Distribution of HLA-A types by country

Maciamo

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I have started a new page listing HLA allele frequencies by country. I have only had time to add HLA-A types so far, but I am planning to add other types too.

There are 14 common HLA-A types in Europe. Some geographic patterns are quite obvious for some types.

HLA-A1 is found at highest frequencies in Northwest Europe, but is also common in central and eastern Europe. Its lowest incidence is observed among the Pasiegos, Sardinians, Saami, Finns, Georgians, Druzes and Saudis. Its presence in the Urals, Siberia and South Asia all hint at an Indo-European origin (both R1a and R1b).

HLA-A2 is the most common type in Europe, ranging from 24% to 34% of the population anywhere. It doesn't show any specific geographic pattern though. A2 is a bit less common among the North Africans, Jews, Armenians, Turks and Greeks. Oddly enough it is lowest in Armenia (18%) but highest in neighbouring Georgia (35%). HLA-A2 was inherited from Neanderthal according to Abi-Rached et al. (2011).

HLA-A3 reaches a maximum frequency of 15-30% in Northern Europe (Saami, Finland, Sweden, Germany) then progressively declines southward to reach in minimum in the Balkans, Sardinia, North Africa, the Levant and Saudi Arabia. Probably linked to Y-haplogroup I1. Note that the North European allele is exclusively A*0301, while Armenia and Georgia have both the European A*0301 and Middle Eastern A*0302.

HLA-A11 is most common among the Russian Saami (14%) and Druzes (11%), followed by Southeast Europe, Turkey and bizarrely also Ireland. Despite its high frequency from the Carpathians to the Levant, A11 is rare in Saudi Arabia and North Africa. Probably due to some founder effect, its highest frequency is observed among the Saami of Murmansk, but its lowest frequency in among Scandinavian Saami. Its origin is probably Near Eastern, but it might have arrived to Europe during the late glacial or immediate post-glacial period, like Y-DNA J2b and E-V13 and mtDNA H, J1c and T2b, among others.

HLA-A23 is most common in the Middle East and North Africa, and is absent from the Saami and oddly also the Sardinian population. It is also high among the Chuvash and Tatars, who have a lot of Y-DNA E1b1b and J2. Within Europe is fairly even, but lower in the north, except for a sharp peak in Norway (founder effect ?). A11 is probably not Neolithic due to its absence from Sardinia. It could have been brought by a later migration (haplogroup J2a in the Late Bronze or Early Iron Age ?).

HLA-A24 peaks both among the Saami and Chuvash as well as in Southeast Europeans (Balkans + Italy), Druzes and Georgians. It is also relatively common among the Basques and Sardinians. It is least common in Northwest Europe. It appears to be pre-Indo-European. Perhaps Epipalaeolithic East Mediterranean like A11.

HLA-A25 is absent from the Sardinian, Georgian, Druze and Saudi population, and is very rare in North Africa, the southern Balkans, Turkey and Armenia as well as in the extreme north of Europe (Lapland, Finland). It peaks mostly in R1a-rich countries (Slavic + Norway, Austria, Romania), then in R1b-rich countries (Ireland, Britain, France). It is almost certainly of Indo-European origin.

HLA-A26 is found chiefly in the Balkans and central Europe, especially in the Danube basin. It peaks among the Jews (8.9%), Saudis (6.4%) and the mysterious Pasiegos of Cantabria (8.6%). It is rarest in western and northern Europe. Very probably of Southwest Asian origin, but not necessarily G2a (could have been spread by J1 and T1a Neolithic herders). HLA-A26 was inherited from Neanderthal according to Abi-Rached et al. (2011).

HLA-A29 is most common in Western Europe, North Africa, Israel and Armenia, with a peak among the Pasiegos (14%) and the Basques (13%). It appears to be rarest in Northeast Europe (Finland, Lapland, Volga-Ural), Danubian Europe (Bosnia, Croatia, Serbia, Albania, Bulgaria), but also Sardinia and Georgia. It might have come from the Near East to Iberia via North Africa, then spread around western Europe with the Megalithic and Bell Beaker cultures. It could be linked to R1b-V88.

HLA-A30 is exceptionally high among the Sardinians (19%), followed by Moroccans (10.6%), Jordanians (8.7%), Druzes (7.5%), the Basques (7.3%) and Bosnians (6.4%), but is almost absent from Finland and Lapland, which hint at a Neolithic dispersal. The higher frequency is southern and central Europe also suggest a Neolithic origin, probably through the Mediterranean route like A26 and A29.

HLA-A32 peaks among the Sardinians (8.7%) as well as in the Balkans, Turkey, Italy and Andalusia. It is rarest among the Basques, Pasiegos and Saami. Also of probable Neolithic origin, but brought directly from the Near East (G2a).

HLA-A33 also peaks among the Libyans, (5.5%), Saudis (5.3%), Moroccans (4.8%), Sardinians (4.5%), Jews (3.5%) and Jordanians (3.5%), but has a wider Mediterranean and eastern European distribution. It is lowest in Northwest Europe and Fennoscandia. It is very surely linked to Neolithic farmers.

HLA-A68 is mostly distinctive by its low incidence among the Sardinians, Basques and Saami. Otherwise, like A23, it doesn't have a clear geographic pattern. Like A31, its highest frequency is found among the Saudis, Sudanese, North Africans, Chuvash, Bashkirs, Swiss and Pasiegos. It's hard to find a connection between those people. Its probably linked to Y-haplogroup E1b1b, or perhaps to Y-DNA G (encompassing both G1 and G2) as A68 is also found in Mongolia.

HLA-A74 is only found at trace frequencies in Europe and is more common in Subsaharan Africa. The highest reported frequency in Europe is in Albania-Kosovo (0.6%), which also happens to have the highest frequency of Y-haplogroup E1b1b. A74 is also found in Greece, Bosnia, Romania, Spain, Portugal, France, Wales, the Netherlands and Germany. In the Middle East it is most common among the Saudis (0.9%) and Jordanians (0.8%), who have the highest frequency of E1b1b in the region.


HLA-A0101.png




Medical conditions associated with HLA-A types


HLA type
Increased risk for...
A1Type-1 Diabetes
A2Spontaneous abortion
A3Multiple sclerosis, Hemochromatosis, Myasthenia gravis
A11Papilloma virus suseptibility
A24Ankylosing spondylitis, Myasthenia gravis, Type-1 Diabetes
A26Adult T-cell leukemia/lymphoma
A30Myasthenia gravis
A68Adult T-cell leukemia/lymphoma
 
Last edited:
Thank you very much for this. My question is how do we know which variant means you have the HLA?
 
Maciamo,is for ex. HLA-A1 the same as HLA-A*0101 ?
 
Maciamo,is for ex. HLA-A1 the same as HLA-A*0101 ?

If you are positive for HLA-A*0101 then you are also HLA-A1. A*0101 is the European subtype of A1.
 
If you are positive for HLA-A*0101 then you are also HLA-A1. A*0101 is the European subtype of A1.

what is a positive marker in CEU group for HLA-A1.A*0101 ??
 
Thank you very much for this. My question is how do we know which variant means you have the HLA?

No easy answer. Try googling the SNP and look which is the minor allele (that's the one positive for the HLA). 95% of the time you'll only have inherited a same HLA allele from only one parent, so you'll be heterozygous (e.g. AG). If you are homozygous (e.g. AA or GG) you can assume that you don't have the allele.
 
No easy answer. Try googling the SNP and look which is the minor allele (that's the one positive for the HLA). 95% of the time you'll only have inherited a same HLA allele from only one parent, so you'll be heterozygous (e.g. AG). If you are homozygous (e.g. AA or GG) you can assume that you don't have the allele.

so, checking my fathers rsnumbers via 23andme, for the CEU group you linked
he has
TT for the first line and
AG for the second line
I did not bother to do anymore

What does this all mean?
 
If you are positive for HLA-A*0101 then you are also HLA-A1. A*0101 is the European subtype of A1.

How do you interpret my results?

HLA-A*0101 rs1611635 No SNPs matching found
rs10947088 - TT
 
so, checking my fathers rsnumbers via 23andme, for the CEU group you linked
he has
TT for the first line and
AG for the second line
I did not bother to do anymore

What does this all mean?

If by first line you mean rs1611635, T is positive. If so it appears that your father has two A1 alleles.
 
Little update: according to Abi-Rached et al. (2011), HLA-A2 and A26 were both inherited from Neanderthals. Interesting that A2 happens to be the most common HLA-A type in Europe today (30% of the population) and progressively decreases in frequency with distance from Europe in the Middle East (just like mtDNA U5). On the other hand A26 peaks in Southeast Europe and the Near East and may have been inherited from Near Eastern Neanderthals.
 
If by first line you mean rs1611635, T is positive. If so it appears that your father has two A1 alleles.
yes, this is what I mean..............he is 85 yo now ..............I always wondered how accurate his dna was when he did his test at 84yo
 
This thread is a great work. We can learn so much about auto-immune deseases like lupus. I have some basque friends rh- with this illness and it seems inherated from neanderthals. Is lupus in rilation to A2?
 

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