HLA Frequencies

[aaron_c]

I'm been reading Shoemaker and doing bits of his protocol lately, with some (limited) success. One aspect of his theory I've been curious about is his assertion that HLA types can play a role in treatment efficacy if not disease severity. Having believed Amy Yasko back in the day I'm more cautious now about giving credence to anything but a clear-cut genetic disorder--but I still want to look into it.

And here's where I need help. I found a database of the HLA's from the control groups of various studies, and it will allow me to search for HLA frequencies...but I'm not familiar enough with the arcane language of HLA's to figure out how, or if I can use this how I'd like. My goal is to look into the frequencies of 11-3-52B and 4-3-53. Any help would be appreciated so much, thank you!

 

[alicec]

I had to refresh my memory about what the 3 sets of numbers mean - ie as used by Shoemaker. You can see more about that here and here.

So the first number is DRB1, the second is DQB1 (Shoemaker doesn't specify DQA1 or DQB1 but if you look on the LabCorp test shown in the second link you can see it is DQB1 that is being singled out), the third number is DRB3 or 4 or 5. There is linkage disequilibrium between these, especially with DRB3,4,5 to DRB1. DR status really means DRB1 status since the other DR loci always associate in certain ways. DR and DQ tend to associate, though with variation leading to different combination frequencies.

Here is the Wikipedia article on HLA DR showing frequencies of the most common DR-DQ haplotypes in Americans of European origin. So from this you can get an idea of the prevalence of the first two of Shoemaker's numbers in this population (the third number is irrelevant) for the haplotypes you are interested in. So 11-3 (52B) is 8.6% and 4-3-(53) is 16.9%.

I've never been able to find any research confirming the HLA linkage to susceptibility that Shoemaker claims. Presumably he based his claims on the observation that his patients had higher prevalence of some HLA haplotypes that the international frequencies that he compared with. He just assumed that these haplotypes were more susceptible to the diseases the patients suffered from. This of course is not a valid assumption, since haplotypes vary greatly with ethnicity. His patients were just exhibiting haplotype frequencies more like Americans of European origin, as you might expect - nothing abnormal at all.

As this and this post makes clear, only 14.1% of the population of Americans of European origin have haplotypes which are NOT risky according to Shoemaker's claims. Really he is making this stuff up as he goes along.

I tried putting DRB1 and DQB1 values into the website you linked and just setting any for the other values but it wouldn't compute. Not sure what it needs to work properly.