I would like to identify specific HLA supertype (e.g. HLA-B44) using whole blood.
1. What would be the best approach?
2. What are the alternatives of determining all associated HLA alleles (in this case HLA-B*4001, B*4402, B*4403 etc.)?
Any thoughts?
Dear Daan,
HLA supertype typing is not so easy, as you think!
You can use HLA typing kits (SSP, SSO) to use DNA isolated from whole blood.
You can not buy HLA typing kits for HLA supertypes!
You only can buy HLA typing kits for different HLA groups or alleles (HLA broads or splits).
To give an example: if you want to look for members of the HLA B44 supertype, you would need HLA typing kits (SSP) for B*15, B*18, B*37, B*40, B*44, B*45, B*47, B*49 and B*50.
If you would use a HLA-B NGS (Next Generation Sequencing) approach, you could find out all HLA-B alleles. After this you can find out, which of these HLA-B alleles are part of the B44 supertype and which are not.
The same would be possible for each HLA locus and each HLA supertype.
Best regards,
Thomas
Dear Daan,
As you aware that, HLA supertypes are classified based on the aminoacid residues present in the anchor position, its not easy to determine.
As suggested by Thomas M.C.Binder you can go HLA typing kits (SSP/SSO) according to your lab setup. If you are new to this field, simply go for SSP kits which is easier to perform but needs to take extreme precautions to avoid cross contamination while typing. Now real time PCR kits are also available, however the cost of the assay will be much higher when compared to SSP kits.
If you have sequencing facility, you can go for that.
with regards
Kalyanaraman
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