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New map of HLA-A1 allele frequency
Here is my first HLA map. I chose to start with HLA-A1 because it is the first chronologically, but also because it is one of the most common HLA types in Europe.
The HLA (Human Leucocyte Antigen) genes are on important component of the immune system regulation. They are cell-surface antigen-presenting proteins present in almost every cell of the body. Their role is to signal to white blood cells (more specifically T cells) that a cell has been contaminated by a pathogen (virus or bacteria) and should be destroyed.
There are many classes of HLA. The main are A, B, C, DP, DQ and DR. Everyone has two copies of each type, one inherited from each parent. Each HLA type (e.g. HLA-A1) has several subtypes (e.g. HLA A*01:01, HLA A*01:02, HLA A*01:03). Subtypes usually vary between continent or racial groups. A*0101 is the variant found in Europe. A*0102 and A*0103 are much rare and mostly confined to Africa and Southwest Asia.
HLA types can play a very significant medical role in some autoimmune diseases. HLA-A1 has been associated with increased risk for diabetes, lymphoma and susceptibility to measles and herpes infections when combined to other HLA types (e.g. HLA-B8). If you have tested your genome with 23andMe (or another company) you can check if you are a carrier of the HLA-A1 type with the SNP rs1611635 (each T represents a copy of HLA-A*01:01).
I have used the HLA allele frequencies database to make the map.
HLA-A1 has an interesting peak of frequency in Northwest Europe, and is much rare among the Saami, Sardinians, Pasiegos, Georgians and Saudis, which hints that it could have been spread by the Indo-Europeans. It is also found at frequencies comparable to the European average (10-15%) in parts of South Asia, notably among the Pathans, Sindhi and North Indians, which reinforces the Indo-European connection. It is also found at high frequency in Mongolia (6 to 14.5%), but is otherwise very rare or absent from East Asian countries. Unfortunately there is no data at all for Central Asia, although I expect that it is above 10% in most places, and especially in the Hindu Kush region.
If I broaden the search to HLA A*01 without subtype, there is more data. It reaches 19% in Gujarat (N-W India), 18% in the South Urals, and 10% in the Samara region.
Oddly enough it is also relatively common among Maghrebis. The fact that it is also found in Jordan (7%), Sudan (5%) and Cameroon (3%) suggests that HLA-A1 could also have been propagated by R1b-V88 cattle herders during the Neolithic. The allele could have been positively selected in Western Europe and the Maghreb if it conferred better protection against local pathogens.
I have checked the above SNP in a dozen Mesolithic, Neolithic, Chalcolithic and Bronze Age genomes from Haak 2015, but all of them were negative.
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