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Crohn's Disease Forum » Parents of Kids with IBD » Have you done DNA analysis?


02-28-2015, 10:25 PM   #1
Crohnick
 
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Have you done DNA analysis?

Have you done a DNA analysis such as 23andMe on your child (or yourself)? If so does it express the gs221 SNP (marker for DQ2 haplotype)? I just want to see how strong the association is between this gene and IBD. Thanks for your response.
02-28-2015, 10:30 PM   #2
my little penguin
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We did it for DS .
I would have to look
If you send the raw data to promethease for $5
They generate a nice report including all SNP ever associated with Ibd crohns or uc.
DS has 148 different Snp associated with Ibd including nod2
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02-28-2015, 10:34 PM   #3
my little penguin
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Also you can have a gene but not the mutation
You have to have a specific SNP number with a specific risk allele combo ( a:g etc...)
Again SNP are extremely primitive in the land of genetics
Most genetist wont touch them .
The SNP association is only based on a single paper study a single group who happened to have that SNP risk allele . Sometimes there are multiple groups or papers so a stronger correlation can be made. Again just a word of caution since for every paper proving one thing there are multiple papers disproving the same thing
03-01-2015, 03:35 PM   #4
Crohnick
 
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Also you can have a gene but not the mutation
You have to have a specific SNP number with a specific risk allele combo ( a:g etc...)
Again SNP are extremely primitive in the land of genetics
Most genetist wont touch them .
The SNP association is only based on a single paper study a single group who happened to have that SNP risk allele . Sometimes there are multiple groups or papers so a stronger correlation can be made. Again just a word of caution since for every paper proving one thing there are multiple papers disproving the same thing
Thanks for shedding some light on this for me. I ran the raw data through Promethease. There was no allele listed with gs221 that I asked about in my original post, just the gene (no letters in parentheses).

As far as Crohn's, 8 showed up, ranging from 1.52 - 1.09 X risk factors. And there were a couple more at normal risk.
03-01-2015, 04:44 PM   #5
Maya142
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So interesting that there's such a large variation -- my daughter had 142 different SNP associated with IBD.

One of the rheumatologists we see (who does a LOT of research) does not like the 23 and me data - says it does not take into account gene to gene interaction, whatever that means. So I just take it with a grain of salt.
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Mom of M (20)
diagnosed with Crohn's Disease at 16
Juvenile Idiopathic Arthritis at 12
Juvenile Ankylosing Spondylitis at 16

Mom of S (23)
dx with JIA at 14
Ankylosing Spondylitis at 18
03-01-2015, 07:04 PM   #6
Crohnick
 
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So interesting that there's such a large variation -- my daughter had 142 different SNP associated with IBD.

One of the rheumatologists we see (who does a LOT of research) does not like the 23 and me data - says it does not take into account gene to gene interaction, whatever that means. So I just take it with a grain of salt.
It's interesting you mention gene-to-gene interaction, because my son's data had a handful of genes that were "protective" against auto-immune and IBD.

If you don't mind my asking, does your daughter's report list the gs221 gene (as a risk for "auto-immune disease")?
03-01-2015, 07:29 PM   #7
Maya142
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Couldn't find it. Would it be under IBD (using the Promethease report)?
03-01-2015, 09:42 PM   #8
Crohnick
 
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Couldn't find it. Would it be under IBD (using the Promethease report)?
My report has a search box at the top left. I type in gs221 and it comes back with this result, highlighted in a red box.

gs221 Autoimmune disorder risk in Europeans
03-01-2015, 10:28 PM   #9
Maya142
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Nope, she doesn't have that particular gene. Many others for autoimmune disease - besides Crohn's and AS, also Lupus, RA and Systemic Sclerosis.
03-01-2015, 10:55 PM   #10
my little penguin
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Everything I googled relates it to celiac
Celiac , RA, As, crohns and sle /scleroderma all overlap sharing the same mutations on genes
Also they way we explain 23&me
It like knowing a grandparent or great great aunt had heart disease or liver disease etc...
You are just at a slightly higher risk but may never contract those diseases

Same with having the gene mutations .
03-02-2015, 12:54 PM   #11
radmap
 
Join Date: Mar 2015
In SNPedia, which Promethease reports are based on, there are both single SNPs and combinations of SNPs. Combinations (sets) of SNPs are called genosets, and the abbreviation is "gs", so Gs221 is genoset #221.

To find out more about the publication that says what the consequence of having that combination of SNPs is, either go to the Gs page in SNPedia or click on the /criteria link from that page, which lists the SNP names.

In this case, the cited publication says your risk is based on which two HLA DQ molecules you are carrying (look at Table 1). Gs221 says you have one DQ2.2 but to get a better estimate of autoimmune risk you need to know what your other HLA-DQ allele is.
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