6.3 or 6.4 on the other. Even if you're unusual and don't have DQ7, A1*0505 is currently considered a celiac risk gene because there are celiacs with only *0505 and not DQ2 or DQ8.
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#4 domesticactivist

 
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Posted 02 November 2011 - 08:05 PM

Thank you!!! You've really helped, Skylark :)
  • 0
Our family is transitioning off the GAPS Intro Diet and into the Full GAPS Diet.
Gluten-Free since November 2010
GAPS Diet since January/February 2011
me - not tested for celiac - currently doing a gluten challenge since 11/26/2011
partner - not tested for celiac
ds - age 11, hospitalized 9/2010, celiac dx by gluten reaction & genetics. No biopsy or blood as we were already gluten-free by the time it was an option.
dd - age 12.5, not celiac, has Tourette's syndome
both kids have now-resolved attention issues.

#5 nora_n

 
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Posted 04 November 2011 - 07:20 AM

It is interesting to follow gene test results over time.

Some years ago they usually only did the beta chains, then Dr. Lewey contacted labs to get them to test alpha chains since he had two patients who were positive on biopsies and symptoms, but negative beta chains. He suspected they had half a gene (which is usually 05* in alpha)

Now we see that they are able or trying to differentiate a bit inside 0301. (0301=DQ7)

by the way, there was one officially diagnosed DQ6 celiac here a long time ago, and one more posted

DQ7 can be celiac
http://www.clinchem..../full/44/8/1755
  • 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 domesticactivist

 
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Posted 04 November 2011 - 07:24 AM

:) nora_n btw Not all labs will do the alpha testing and tell the full results. I used Kimball Genetics division of Labcorp for this reason. I did have to call the councilor for the full results after just receiving the summary they sent to my dr.
  • 0
Our family is transitioning off the GAPS Intro Diet and into the Full GAPS Diet.
Gluten-Free since November 2010
GAPS Diet since January/February 2011
me - not tested for celiac - currently doing a gluten challenge since 11/26/2011
partner - not tested for celiac
ds - age 11, hospitalized 9/2010, celiac dx by gluten reaction & genetics. No biopsy or blood as we were already gluten-free by the time it was an option.
dd - age 12.5, not celiac, has Tourette's syndome
both kids have now-resolved attention issues.

#7 Skylark

 
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Posted 04 November 2011 - 09:11 AM

It is interesting to follow gene test results over time.

Some years ago they usually only did the beta chains, then Dr. Lewey contacted labs to get them to test alpha chains since he had two patients who were positive on biopsies and symptoms, but negative beta chains. He suspected they had half a gene (which is usually 05* in alpha)

Now we see that they are able or trying to differentiate a bit inside 0301. (0301=DQ7)

It is interesting to see all the genetic variation. A lot of the variants are single nucleotide changes and they don't even change the protein, like *0501 and *0505. Others are single amino acid changes and it's hard to know for sure whether or not the amino acid could change how well HLA binds to deamidated gliadin.

What will be REALLY interesting is when sequencing becomes the standard for genetic testing rather than PCR. It's probably only a matter of time as sequencing gets cheaper and cheaper. Then the number of tiny polymorphisms in the HLA alleles will really explode.
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#8 nora_n

 
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Posted 05 November 2011 - 01:39 AM

Yes, several people have posted they had to get the full results themselves!

I was just thinking, we have these huge discussions in Northern Europe on the celiac boards and celiac facebook pages about difference in sensitivity (wheat starch vs food not originally made from wheat, typically glucose and other sugars also bother the sensitive glunten intolerant people)

Now I was thinking that all these variations in the HLA DQ where the binding sites for gliadin and gliadin-like peptides are, these variations can explain that some do not tolerate wheat starch andn glucose etc.
--They say that the government food agency has not found any gluten in items that contain glucose from wheat, and that we believe in superstition (se who get sick from for example glucose from wheat starch) but I tried to point out that gliadin tests are notorious for not being accurate for small amounts of gluten, and that highly processed gluten and hydrolyzed gluten is almost not picked up by the tests.

In wheat there is about half gliadin and half glutenin, and other gliadin-and glutenin-like peptides, and luckily the wikipedia page on wheat allergy lists some http://en.wikipedia....i/Wheat_allergy likewise different gluten sensitive people may react to different forms of gliadins.
http://en.wikipedia.org/wiki/Gliadin

I only used wikipedia because it is easy to look there
  • 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)

#9 Di2011

 
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Posted 05 November 2011 - 02:26 AM

Yes, several people have posted they had to get the full results themselves!

I was just thinking, we have these huge discussions in Northern Europe on the celiac boards and celiac facebook pages about difference in sensitivity (wheat starch vs food not originally made from wheat, typically glucose and other sugars also bother the sensitive glunten intolerant people)

Hi Nora_N
I can't seem to tolerate the so-called "Gluten-Free" deriviatives such a glucoses, gums, thickeners, E400 additives etc and wonder if there is any such discussion amongst you Northern European board members?
Di
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#10 nora_n

 
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Posted 06 November 2011 - 04:26 AM

Yes, right now there are heated discussions on facebook , swedish celiacs about glucoses etc.

We have had them on norwegian forums too, but not so much about glucose.

The majority does seem to tolerate wheat starch and glucose, but the minority, we do not know how many, do not tolerate wheat starch or things that are originated from it.
Maltodextrin too, anything originally from wheat.
I also react to citric acid (which is made from moldy starch)
  • 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 domesticactivist

 
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Posted 28 January 2012 - 11:16 AM

Bump for all the people thinking about genetics right now.
  • 0
Our family is transitioning off the GAPS Intro Diet and into the Full GAPS Diet.
Gluten-Free since November 2010
GAPS Diet since January/February 2011
me - not tested for celiac - currently doing a gluten challenge since 11/26/2011
partner - not tested for celiac
ds - age 11, hospitalized 9/2010, celiac dx by gluten reaction & genetics. No biopsy or blood as we were already gluten-free by the time it was an option.
dd - age 12.5, not celiac, has Tourette's syndome
both kids have now-resolved attention issues.




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