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HLA DR in 23andMe Gene Set

Valentijn

Senior Member
Messages
15,786
@Valentijn can I be cheeky and ask if you could do the same for me? The only problem is I have tried to upload my raw data file from 23andme but I can't seem to upload the file on here. I am on an iPad I don't know whether that makes any difference. Is there a way I can just copy and paste the Missence mutations data to you? How would find them in my raw data on 23andme? Thank you very much.
One thing you can try is directly using the program downloaded from https://sourceforge.net/projects/analyzemygenes/ and also download and unzip ten_percent.zip and remarks.zip from https://sourceforge.net/projects/analyzemygenes/files/Databases/ into the same folder.

Then it can run with your raw text results, and generate a text file or pdf with the rare results. If the text file is opened with Excel (comma separations) then you can sort based on BLOSUM scores to get a shorter list of missense mutations. -4 is mostly likely to cause problems (but often doesn't), and 4 is no change to the gene's product. Then you can look up the mutations on dbSNP or by gene on OMIM.

But if you're struggling with any of that, I'm happy to take a look.
 

btdt

Senior Member
Messages
161
Location
Ontario
I really need to do this
https://sourceforge.net/projects/analyzemygenes/ and also download and unzip ten_percent.zip and remarks.zip from https://sourceforge.net/projects/analyzemygenes/files/Databases/ into the same folder.

but last chance I failed... I need to get to this thread first when I have what it takes to get here and do it before I am tired I only have so much brain resource... I want to have it on hand so I can drag it places with me.. should I need too...

Still I open to having help too I just don't know how to do that either... maybe get help with both as I can manage it... this in not only a personal body brain resource issue it is lack of computer knowledge and skill issue and not understanding terms ect... I could learn maybe but it would take time... how much depends on ... go back to go and do not collect 200 $...

I am too tire to go one but I will have a rest and come back... if I knew how to put this page on the front of my computer with a do first post it I would... gain... do not pass go.. I don't know how... If I ever did I forget now.

I will be back
 

anniekim

Senior Member
Messages
779
Location
U.K
One thing you can try is directly using the program downloaded from https://sourceforge.net/projects/analyzemygenes/ and also download and unzip ten_percent.zip and remarks.zip from https://sourceforge.net/projects/analyzemygenes/files/Databases/ into the same folder.

Then it can run with your raw text results, and generate a text file or pdf with the rare results. If the text file is opened with Excel (comma separations) then you can sort based on BLOSUM scores to get a shorter list of missense mutations. -4 is mostly likely to cause problems (but often doesn't), and 4 is no change to the gene's product. Then you can look up the mutations on dbSNP or by gene on OMIM.

But if you're struggling with any of that, I'm happy to take a look.

@Valentijn, thank you but I confess I am at complete loss as to what to do from your instructions. They are good instructions but I just don't have the intelligence to understand.

I take it you believe the Missence mutuations can indicate problems with the asper. Mold you mentioned earlier in the thread? I am writing Missence mutations but I don't have a clue what it all means. Any ideas why I can't seem to upload the raw data file on here? Thank you very much for your time and help.
 

Jenny TipsforME

Senior Member
Messages
1,184
Location
Bristol
Has anyone read https://www.nature.com/nature/journal/vaop/ncurrent/full/nature22329.html

Susceptibility and protection against human autoimmune diseases, including type I diabetes, multiple sclerosis, and Goodpasture disease, is associated with particular human leukocyte antigen (HLA) alleles. However, the mechanisms underpinning such HLA-mediated effects on self-tolerance remain unclear. Here we investigate the molecular mechanism of Goodpasture disease, an HLA-linked autoimmune renal disorder characterized by an immunodominant CD4+ T-cell self-epitope derived from the α3 chain of type IV collagen (α3135–145)1, 2, 3, 4. While HLA-DR15 confers a markedly increased disease risk, the protective HLA-DR1 allele is dominantly protective in trans with HLA-DR15 (ref. 2). We show that autoreactive α3135–145-specific T cells expand in patients with Goodpasture disease and, in α3135–145-immunized HLA-DR15 transgenic mice, α3135–145-specific T cells infiltrate the kidney and mice develop Goodpasture disease. HLA-DR15 and HLA-DR1 exhibit distinct peptide repertoires and binding preferences and present the α3135–145 epitope in different binding registers. HLA-DR15-α3135–145 tetramer+ T cells in HLA-DR15 transgenic mice exhibit a conventional T-cell phenotype (Tconv) that secretes pro-inflammatory cytokines. In contrast, HLA-DR1-α3135–145 tetramer+ T cells in HLA-DR1 and HLA-DR15/DR1 transgenic mice are predominantly CD4+Foxp3+ regulatory T cells (Treg cells) expressing tolerogenic cytokines. HLA-DR1-induced Treg cells confer resistance to disease in HLA-DR15/DR1 transgenic mice. HLA-DR15+and HLA-DR1+ healthy human donors display altered α3135–145-specific T-cell antigen receptor usage, HLA-DR15-α3135–145 tetramer+ Foxp3− Tconv and HLA-DR1-α3135–145 tetramer+Foxp3+CD25hiCD127lo Treg dominant phenotypes. Moreover, patients with Goodpasture disease display a clonally expanded α3135–145-specific CD4+ T-cell repertoire. Accordingly, we provide a mechanistic basis for the dominantly protective effect of HLA in autoimmune disease, whereby HLA polymorphism shapes the relative abundance of self-epitope specific Treg cells that leads to protection or causation of autoimmunity.

Lay version here
http://www.sciencealert.com/researchers-have-discovered-a-key-mechanism-behind-autoimmune-diseases
 

btdt

Senior Member
Messages
161
Location
Ontario
I have been away sick again as I come back I can't recall why I wanted to know at this point it would be a useless as the 23 and me results I got.
I am looking for a doctor in Ontario Canada what knows what to do about all this and I can't travel far... sadly... if anyone knows of one please let me know.
all the results in the world won't help me if I can't sort it and so far I can't... I have had a lot of infected teeth and have had them out in the last few months since I have been here.. I think my lack of brain power could be related to those teeth we will see if I come back online soon or not. I have not been able to think properly recently it could of course be caused by something else. Time will tell.
 

tango

Senior Member
Messages
165
Location
New Zealand
One thing you can try is directly using the program downloaded from https://sourceforge.net/projects/analyzemygenes/ and also download and unzip ten_percent.zip and remarks.zip from https://sourceforge.net/projects/analyzemygenes/files/Databases/ into the same folder.

Then it can run with your raw text results, and generate a text file or pdf with the rare results. If the text file is opened with Excel (comma separations) then you can sort based on BLOSUM scores to get a shorter list of missense mutations. -4 is mostly likely to cause problems (but often doesn't), and 4 is no change to the gene's product. Then you can look up the mutations on dbSNP or by gene on OMIM.

But if you're struggling with any of that, I'm happy to take a look.
Thanks, I will try this tomorrow. I know a researcher told me I have a high % of rare genes and I'm very curious to check it out.
 

tango

Senior Member
Messages
165
Location
New Zealand
Can anyone help me interpret the Shoemaker genes? I have a couple of homozygous SNPs

I've always dismissed the idea of mold illness but I do fit a lot of the symptoms so I am looking into it...

I have ancestry.com and 23andme so if anyone knows any other relevant SNPs I can add them to the list

HLA-DRA rs11544315 T CC -/-
HLA-DRA rs2395182 G TT -/-
HLA-DRA rs3135391 A GG -/-
HLA-DRA rs7192 T TT +/+
HLA-DRA rs8084 A AA +/+
 

btdt

Senior Member
Messages
161
Location
Ontario
@Jenny TipsforME
do they interpret or is it the same deal as 23 and me? all the test results in the world are useless if you can't put them to use.
I do not have the computer skills to download a bunch of stuff or is it brain skill... I am looking for something like genetic genie where I can just join it to 23 and me and let it read what is there. I also have a security issue with this computer which is shared access and I do not want to mess about with my genetic code... like anybody wants it I don't even want it.. cause it sucks.