The most basic definition is that they are markers that identify cells as friendly and prevent the immune system from attacking them.

Many times you'll hear about HLA when someone is needing a bone marrow and are tested against others to identify a match. The same principle applies in that when someone is given a bone marrow transplant, the old immune system is rebooted with the "good" bone marrow.

The HLA-DR2 and/or HLA-DR4 immune response genes are seen in some with MS and may be linked to other diseases such as Diabetes. I don't know the medical background or the exact reasoning behind these genes but suspect it has something to do with how ms or other diseases are linked to them. It gets confusing and maybe someone else will come in to shed a better light on it.