Nod2 without card 15 gene

[my little penguin]

Ds has multiple variants of the nod 2 gene ( per 23 & me)
But no card 15
So anyone know if it's worse to have more than nod 2 variants
Or have the combo

Or does it even matter .

 

[Mehita]

Don't know the answer to your question, but going to look it up on DS's report! Where did you find that data?

 

[my little penguin]

I used Promethease -submitted raw data and got a report
Ds has 149 genes assosciated with crohns
Some are nod 2
Ibd5
IL23R
Etc

It also pickup his arthritis including spondyloarthritis

 

[DustyKat]

My understanding is that NOD2 is also known as Card15, so one and the same.

I don’t know the significance of multiple variants but since it is associated with Crohn’s perhaps the variants influence the time of onset, location, severity and phenotype but that is just me guessing. :shifty-t:

Dusty. xxx

 

[my little penguin]

Thanks Dusty
It is kinda cool to see the DNA confirm the dx which we knew about but still cool.
Gives hope for the future
Much easier to spit in a tube KWIM .

 

[my little penguin]

http://onlinelibrary.wiley.com/stor...087A9E19DCC3D2.f04t02?v=1&t=i2j0k5cr&d327f194

Paper on ibd5

 

[my little penguin]

Backgroud/Purpose

Three common mutations of the NOD2/CARD15 gene have been associated with Crohn disease (CD), ileal disease location, and fibrostenotic behavior. The aim of this study was to investigate the effect of these mutations on disease manifestation and the risk of surgery in a cohort of German childhood–onset CD patients.

Methods

Genotyping for the NOD2 mutations p.Arg702Trp, p.Gly908Arg, and p.1007fs was performed in 171 CD children (onset of disease <17 years; mean 11.8 years) and in 253 controls. NOD2 mutation status was correlated with the need for surgery during childhood.

Results

Seventy-eight children (45.6%) were carriers of at least 1 NOD2 mutation versus 36 (14.2%) in the control group (P < .0001). NOD2 mutations were highly associated with CD and stricturing behavior (P < .0001), with the p.1007fs mutation also conferring a risk for isolated ileal disease (P = .003). Thirty-two children (18.7%) needed an intestinal resection with a significant association between the need of surgery and NOD2 carrier status. Surgery occurred at an earlier stage of disease in children with p.1007fs mutations.

Conclusions

In children with pediatric-onset CD, the need for surgical therapy younger than 17 years is associated with the NOD2 genotype. Genetic testing therefore may identify children with CD who are at risk.

Key words:

Crohn disease, Inflammatory bowel disease, NOD2, CARD15, Mutation, p.1007fs, Strictures, Surgery

☆Presented at the joint congress of the European Paediatric Surgeons' Association and the British Association of Paediatric Surgery, June 2009 in Graz/Austria.

☆☆Authors have no conflicts of interest and no financial relationships relevant to this article to declar

NOD2 mutations predict the risk for surgery in pediatric-onset Crohn's disease☆☆☆

Martin Lacheremail, Johanna Helmbrecht, Sebastian Schroepf, Sibylle Koletzko, Antje Ballauff, Martin Classen, Holm Uhlig, Jochen Hubertus, Dominik Hartl, Peter Lohse, Dietrich von Schweinitz, Roland Kappler
Received: September 7, 2009; Received in revised form: October 9, 2009; Accepted: October 10, 2009;
DOI: http://dx.doi.org/10.1016/j.jpedsurg.2009.10.046



From
http://www.jpedsurg.org/article/S00...tract#/article/S0022-3468(09)00829-X/abstract

 

[my little penguin]

Background
Influence of genetic variants in the NOD2 gene may play a more important role in disease activity, behaviour and treatment of pediatric- than adult-onset Crohn’s disease (CD).
Methods
85 pediatric- and 117 adult-onset CD patients were tested for the three main NOD2 CD-associated variants (p.R702W, p.G908R and p.10007fs) and clinical data of at least two years of follow-up were compared regarding disease behaviour and activity, response to therapy and bone mineral density (BMD).
Results
Chronic active and moderate to severe course of CD is associated in patients with pediatric-onset (p=0.0001) and NOD2 variant alleles (p=0.0001). In pediatric-onset CD the average PCDAI-Score was significantly higher in patients carrying NOD2 variants (p=0.0008). In addition, underweight during course of the disease (p=0.012) was associated with NOD2 variants. Interestingly, osteoporosis was found more frequently in patients carrying NOD2 variant alleles (p=0.033), especially in pediatric-onset CD patients with homozygous NOD2 variants (p=0.037). Accordingly, low BMD in pediatric-onset CD is associated with a higher PCDAI (p=0.0092), chronic active disease (p=0.0148), underweight at diagnosis (p=0.0271) and during follow-up (p=0.0109). Furthermore, pediatric-onset CD patients with NOD2 variants are more frequently steroid-dependent or refractory (p=0.048) and need long-term immunosuppressive therapy (p=0.0213).
Conclusions
These data suggests that the presence of any of the main NOD2 variants in CD is associated with osteoporosis and an age of onset dependent influence towards underweight, higher disease activity and a more intensive immunosuppressive therapy. This observation supports the idea for an early intensive treatment strategy in children and adolescent CD patients with NOD2 gene variants.

Date: 02 May 2013
Age-of-onset-dependent influence of NOD2 gene variants on disease behaviour and treatment in Crohn’s disease

Carsten Posovszky, Veronika Pfalzer, Georgia Lahr, Jan Hendrik Niess, Jochen Klaus, Benjamin Mayer, Klaus-Michael Debatin, Georg BT von Boyen


From
http://link.springer.com/article/10.1186/1471-230X-13-77

 

[my little penguin]

http://biologie.univ-mrs.fr/upload/p87/Economou.pdf

Paper on genes in crohns

 

[my little penguin]

Very cool predicts severity and location
But you need to have more than one nod2
Ds has three


http://deepblue.lib.umich.edu/bitstream/handle/2027.42/83256/Adler-2011-The Prognostic Power.pdf

 

[my little penguin]

Genetic variants in pediatric Crohn’s disease

Phenotypic differences between adult and pediatric onset CD suggest a different genetic predisposition. Pediatric IBD is characterized by extensive intestinal involvement and rapid early progression.80 The increased risk of CD among family members with early-onset disease and the stratification of disease by age of onset has been the focus of many studies in the effort to further ascertain the genetic influence of CD.

Genetic susceptibility may play a more important role in the etiology of early-onset IBD than in late-onset IBD, and therefore pediatric-onset IBD patients can be expected to have a higher frequency of gene mutations. De Ridder and colleagues81 investigated genetic polymorphism in CARD15 and DLG5 and described more frequent occurrence of polymorphisms, 3020insC, in CARD15 and SNP, rs3792876, in SLC22A4/5 in patients with pediatric-onset CD than in patients with adult-onset CD. Polymorphisms 3020insC in CARD15 and SNP rs2165047 in DLG5 were associated with specific phenotypes such as ileal and perianal disease, respectively. In another pediatric study in the GWAS literature,82 a previously unreported susceptibility locus for pediatric-onset IBD at 20q13 and 21q22 was identified, suggesting that TNFRSF6B is the most plausible candidate within the 20q13 locus, involved in both antigen-presenting cell differentiation and lymphocyte function. Autophagy-associated genes (ATG16L1 and IRGM) were also seen in early-onset CD cases, further confirming autophagy as an important contributor in the pathogenesis of pediatric CD.83

Dubinsky et al84 examined associations between the R381Q variant of the IL-23R gene and CD in a pediatric cohort and reported significant associations using a family-based study. Similarly, Van Limbergen et al85 also reported associations with the same SNP in a Scottish cohort of pediatric CD using the case-control design. These reports provide strong evidence that the IL-23R gene is not only associated with adult-onset CD, but similar associations exist for children among most Caucasian populations.

Appl Clin Genet. 2013; 6: 25–32.
Published online Jul 16, 2013. doi: 10.2147/TACG.S33966
PMCID: PMC3735034
Genetic variants associated with Crohn’s disease
Sonia Michail,1 Gilberto Bultron,1 and R William DePaolo2




From

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3735034/

 

[my little penguin]

BACKGROUND AND OBJECTIVES: Interleukin (IL)-23 is a key regulator of inflammation and influences the activities of T-helper 17 (Th-17) lymphocytes. Recent reports indicate that variants in the gene coding for its receptor (IL-23R) are strongly associated with Crohn's disease (CD). We investigated whether DNA variants in the IL-23R gene determine susceptibility for CD in Canadian children.

DESIGN AND METHODS: A case-control and case-parent trio design was implemented at three pediatric centers across Canada. Cases of CD (</=20 yr) along with their parents and controls were recruited. DNA samples were collected and genotyped for 10 single nucleotide polymorphisms (SNPs) in the IL-23R gene and three common SNPs in the CARD15 gene. Transmission disequilibrium-based tests were applied to the case-parent data and logistic regression models to the case-control data to study the association between the SNPs and CD.

RESULTS: A total of 259 CD cases, 139 controls, and 232 families (167 trios and 65 dyads) were studied. The mean age at diagnosis was 13.3 yr (range 2.6-20 yr). The majority of the patients were Caucasian. Case-control analysis revealed significant associations with three SNPs (rs1004819, rs7517847, and rs11209026 [R381Q]) and borderline nonsignificant associations with three other SNPs (rs10489629, rs10889697, and rs11465804) in the IL-23R gene. Having any CARD15 variant was associated with a significant risk for CD (P < 0.0001). Analyses of case-parent data confirmed the findings from the case-control analysis including significant associations with the R381Q SNP (P= 0.002). The common variant in this SNP conferred risk for CD. These associations were largely independent of the CARD15 gene.

CONCLUSIONS: Our findings confirm recently reported genome-wide associations between the IL-23R gene and CD. They suggest that the gene is also associated with pediatric-onset CD among Canadian children.

From
http://www.ncbi.nlm.nih.gov/m/pubmed/18047539/

 

[DustyKat]

Thanks so much for all the research references mlp! :thumleft:

Thanks Dusty
It is kinda cool to see the DNA confirm the dx which we knew about but still cool.
Gives hope for the future
Much easier to spit in a tube KWIM .

Oh yeah, a spit is so much more user friendly than a needle! :lol:

I wish we had access to the 23 and me study.

I am with you mlp, as much as I hate the confirmation I do love to see the marry up with these sort of tests and the thoughts of where this may take us in the future.

The ASCA tests weren’t available here when my kids were diagnosed but when Sarah was unwell with gastro symptoms back in August the GP ordered it. I wasn’t sure why he did as we knew what we were dealing with but it surely did pique my curiosity as to what the results would be. She was indeed positive. I imagine Matt would be positive too.

I have been having my own abdo issues of late. The GP thinks its Crohn’s but I don’t agree. As a result he ran the ASCA test and I am negative but of course it is far from a decisive test and not one to diagnose so scopes for me it is! :eek2:

Matt has just had his regular bloods drawn and although neither of the kids have had confirmed arthritic associations with their CD they do occasionally complain of lower back pain. The GP and GI don’t think it is a Crohn’s related arthropathy but I have had the GP run HLA B27 just out of curiosity, so it will be interesting to see if he does carry the antigen. Forewarned is forearmed as they say! :lol:

I can’t sign off though mlp without making mention of how sorry I am to see that your lad carries three variations of NOD2. The upside is that he has such a formidable advocate :thumright: and knowledgable and caring Mum :rosette1: to help him navigate through the maze of what life has already thrown at him and with whatever the future holds. It goes without saying that I hope the future is a bright and smooth sailing one. :ghug:

Dusty. xxx

 

[my little penguin]

I was tired and didn't count right
Ds has
5 variants of NOD 2
3 variants of ATG16 L1
14 variants. IL23R
4 variants of IBD 5
1 variants SLC 22A4
1 variant CDKALI
1 variant BSN

Among the known ( published ones )
Plus more
Kiddo didn't stand a chance

Dusty
Most SpA kids do not have HLA B27 when they have crohns ...

 

[Pilgrim]

I hope we can access the tests when our daughter is 6 in a few years.

What an incredible amount of information.

 

[Maya142]

I believe ASCA is associated with AS (and IBD of course) though. Both my daughters are HLA B27+ and my husband is HLA B27+ and ASCA+ (we never tested the girls).

Dusty, if your son does happen to be HLA B27+ and continues to have lower back pain (even if it is mild), I would get him to a rheumatologist fast. Just to be safe...

 

[my little penguin]

Genomic DNA from 2700 Caucasians including 812 patients with Crohn's disease (CD), 442 patients with ulcerative colitis (UC), and 1446 healthy controls was analyzed for the NOD2 SNPs rs2066843 and rs2076756 and the three main CD-associated NOD2 variants p.Arg702Trp (rs2066844), p.Gly908Arg (rs2066847), and p.Leu1007fsX1008 (rs2066847). Haplotype and genotype-phenotype analyses were performed. The SNPs rs2066843 (p = 3.01×10−5, OR 1.48, [95% CI 1.23-1.78]) and rs2076756 (p = 4.01×10−6; OR 1.54, [95% CI 1.28-1.86]) were significantly associated with CD but not with UC susceptibility. Haplotype analysis revealed a number of significant associations with CD susceptibility with omnibus p values <10−10. The SNPs rs2066843 and rs2076756 were in linkage disequilibrium with each other and with the three main CD-associated NOD2 mutations (D'>0.9). However, in CD, SNPs rs2066843 and rs2076756 were more frequently observed than the other three common NOD2 mutations (minor allele frequencies for rs2066843 and rs2076756: 0.390 and 0.380, respectively). In CD patients homozygous for these novel NOD2 variants, genotype-phenotype analysis revealed higher rates of a penetrating phenotype (rs2076756: p = 0.015) and fistulas (rs2076756: p = 0.015) and significant associations with CD-related surgery (rs2076756: p = 0.003; rs2066843: p = 0.015). However, in multivariate analysis only disease localization (p<2×10−16) and behaviour (p = 0.02) were significantly associated with the need for surgery.

The NOD2 Single Nucleotide Polymorphisms rs2066843 and rs2076756 Are Novel and Common Crohn's Disease Susceptibility Gene Variants
Jürgen Glas, Julia Seiderer, Cornelia Tillack, Simone Pfennig, Florian Beigel, Matthias Jürgens, [...view 9 more...], Stephan Brand


From
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0014466

 

[my little penguin]

RESULTS: ATG16L1, IBD5, and IL23R SNPs were significantly associated with CD. Multivariate analysis showed independent CD association for carriers of ATG16L1 (odds ratio [OR] = 1.8, 95% confidence interval [CI] 1.09-3.24), IBD5-IGR2230 (OR = 2.16, 95% CI 1.30-3.59), and IL23R-rs10889677 (OR = 2.13, 95% CI 1.39-3.28) while retaining association for NOD2 mutation carriers (OR = 4.45, 95% CI 2.68-7.38), IBD family history (OR = 2.75, 95% CI 1.42-5.31), tobacco (OR = 2.06, 95% CI 1.35-3.14), and Jewish ethnicity (OR = 20.1, 95% CI 2.16-186.8). IL23R minor variants for Arg381Gln and Intron 6 rs7517848 showed independent, CD protection and 3' untranslated variant rs108896778 showed risk. MDR analysis suggested an interaction between IBD5, ATG16L1, and IL23R risk alleles. Penetrance values for ATG16L1 and IBD5 were 0.27% for heterozygotes, and 0.35% and 0.44%, respectively, for homozygotes. IL23R rs108896778 penetrance was 0.37%

Contributions of IBD5, IL23R, ATG16L1, and NOD2 to Crohn's disease risk in a population-based case-control study: evidence of gene-gene interactions.

Authors
Okazaki T1, Wang MH, Rawsthorne P, Sargent M, Datta LW, Shugart YY, Bernstein CN, Brant SR.
Author information
Journal
Inflamm Bowel Dis. 2008 Nov;14(11):1528-41. doi: 10.1002/ibd.20512.


From
http://www.ncbi.nlm.nih.gov/m/pubmed/18521914/

 

[my little penguin]

https://www.scienceopen.com/documen...tral/7ca28ec8-2b6b-4889-930a-d29bf0aeb1e6.pdf

Gene mutations pediayric crohns

 

[DustyKat]

Matt’s HLA B27+ result: Not detected.

 

[Brian'sMom]

Thanks MLP for all the research!

 

[kimmidwife]

Thanks MLP!
We got the 23 and me results and now have to do the second part to see the medical genetics. I plan to do it tomorrow.

 

[Mehita]

I'm confused. I have DS's SNPedia report which we saved as an Excel file. Where are you seeing all the IBD related info, MLP? I see it in the notes column, but how do I know what gene and node I'm looking at?

Some things I found interesting...
- as expected, IBD came up several times
- has an issue metabolizing NSAIDS
- has a high metabolism in general
- cannot process warfarin
- the known health issues we have in our family showed up in one form or another (cholesterol, heart disease)
- he's male (*LOL*)
- lacks empathy
- chance of Celiac (!)

 

[Maya142]

M had some of the same things - issues metabolizing NSAID (she's been on an NSAID for the last 5 years, no real problems), IBD genes, AS genes, heart disease etc.

If you used Prometheus ("Promethease") to interpret the raw data from 23 and me, there is a Table function on the right which displays the genes for particular illness (for example: Crohns) and will tell you the genes (NOD2, IL23R etc.).