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Thread: Promethease report on c(o)eliac disease

  1. #1
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    Promethease report on c(o)eliac disease

    I ran Promethease on my AncestryDNA data the other day. My sister is apparently positive for coeliac disease. My report says this at the top:


    rs2187668(A;G)
    Magnitude: 2.1
    Frequency: 15.9%
    Repute:Bad
    References:10
    Somewhat increased autoimmune disorder (lupus, celiac disease) risk; 1 HLA-DRB1*0301 allele
    In at least UK populations, and perhaps others, SNP rs2187668 is a tag SNP for the HLA-DRB1*0301 allele. The HLA-DRB1*0301 allele is the allele presenting the highest risk for developing lupus, and it appears to act in a dominant manner (i.e. inheriting 2 copies is no worse than inheriting 1 copy). In dbSNP orientation, the risk allele is rs2187668(A), with an odds ratio of 2.3x (CI: 1.7 - 3.2, permuted p < 0.0001). From individuals with the most common rs2187668(G;G) genotype, risk is reduced for celiac disease, with an odds ratio of 0.30x according to a study of ~800 patients. rs2187668(A) also tags the tightly linked DQB1*0201 allele, which in turn is linked to DQA1*0501; together, these are known as the DQ2.5 haplotype. This is the most common haplotype associated with celiac diseas...

    Our local health website says this:
    It is a multigenetic disorder, associated with HLA types HLA-DQ2 (90%) or HLA-DQ8, plus other genetic or environmental factors. HLA typing indicating lack of DQ2 or DQ8 has a high negative predictive value, which may be useful if trying to exclude coeliac disease.[2]

    However I don't have any symptoms of the disease.
    Last edited by MacUalraig; 10-12-2015 at 12:55 PM.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019, Chronomics Jan 2020, Sano Genetics Feb 2020, Nebula Genomics June 2020, YSEQ WGS400 Feb 2022)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content
    FBIMatch: A------ (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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     paulgill (10-13-2015)

  3. #2
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    "Approximately 95% of patients express HLA-DQ2 and the remainder express DQ8. Twenty to thirty percent of the general population are HLA-DQ2 positive, so clearly there are other, as yet, unidentified factors determining the onset of coeliac disease in a fraction of this group. It is estimated by linkage studies that HLA genes account for only 40% of the heritability of coeliac disease."

    http://www.bsg.org.uk/images/stories...coeliac_10.pdf

    What confused me a bit was my family suggestion I should test for it - but it seems there isn't any point unless you have the symptoms ;-)
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019, Chronomics Jan 2020, Sano Genetics Feb 2020, Nebula Genomics June 2020, YSEQ WGS400 Feb 2022)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content
    FBIMatch: A------ (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

  4. The Following User Says Thank You to MacUalraig For This Useful Post:

     paulgill (10-13-2015)

  5. #3
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    I just ran Promethease, and also have a celiac factor, with no symptoms.

    rs3184504(T;T)
    increased risk for celiac disease increased resistance to bacterial infections

    Bad Repute
    3 Magnitude
    21.4% Frequency
    0.2181 GMAF
    33 References

    Of course, with a 450 page report of medical conditions, you would think I would have died at least 40 years ago.

  6. The Following User Says Thank You to Torc Seanathair For This Useful Post:

     MacUalraig (12-08-2015)

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    HV0

    Turkey Iraq Azerbaijan Turkmenistan Transcaucasian Federation Catalonia
    Bad Repute
    2 Magnitude
    45.5% Frequency
    0.2181 GMAF
    31 References
    SH2B3 Gene
    12 Chromosome
    111446804 Position
    3 Max Magnitude

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