HLA-DR test results interpretation -- HELP?!?!

[spaceboy3000]

Hi,

I just got back my HLA-DR results from Labcorp, and I am trying to figure out how to interpret them. I'm trying to follow Shoemaker's protocols, and specifically his "rosetta stone" for interpreting the labwork, but I am COMPLETELY confused by it!! I'm not a stupid guy, but guess what? I've had brain fog pretty badly over the past few months, so I'm really not figuring it out - can you guys help me figure out the haplotype and the basic "interpretation" according to Shoemaker's "rosetta stone"? It would really help!!

Here's the info from Labcorp:

DRB1 08
DRB1 11

DRB3 02
DRB3 --

DRB4 --
DRB4 --

DRB5 --
DRB5 --

DQB1 Allele 1: 03
DQB2 Allele 2: 04

(I gather that the above info is what we need to figure this out. Please let me know if you need all the rest of the codes, etc., and I will post that too. Thanks!)

 

[Valentijn]

@spaceboy3000 - Please post the codes too!

 

[spaceboy3000]

Here is all the info (minus the personally identifying info.....)

 

[Valentijn]

So if I'm remembering correctly, this means that you have DRB1*08:01 or DRB1*08:50, and DRB1 11:??? (one of the options listed under ABZYG). So you're heterozygous for that one.

You also have DRB3*02:?? (one of the UZTH).

And you have DQB1*03:?? and DQB1*04:??.

So DRB1*08/DRB1*11, DRB3*02, DQB1*03/DQB1*04.

 

[roxie60]

I have been trying to find out my HLA gene info as it relates to lyme. Ive read certain HLA genes can suppress antibody generation. If I have those genes it doesnt make sense for me to get another IGenex WB test cause it will probably be negative. Anyone gone down this rabbit hole here at PR, please provide a link to the thread/discussion. HLA genes seem much more difficult to understand and find in 23and me, I know the code index is needed but so are specific snps RS#s which Im not finding many.

 

[spaceboy3000]

Hi Roxie,

I started this thread about 6 weeks ago - and have gotten a lot more info since then.

First off, regarding HLA DR, 23andMe testing apparently does NOT cover the specific testing required. Unfortunately that is still done through a blood test. Labcorp quoted me around $600-700, but I have a doctor friend so luckily for me I was able to get it cheaper.

SO, I have one multi-susceptible haplotype, 11-3-52b. I'm trying to upload a copy of the worksheet that my doctor uses, but for some reason it won't take the file.... I just got back from visiting this doctor in the South Western US. She is one of Ritchie Shoemaker's "trained" specialists, and a number of us are very impressed with her.

Basically, Shoemaker has a very complete protocol for investigating and fixing the numerous problems that crop up with some of these haplotypes. My friend is further into the process and so far is reporting dramatic improvements.

**** I think this part is really important**** --- I have some definite methylation problems myself (a double mutation on the A1298C gene) and had been diligently trying to address some of the issues directly with it, with the help of this forum, and a few methylation specialists. After a year, I haven't noticed any improvements. Very interestingly, this "mold" specialist reports that probably 90% of her patients that she apparently is successful in treating also have methylation problems. But she has had much better luck improving her patients' health by treating the biotoxin illness ("mold") rather than addressing the methylation concerns as a primary focus. I guess I am going to be putting this approach to the test!!

Put another way, it has always seemed to me to be that there must be a misunderstanding with lyme disease. From a bunch of sources, including my own common sense, it seems apparent that a VERY BIG percentage of the population has been exposed at some time to lyme disease. However, only a relatively small percentage of us get truly sick and/or don't respond well to lyme treatment. It seems to me that there are other VERY IMPORTANT factors that actually make the difference. For example, this search led me to looking into methylation and the related genetics, etc. I found that I have problems in that area too. Addressing those factors for more than a year hasn't seemed to make a positive difference for me. A few bad experiences in the past year have led me to consider biotoxin illness and mold as a bigger factor than I had thought. And for what its worth, Shoemaker's approach to mold is quite parallel to the methylation issue research and approach. (Looking into specific genetic markers, and the usual problem areas that are resultant.)

Basically, you always have to start by making VERY sure you are out of exposure to the mold. Of all the things I've attempted to do for my health in the past five years, this seems to be the most difficult, expensive, and frustrating thing I've had to tackle. Meanwhile, there are a number of different blood tests that measure different types of inflammation. It is pretty complex, and apparently has to be done in the right order, or you have to start over.

After getting out of the mold exposure, you begin taking a lot of cholestyramine (3 or 4 times a day for a LONG time) to soak up and get rid of the buildup of specific toxins that collect in your body with this type of exposure combined with the genetic inability to deal normally with them. Ritchie Shoemaker has written a few books on the subject, so I will shut up about the process.

ANYWAY, that is what I have learned, and where I am at with the process. It will probably take a while to move through this process, especially since Medicare is almost zero help with any of this. And if I have good results, I will certainly share them!

I would love to hear from anybody with other specific experiences with this issue too....!

Thanks,

Jed

 

[Valentijn]

I have been trying to find out my HLA gene info as it relates to lyme. Ive read certain HLA genes can suppress antibody generation. If I have those genes it doesnt make sense for me to get another IGenex WB test cause it will probably be negative. Anyone gone down this rabbit hole here at PR, please provide a link to the thread/discussion. HLA genes seem much more difficult to understand and find in 23and me, I know the code index is needed but so are specific snps RS#s which Im not finding many.

The relevant SNPs have multiple mutations - hence instead of just being "A" or "G", an SNP might be capable of being "A", "G", "C", or even "T", resulting in different HLA types. 23andMe doesn't seem capable of handling more than two alleles per SNP, and doesn't test any of these.

The only HLA gene which is tested enough to sometimes figure out one or both of your types is HLA-DRA. With 23andMe data I was able to fully figure out DRA types for 6 ME patients and narrow it down to having two out of three possibilities for the other 5.

According to my notes, these were the relevant SNPs which narrow down the possibilities:
rs7192 - G = DRA*010101 or DRA*010102
rs7192 - T = DRA*010201 or DRA*010202 or DRA*010203

rs8084 - C = DRA*010101 or DRA*010201
rs8084 - A = DRA*010202 or DRA*010102 or DRA*010203

rs11544315 - C = DRA*010101 or DRA*010201 or DRA*010202 or DRA*010203
rs11544315 - T = DRA*010102

rs3135391 - A = DRA*010203
rs3135391 - G = DRA*010101 or DRA*010201 or DRA*010202 or DRA*010102

So basically you have to look at the SNP results in combination to figure out which two types (sometimes both are the same) apply to you.

 

[Valentijn]

@roxie60 - I took a 2nd look at the DLA-DRA data I have, and was able to get a bit further with it now, probably due to far less brain fog than the last time I checked them. Basically by "subtracting" the alleles used for the types which can easily be figured out, the remainder must belong to the 2nd type which is also then easily identified.

So by checking for a "T" at rs11544315 (DRA*010102) and an "A" at rs3135391 (DRA*010203), and either finding those or ruling them out, there are only three options left.

Step 1: determine if one or both types are as follows, with the allele unique to that set underlined and bolded (order is rs7192 rs8084 rs11544315 rs3135391):
GATG = DRA*010102
TACA = DRA*010203

So if someone has "GG AA TT GG" then they are homozygous for DRA*010102, for example. Or if they have "GT AA CT AC" then they are heterozygous for both DRA*010102 and DRA*010203.

But in the event that they are only heterozygous for one of the above, such as with "GT AC CC AG", we can see that the "A" in the last pair means that they are heterozygous for DRA*010203 and can then subtract the known type from the alleles to see what remains. So if we subtract the DRA*010203 alleles of TACA from "GT AC CC AG" we're left with GCCG, which can be used to determine the DLA-DRA type.

Alternatively, neither DRA*010102 nor DRA*010203 are present, and the remaining options are two of the following three possibilities. Because the other two options have been found or ruled out, we now have some additional unique alleles in Step 2 which are underlined and bolded.

Step 2:
GCCG = DRA*010101
TCCG = DRA*010201
TACG = DRA*010202

If one of the types was already determined in Step 1, we subtract the known alleles to see what the remaining type is. In the "GT AC CC AG" example, we found DRA*010203 and were left with GCCG. Hence the 2nd type for that person must be DRA *010101.

But if neither type has been determined yet, we look for the now unique alleles in the remaining options. If rs7192 has one or two "G" alleles at this point, we know the person is respectively heterozygous or homozygous for DRA*010101. And if they have one or two "A" alleles at rs8084, we know they are heterozygous or homozygous for DRA*010202. But this only applies if Step 1 was completed first!

Step 3: Now that DRA*010101, DRA*010102, DRA*010202, and DRA*010203 have been definitely included or excluded for the patient, anything that is left should be TCCG, indicating DRA*010201. If trying to find this result prior to excluding everything else, all you get is a big mess and a bunch of guesswork. But by ruling out the other options first, in the proper order, it's possible to determine both HLA-DRA types with certainty.

 

[Valentijn]

Using the above methodology I was able to figure out the HLA-DRA types for 31 ME patients and controls.

Each person can have two types, or two of one type, so there's 62 types for patients (Ps) and 62 types for controls (Cs).
HLA-DRA Ps Cs
*010101 38 32
*010102 00 01
*010201 00 00
*010202 16 24
*010203 08 05