HLA DQ4 is an HLA-DQ serotype grouping based on antibody recognition of the HLA DQ beta chain. It is synonymous with the HLA-DQB1*04 allelegroup. This group is composed of two similar beta chains. HLA DQB1*0401, and HLA DQB1*0402. These beta chains are linked to certain alpha chain genes (alleles) such as DQB1*0302, *0303, and *0401.
DQA1*0303:DQB1*0401 is linked to DRB1*0405 and is commmon on the west pacific rim, from Indonesia to Japan and inland areas of Eastern Asia. In Japan it confers susceptibility
to type 1 diabetes.
DQA1*0303:DQB1*0402 is primarily found in Northeastern Asia and the west pacific rim.
It is similar to DQA1*0303:DQB1*0402.
DQB1*0401:DQB1*0402 has a trimodal global distribution. The highest frequencies
are found in the highland reagions of the new world, peaking in NW Mexico and in the Andes. It is also found at high levels in Namibia and Botswana. Between these two population it is moderatedly high in the Ainu of northern Japan.
The table to the left shows the values of Japanese(values converted from phenotype frequencies to haplotype frequencies for sake of consistency) DR-DQ types. This table is presented here because of the diversity of DQ4 types in the Japanese population not seen elsewhere.
DQ4 is typically rare most of the world but where it appears more frequently is something of interest. The node of DQ4 is with the DQA1*0401:DQB1*0402 (DQ4.24 for this page) haplotype in Northwestern Mexico and the highland region of western South America reaching 40% haplotype frequencies in that area. Outside of the Indigenous American population DQ4.24 is elevated
at 10% in the Ainu of Hokkaidō, Japan. There are a number of other A-B haplotypes that suggest a connection between the Ainu and the Meso-American and Andean populations as well as Lakota Souix all have DQ4 levels higher than the Ainu. The linkage of DQ4 in Asia appears to be heaviest with DR8 (DR*0801, DR*0802, DR*0804) for DQ4.24 and the frequency is elevated from
the Ryukyu Islands to Okhotsk, Ulchi, Negidal, Tofalar at approximately 10% falling off in the Mansi at 4% and punctate levels in between. Haplotype diversity of DQB1*0402 appears to be centered around the Amur River/Japanese Island Chain, and diversity of DQB1*0401 very roughly follows a similar pattern. DQ4.24 is also high in the Swedes however this may be due to east to west gene flow tracable at other HLA loci.
Since DQA1*0401:DQB1*0402 is found in the !Kung, one reasonably assumes it evolved in Africa and migrated with one of several potential waves, probably the earliest. Tracing the migration route is excessively difficult, but it appears that a possible second node of expansion in Central Asia and not the West Pacific Rim/Austro-Indic route postulated as the early human distribution. The most common haplotypes in the !Kung (for example Cw-B) that also appear in Eurasia appear to have been associated with the earliest migration, and is suggestive of a coastal migration; however the relatively high frequencies in the Ainu and Amur basin suggest a migration through the Transbaikal that is consistent with archaeology from about 18 kya. One expects with such a route that Korean would be higher than Japanese and Japanese higher the Ryukuans still higher than Taiwan aboriginals. From the west gene frequencies in the Levant and Black Sea region are at 'diffusive' levels whereas there are pockets of increased frequency in the Zoroastrians of Yadz region (DQA1*0401 and DQB1*0402). Thus the DR8-DQ4.24 haplotype is probably one of western origin.
The DR4-DQA1*0303:DQB1*040X can be found at high frequencies in PNG highland groups  but not DQ4.24. The DR*0405 and DR*410 are found specifically associated with these DQ types and there is some haplotype diversity. So that it appears the presence of the DQA1*03:DQB1*04 is of West Pacific Rim origins in Japanese and proximal Siberians, but unfortunately there is no current typing of these haplotypes in the Taiwan aboriginal population. The presence in Indonesia may be the result of retrograde gene flow that can be established by other HLA types as well as mtDNA.
^ Mimura T, Funatsu H, Uchigata Y, Kitano S, Noma H, Shimizu E, Konno Y, Amano S, Araie M, Yoshino O, Iwamoto Y, Hori S (2003). "Relationship between human leukocyte antigen status and proliferative diabetic retinopathy in patients with younger-onset type 1 diabetes mellitus.". Am J Ophthalmol135 (6): 844-8. PMID 12788125.
^ Mimura T, Funatsu H, Uchigata Y, Kitano S, Shimizu E, Amano S, Yamagami S, Noma H, Araie M, Hori S (2005). "Glutamic acid decarboxylase autoantibody prevalence and association with HLA genotype in patients with younger-onset type 1 diabetes and proliferative diabetic retinopathy.". Ophthalmology112 (11): 1904-9. PMID 16157380.
^ Porto T, Coelho I, Boavida J, Pereira C, Nunes J, Mendonça D, Martins B, Sobrinho L, Leite V (2006). "Association of HLA DQ4-DR8 haplotype with papillary thyroid carcinomas.". Clin Endocrinol (Oxf)64 (2): 179-83. PMID 16430717.
^ Smerdel A, Lie B, Finholt C, Ploski R, Førre Ø, Undlien D, Thorsby E (2003). "An additional susceptibility gene for juvenile idiopathic arthritis in the HLA class I region on several DR-DQ haplotypes.". Tissue Antigens61 (1): 80-4. PMID 12622778.
^ Smerdel A, Ploski R, Flatø B, Musiej-Nowakowska E, Thorsby E, Førre Ø (2002). "Juvenile idiopathic arthritis (JIA) is primarily associated with HLA-DR8 but not DQ4 on the DR8-DQ4 haplotype.". Ann Rheum Dis61 (4): 354-7. PMID 11874841.
^ Betsou F, Borrego M, Guillaume N, Catry M, Romão S, Machado-Caetano J, Sueur J, Mention J, Faille N, Orfila J (2003). "Cross-reactivity between Chlamydia trachomatis heat shock protein 10 and early pregnancy factor.". Clin Diagn Lab Immunol10 (3): 446-50. PMID 12738647.
^ Birol A, Anadolu R, Tutkak H, Gürgey E (2002). "HLA-class 1 and class 2 antigens in Turkish patients with pemphigus.". Int J Dermatol41 (2): 79-83. PMID 11982641.
^ Kawa S, Ota M, Yoshizawa K, Horiuchi A, Hamano H, Ochi Y, Nakayama K, Tokutake Y, Katsuyama Y, Saito S, Hasebe O, Kiyosawa K (2002). "HLA DRB10405-DQB10401 haplotype is associated with autoimmune pancreatitis in the Japanese population.". Gastroenterology122 (5): 1264-9. PMID 11984513.
^ Kikuoka N, Sugihara S, Yanagawa T, Ikezaki A, Kim H, Matsuoka H, Kobayashi Y, Wataki K, Konda S, Sato H, Miyamoto S, Sasaki N, Sakamaki T, Niimi H, Murata M (2001). "Cytotoxic T lymphocyte antigen 4 gene polymorphism confers susceptibility to type 1 diabetes in Japanese children: analysis of association with HLA genotypes and autoantibodies.". Clin Endocrinol (Oxf)55 (5): 597-603. PMID 11894970.
^ Tsuchiya K, Kimura A, Kondo M, Nishimura Y, Sasazuki T (2001). "Combination of HLA-A and HLA class II alleles controls the susceptibility to rheumatoid arthritis.". Tissue Antigens58 (6): 395-401. PMID 11929590.
^ Matake H, Okabe N, Naito S, Yao T (1992). "An HLA study on 149 Japanese patients with Crohn's disease.". Gastroenterol Jpn27 (4): 496-501. PMID 1526431.
^ Nakajima A, Matsuhashi N, Kodama T, Yazaki Y, Takazoe M, Kimura A (1995). "HLA-linked susceptibility and resistance genes in Crohn's disease.". Gastroenterology109 (5): 1462-7. PMID 7557126.
^ ab Tanaka T, Ohmori M, Yasunaga S, Ohshima K, Kikuchi M, and Sasazuki T. (1999). "DNA typing of HLA class II genes (HLA-DR, -DQ and -DP) in Japanese patients with histiocytic necrotizing lymphadenitis (Kikuchi's disease).". Tissue Antigens54 (3): 246-253. PMID 10519361.
^ Bannai M, Tokunaga K, Imanishi T, Harihara S, Fujisawa K, Juji T, and Omoto K. (1996). "HLA class II alleles in Ainu living in Hidaka District, Hokkaidō, northern Japan.". Am J Phys Anthropol101 (1): 1-9. PMID 8876810.
^ Uinuk-Ool TS, Takezaki N, Sukernik RI, Nagl S, Klein J. (2002). "Origin and affinities of indigenous Siberian populations as revealed by HLA class II gene frequencies.". Human Genetics110 (3): 209-226. PMID 11935333.
^ Gao X, Bhatia K, Trent RJ, and Serjeantson SW. (1992). "HLA-DR, DQ nucleotide sequence polymorphisms in five Melanesian populations.". Tissue Antigens40 (1): 31-37. PMID 1440559.