CFS SNP Study - PubMed

[roxie60]

Found this while doing some research today. Interesting and glad to see some published research being done even if they consider the sample too small. If you scroll down and click on 'Table 2' if you have the Firefix Addon for SNPs you can quickly see your snp values for the ones they researched to fin a connection between SNPs and CFS. FWIW

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765429/

 

[roxie60]

For those interested in sharing here is table 2, if you have the SNPs addon you should be able to scroll over and see your values. I am curious, for those with their SNPs , maybe we could put our results for these SNPs in a thread and see how they compare. So far of the 42 SNPs, my chip did not have ~25% of the SNPs they looked at (N=11). Of the remaining ~75% of SNPs I did have they broke down as N=22 of 31 snps were Homo and/or Hetero for the risk alleles (71% of reportable SNPs). N=10 risk alelles were homozygous and N=12 were heterozygous. If you are interested I will start a post where anyone wanting to participate can add their results for these specific SNPs. Anyone with 23andME (with or without CFS diagnosis). If you have been formally diagnosed (not just suspected like me, is there a dx code for CFS?) you might want add an asterisk at end of your name in the name list.

Table 2
 
A panel of 42 SNPs by the CDC Chronic Fatigue Syndrome Research Group.
Gene    SNPs
COMT    rs4646312, rs740603, rs6269, rs4633, rs165722, rs933271, rs5993882
CRHR1    rs110402, rs1396862, rs242940, rs173365, rs242924, rs7209436
CRHR2    rs2267710, rs2267714, rs2284217
MAOA    rs1801291, rs979606, rs979605
MAOB    rs3027452, rs2283729, rs1799836
NR3C1    rs2918419, rs1866388, rs860458, rs852977, rs6196, rs6188, rs258750
POMC    rs12473543
SLC6A4    rs2066713, rs4325622, rs140701
TH    rs4074905, rs2070762
TPH2    rs2171363, rs4760816, rs4760750, rs1386486, rs1487280, rs1872824, rs10784941
 
The "rs number" means the NCBI SNP ID.
 
COMT = catechol-O-methyltransferase, CRHR1 = corticotropin releasing hormone receptor 1, CRHR2 = corticotropin releasing hormone receptor 2, MAOA = monoamine oxidase A, MAOB = monoamine oxidase B, NR3C1 = nuclear receptor subfamily 3, group C, member 1 glucocorticoid receptor, POMC = proopiomelanocortin, SLC6A4 = solute carrier family 6 member 4, SNP = Single nucleotide polymorphism, TH = tyrosine hydroxylase, TPH2 = tryptophan hydroxylase 2.

 

[roxie60]

Bear with me, it will take a bit of time for me to get the formatted list of SNPs created so we can just add to the end like we have done in other threads. Thx

 

[roxie60]

Here is the list of 42 SNPs studied to see if they 'could' be a predictor of CFS based on above study posted at PubMed. This will be our own PR sample to see if indeed many of us have the risk alelles for the SNPs they suspect maybe a predictor of CFS. (My apologies to those with ME, they did not mention ME in the study so I'm not mentioning it here but encourage you to add your SNPs for comparison). When a name is added a number will be assigned and 'should' correlated with the SNP column. So I will be PR member 1, Roxie60=1, and my SNPs will be in column one. If you are formally diagnosed with CFS/CFIDS add a -C after your #, if you are ME diagnosed add a -M after your number, if you are FM diagnosed add a -F. If you are diagnosed with all three add a -CMF after your number. e.g. Roxie60=1; Roxie60=1-F; Roxie60=1-M; Roxie60=1-C; Roxie60=1-CFM. Nothing after your number means no formal diagnosis yet. This data gathering is for informational purposes only. I'm listing all 42 since some of you may have SNPs that 23andMe do not provide, (NA) means SNP info not available.

Name: Roxie60=1-F; next member=2;


COMT
rs4646312 - (TT);
rs740603 - (NA);
rs6269 - (AA);
rs4633 - (CT);
rs165722 - (CT);
rs933271 - (CC);
rs5993882 - (GG);

CRHR1
rs110402 - (AA);
rs1396862 - (GG);
rs242940 - (NA);
rs173365 - (AA);
rs242924 - (TT);
rs7209436 - (CT);

CRHR2
rs2267710 - (TT);
rs2267714 - (NA);
rs2284217 - (AG);

MAOA
rs1801291 - (NA);
rs979606 - (NA);
rs979605 - (AG);

MAOB
rs3027452 - (GG);
rs2283729 - (AG);
rs1799836 - (CT);

NR3C1
rs2918419 - (TT);
rs1866388 - (AG);
rs860458 - (GG);
rs852977 - (AG);
rs6196 - (AA);
rs6188 - (AC);
rs258750 - (AG);

POMC
rs12473543 - (NA);

SLC6A4
rs2066713 - (AA);
rs4325622 - (NA);
rs140701 - (CC);

TH
rs4074905 - (NA);
rs2070762 - (AG);

TPH2
rs2171363 - (GG);
rs4760816 - (TT);
rs4760750 - (NA);
rs1386486 - (GG);
rs1487280 - (NA);
rs1872824 - (GG);
rs10784941 - (NA);

 

[roxie60]

I found this interesting:

An interesting finding was that an association of NR3C1 with CFS compared to non-fatigued controls appeared to be consistent across several studies. Thus, this significant association strongly suggests that NR3C1 may be involved in biological mechanisms with CFS. The NR3C1 gene encodes the protein for the glucocorticoid receptor, which is expressed in almost every cell in the body and regulates genes that control a wide variety of functions including the development, energy metabolism, and immune response of the organism [36]. A previous animal study has observed that age increases the expression of the glucocorticoid receptor in neural cells [37], and increases in glucocorticoid receptor expression in human skeletal muscle cells have been suggested to contribute to the etiology of the metabolic syndrome [38].

Of the 7 NR3C1 SNPs, 86% of my SNPs are Homo or Hetero for the risk alelle.

 

[roxie60]

Curious what others think of the study article.

 

[roxie60]

also from the study article

Candidate genes

In the present study, we only focused on the 42 SNPs as described in Table ​Table22[18]. As shown in Table ​Table22[18], there were ten candidate genes including COMT, corticotropin releasing hormone receptor 1 (CRHR1), corticotropin releasing hormone receptor 2 (CRHR2), MAOA, MAOB, NR3C1, POMC, solute carrier family 6 member 4 (SLC6A4), tyrosine hydroxylase (TH), and TPH2 genes. Six of the genes (COMT, MAOA, MAOB, SLC6A4, TH, and TPH2) play a role in the neurotransmission system [8]. The remaining four genes (CRHR1, CRHR2, NR3C1, and POMC) are involved in the neuroendocrine system [8]. The rationale of selecting these SNPs is described in detail elsewhere [8]. Briefly, most of these SNPs are intronic or intergenic except that rs4633 (COMT), rs1801291 (MAOA), and rs6196 (NR3C1) are synonymous coding changes [8].

 

[roxie60]

PR has a lot of info about gene expression studies, I've just been reading some. I'm not sure this study has validation in potential for determining/verifying CFS/ME but I still think it would be interesting to see how folks here genes line up with the study.

 

[Allyson]

PR has a lot of info about gene expression studies, I've just been reading some. I'm not sure this study has validation in potential for determining/verifying CFS/ME but I still think it would be interesting to see how folks here genes line up with the study.

Hi Roxie, thanks for posting


sorry i do not understand much about genetics yet so can t really add much

but it is great to see they are doing this

we will never know if there is a gentic link unless we look for one.

ANd i think gentics and epigentics is our only concrete hope of a cure

so please keep the info coming

thanks

Ally

 

[Diana S.]

Here is the list of 42 SNPs studied to see if they 'could' be a predictor of CFS based on above study posted at PubMed. This will be our own PR sample to see if indeed many of us have the risk alelles for the SNPs they suspect maybe a predictor of CFS. (My apologies to those with ME, they did not mention ME in the study so I'm not mentioning it here but encourage you to add your SNPs for comparison). When a name is added a number will be assigned and 'should' correlated with the SNP column. So I will be PR member 1, Roxie60=1, and my SNPs will be in column one. If you are formally diagnosed with CFS/CFIDS add a -C after your #, if you are ME diagnosed add a -M after your number, if you are FM diagnosed add a -F. If you are diagnosed with all three add a -CMF after your number. e.g. Roxie60=1; Roxie60=1-F; Roxie60=1-M; Roxie60=1-C; Roxie60=1-CFM. Nothing after your number means no formal diagnosis yet. This data gathering is for informational purposes only. I'm listing all 42 since some of you may have SNPs that 23andMe do not provide, (NA) means SNP info not available.

Name: Roxie60=1-F; Diana=2-FC;


COMT
rs4646312 - (TT); (TT)
rs740603 - (NA); (NA)
rs6269 - (AA); (AA)
rs4633 - (CT); (TT)
rs165722 - (CT); (TT)
rs933271 - (CC); (CT)
rs5993882 - (GG); (GT)

CRHR1
rs110402 - (AA); (AG)
rs1396862 - (GG); (GG)
rs242940 - (NA); (NA)
rs173365 - (AA); (GG)
rs242924 - (TT); (GT)
rs7209436 - (CT); (CT)

CRHR2
rs2267710 - (TT); (CC)
rs2267714 - (NA); (NA)
rs2284217 - (AG); (AA)

MAOA
rs1801291 - (NA); (NA)
rs979606 - (NA); (NA)
rs979605 - (AG); (GG)

MAOB
rs3027452 - (GG); (GG)
rs2283729 - (AG); (AG)
rs1799836 - (CT); (CT)

NR3C1
rs2918419 - (TT); (TT)
rs1866388 - (AG); (AA)
rs860458 - (GG); (GG)
rs852977 - (AG); (AA)
rs6196 - (AA); (AA)
rs6188 - (AC); (CC)
rs258750 - (AG); (AA)

POMC
rs12473543 - (NA); (NA)

SLC6A4
rs2066713 - (AA); (AG)
rs4325622 - (NA); (NA)
rs140701 - (CC); (CT)

TH
rs4074905 - (NA); (NA)
rs2070762 - (AG); (AA)

TPH2
rs2171363 - (GG); (AA)
rs4760816 - (TT); (CC)
rs4760750 - (NA); (NA)
rs1386486 - (GG); (AG)
rs1487280 - (NA);(NA)
rs1872824 - (GG); (NA)
rs10784941 - (NA); (NA)

 

[Sea]

Looks interesting Roxie, I will get back to this thread when I have enough stamina to find my snps and post them

 

[Wolfiness]

Does anyone know if there's any online Compendium Of Significant ME Genes saying which are the risky alleles so I can check my 23andMe raw data, or a widget that will do it for me on Android, please? I can't use the Firefox SNPTips addon on Android. I'm not particularly interested in Yasko, just the general picture, mitochondrial and neurological function in particular.

 

[pattismith]

Name: Roxie60=1-F; Diana=2-FC; Pattismith = 3-F

COMT
rs4646312 - (TT); (TT) (CT) (T=wild)
rs740603 - (NA); (NA); (NA)
rs6269 - (AA); (AA); (AG) (A = wild)
rs4633 - (CT); (TT); (CT) (C = wild)
rs165722 - (CT); (TT); (NA)
rs933271 - (CC); (CT); (CT) (T = wild?)
rs5993882 - (GG); (GT); (NA) (T = Wild)