Molecular analysis of HLA-DRB1, DQA1, DQB1, DQ promoter polymorphism and extended class I/class II haplotypes in the Seri Indians from Northwest Mexico

The study of the genetics of the Major Histocompatibility Complex (MHC) in Amerindians is of great value in understanding the origins and migrations of these native groups, as well as the impact of immunogenetics on the epidemiology of diseases affecting these populations. We analyzed, using Polymerase Chain Reaction and Sequence Specific Oligonucleotide Probes (PCR-SSOP), DRB1, DQA1, DQB1 alleles and the promoter regions of DQA1 and DQB1 genes in 31 unrelated and 24 related Seri, a Mexican Indian group, from the state of Sonora (Northwest Mexico). The class II genotypes of this population were found to be in genetic equilibrium. The allele frequency (AF) of the prevalent DRB1 alleles were DRB1*0407 (48.4%), DRB1*0802 (33.9%) and DRB1*1402 (16.1%). The most frequent DQA1 and DQB1 alleles were DQA1*03011 (AF = 50.00%), DQA1*0401 (AF = 33.87%) and DQA1*0501 (AF = 16.13%); DQB1*0302 (AF = 50.00%), DQB1*0402 (33.87%) and DQB1*0301 (16.13%); which were in combination with DRB1*0407, DRB1*0802 and DRB1*1402, respectively. Three QAP and three QBP alleles were present (QAP 3.1, 4.1, 4.2; QBP 3.1, 3.21, 4.1) associated with the typical published DQA1 and DQB1 alleles. Four class II haplotypes were present in family members: DRB1*0407-QAP-3.1-DQA1*03011-QBP-3.21-DQB1*0302; DRB1*0802-QAP-4.2-DQA1*0401-QBP-4.1-DQB1*0402; DRB1*1402-QAP-4.1-DQA1*0501-QBP-3.1-DQB1*0301 and DRB1*0701-QAP-2.1-DQA1*0201-QBP-2.1-DQB1*0201. The family data were used to confirm extended haplotypes. A total of 21 haplotypes were found when A* and B* loci were also considered. The three most frequent combinations included A*0201-B*3501-DRB1*0407, A*3101-B*5101-DRB1*0802, and A*0201-B*40-DRB1*1402.     

DQA1 and DQB1 promoter diversity and linkage disequilibrium with class II haplotypes in Mexican Mestizo population

The upstream sequences in the 5' flanking region of HLA class II genes, regulate their expression and contribute to the development of immunological diseases. We analyzed 105 healthy unrelated Mexican Mestizos for QAP and QBP polymorphism. DNA typing for DRB1, DQA1, DQB1, QAP1 and QBP1 was done using a standardized PCR-SSOP. Although all QAP alleles previously described were found in Mexicans, the distribution differed as compared to other populations. QAP-3.1, 4.1 and 4.2 were the most frequent alleles and were associated with DQA1*03, *0501 and *0402 respectively. The prevalent QBP alleles were 3.21, 3.1 and 4.1 found mainly associated with DQB1*0302, *0301 and *0501. Linkage disequilibria between the promoter and the corresponding DQA1 and DQB1 allele, are in general the same as described by others. A total of 61 different haplotypes were defined, only six of them with a frequency above 4%. The haplotypes DRB1*0407-QAP-3.1-DQA1*03-QBP-3.21-DQB1*0302 (HF = 14.37%) and DRB1*0802-QAP-4.2-DQA1*0401-QBP-4.1-DQB1*0402 (HF = 14.22%), which have an Amerindian ancestry, are the most frequent in Mexicans. Some rare combinations were detected such as DRB1*0405-QAP-1.3-DQA1*0101/4-QBP-5.11/5.12-DQB1*0501 and DRB1*0403-QAP-3.2-DQA1*03-QBP-3.21-DQB1*0302, probably due to ancient recombination events. This knowledge is relevant as a basis to evaluate functional implications and to explore the role of promoter diversity in disease expression.     

Major histocompatibility complex class II alleles and haplotypes and blood groups of four Amerindian tribes of Northern Colombia

MHC class II alleles and haplotypes were determined from unrelated individuals and families of the Arhuaco (n = 107), Kogi (n = 42), Arsario (n = 18), and Wayú (n = 88) tribes located in the northern part of Colombia. Class II DRB, DQA1, and DQB1 alleles were determined by PCR-SSO and PCR-RFLP based methods. Four haplotypes, [DRB1^*0407, DRB4^*0101, DQA1^*03, DQB1^*0302]; [DRB1^*0403, DRB4^*0101, DQA1^*03, DQB1^*0302]; [DRB1^*1402/1406, DRB3^*0101, DQA1^*0501, DQB1^*0301]; and [DRB1^*0802, DQA1^*0401, DQB1^*0402], were observed among these four tribes. In addition to these haplotypes, the Wayú Indians showed a frequency of 21.3% for the [DRB1^*1602, DRB5^*02, DQA1^*0501, DQB1^*0301] haplotype, 13.1% for the [DRB1^*0411, DRB4^*0101, DQA1^*03, DQB1^*0302] haplotype, and 8.1% for the [DRB^*0411, DRB4^*0101, DQA1^*03, DQB1^*0402] haplotype. Red cell antigen typing was used to calculate genetic admixture. The Kogi and Arsario showed no genetic admixture while the Arhuaco tribe showed admixture with genes of African origin and the Wayú showed admixture with Caucasians as well as genes of African origin. These findings were confirmed by the MHC class II allele and haplotype data obtained, as alleles and haplotypes of Caucasian and African origin were detected in the Wayú and Arhuaco and not in the Kogi or Arsario. These studies will be important in disease association and transplantation studies for Amerindian and Colombian populations and for correlating genetic traits with the anthropologic and linguistic data available in order to better understand the Amerindian populations.     

Distribution of HLA Class II Alleles and Haplotypes in Mexican Mestizo Population: Comparison with Other Populations

We describe the analysis of the Major Histocompatibility Complex (MHC) class II polymorphism in Mexican Mestizo population. The study provides the HLA-DRB1, DQA1 and DQB1 allele frequencies in 99 Mexican Mestizos. DNA from these individuals was typed by PCR followed by hybridization using sequence specific oligonucleotides (PCR-SSO). The relationship with other worldwide populations was studied by using HLA data from 69 different populations and calculating neighbor-joining dendrograms and correspondence multidimensional values. The highest frequencies were for DRB1*0802 (allele frequency = 0.151), DRB1*0701 (allele frequency = 0.111) and DRB1*0407 (allele frequency = 0.106). Among the eight DQA1 alleles detected, the most frequent were DQA1*03011 (allele frequency = 0.257), DQA1*0501 (allele frequency = 0.227) and DQA1*0401 (allele frequency = 0.166). Twelve DQB1 alleles were found and four of them, DQB1*0302 (allele frequency = 0.237), DQB1*0301 (allele frequency = 0.176), DQB1*0201 (allele frequency = 0.166) and DQB1*0402 (allele frequency = 0.166) showed the highest frequencies. The haplotype DRB1*0802-DQA1*0401-DQB1*0402 (0.151) predominated clearly, followed by DRB1*0701-DQA1*0201-DQB1*0201 (0.111) and DRB1*0407-DQA1*03011-DQB1*0302 (0.101). Both genetic distances and correspondence analyses showed that Mexicans clustered with Amerindian population. These results suggest that the Mexican Mestizo population be principally characterized by haplotypes presents in Amerindian and Caucasian populations with a low frequency of Black haplotypes. In summary, the HLA class II haplotype frequencies demonstrated the tri-racial component existing in Mexican Mestizos.     

Polymorphism of DQA1 promoter in Italian population

We have investigated polymorphism in the 5′-URR of the DQA1 gene by PCR-SSO method in a group of 55 Italian healthy individuals olygotyped for DRB1, DQA1, DQB1 genes and in 20 10th IHWS cell lines as controls. We used primers and oligos (X and Y box) supplied by 12th IHWS and a DIG-11-ddUTP/AMPPD method. We have detected eight QAP variants (1.1,1.2,1.3,1.4,2.1,3.1,4.1,4.2) in our samples. As far as the association of DR/DQ haplotype and QAP sequences, we observed cases of one to one relationship (DQA1^*0201 and QAP2.1, DQA1^*0301 and QAP3.1, DQA1^*0401 and QAP4.2, DQA1^*0501 and QAP4.1); cases in which the same QAP allele was present in different DQA1-DRB1 haplotypes (QAP1.2 with DQA1^*0102 in DRB1^*15-DQB1^*0602 and DRB1^*16-DQB1^*0502 haplotypes or with DQA1^*0103 in the DRB1^*15-DQB1^*0601 haplotypes; QAP1.3 linked to DQA1^*0102, DQA1^*0103 or DQA1^*0104 in different haplotypes; QAP4.1 linked to DQA1^*0501 in DRB1^*11-DQB1^*0301, DRB1^*0301-DQB1^*0201, DRB1^*1303-DQB1^*0301 haplotypes or to DQA1^*0601 in DRB1^*0803-DQB1^*0301); cases where the same DQA1 allele is associated with different QAP sequences according to the DRB1 specificity (DQA1^*0102 allele with QAP1.2 or QAP1.4 in DRB1^*1302). Besides, we have observed that the QAP1.3, previously reported associated with DQA1^*0101-DRB1^*1401 haplotype, is really linked to DQA1^*0104-DRB1^*1401 haplotype. An intriguing data is that sometimes the same QAP is linked to different DQA1 alleles but to the same generic DRB1 allele: DRB1^*02 haplotype includes always the QAP1.2 variant but can bring different DQA1 alleles (^*0102 or ^*0103) and DRB1^*08 haplotype has always the QAP4.2 variant with different DQA1 alleles (^*0401 or ^*0601). The variability of linkage QAP-DQA1 can give further informations about HLA susceptibility in autoimmune diseases and in regulation of immune response in transplantation and oncology.     

DQA103 subtypes have different associations with DRB1 and DQB1 alleles

Polymorphisms outside the hypervariable regions of HLA class II alleles that do not affect the peptide-binding site are probably not under selective pressure and could therefore be useful as markers of the evolutionary pathways of the HLA class II haplotypes. We have analyzed such a polymorphism in the variants of DQA1^*03, which differ at residue 160 encoded in exon 3. Our study included homozygous BCLs of the 10th IHWS and samples of a multiracial panel of 723 unrelated subjects which were also typed for allelic variations in exon 2 by hybridization with SSOP. BCLs having DQA1^*03 and 131 selected DQA1^*03-positive samples were typed for the dimorphism in exon 3 that distinguishes DQA1^*0301 and DQA1^*0302. DQA1^*0301 was found to be exclusively associated with DQB1^*0302, while samples carrying DQB1^*0201, 0301, 0303, and 0401 always had DQA1^*0302. A few haplotypes carrying DQB1^*0302 had DQA1^*0302. The fact that DQA1^*0301 is completely included in DQB1^*0302, and not vice versa, suggests that DQA1^*0301 may have arisen from a mutation in a haplotype containing DQA1^*0302-DQB1^*0302. DQB1^*0302 was found to be associated with all DR4 subtypes, suggesting possibly that the current variants of DRB1-DR4 may be of more recent origin. DRB1^*0405 was the only subtype of DR4 which was not associated with DQA1^*0301 and had multiple associations with the DQB1 alleles, therefore, perhaps representing the oldest allele of this group.     

Endogenous retroviral long terminal repeats of the HLA-DQ region are associated with susceptibility to insulin-dependent diabetes mellitus

HLA-DQ genes are the main inherited factors predisposing to IDDM. This gene region harbors long terminal repeat (DQ LTR) elements of the human endogenous retrovirus HERV-K, which we analyzed for a possible association with disease. We first investigated whether LTR segregate with DQ alleles in families. Members (n = 110) of 29 families with at least one diabetic child, unrelated patients with IDDM (n = 159), and healthy controls (n = 173) were analyzed. Genomic DNA was amplified for DQ LTR3 by a nested primer approach as well as for DQA1 and DQB1 second exons, to assign DQA1 and DQB1 alleles. DQ LTR segregated in 24 families along with DQ alleles. Of the 29 families, 20 index patients were positive for DQ LTR. The DQ LTR was in all patients on the haplotype carrying the DQA1 ^*0301 and DQB1 ^*0302 alleles. A majority of patients had DQ LTR (62%) compared with controls (38%) (p < 1.3 × 10^{− 5}), even after matching for the high-risk alleles DQA1 ^*0501, DQB1 ^*0201-DQA1 ^*0301, and DQB1 ^*0302 (79% of patients and 48% of controls; p < 0.02). Subtyping for DRB1 ^*04 alleles in all DQB1 ^*0302 ⁺ individuals showed 56% DRB1 ^*0401, DQB1 ^*0302 [LTR⁺ patients vs. 29% controls with the same haplotype (p < 0.002). In conclusion, these data demonstrate the segregation of DQ LTR with DQA1, DQB1 alleles on HLA haplotypes. Furthermore their presence on DRB1 ^*0401-, DQA1 ^*0301-, and DQB1 ^*0302-positive haplotypes suggest that they contribute to DQ-related susceptibility for IDDM. Human Immunology 50, 103–110 (1996)     

Polymorphism in the upstream regulatory region of the DQB1 gene (QBP) and four point (DRB1, QBP, DQA1, DQB1) haplotypes in the Dai minority population in China.

Using polymerase chain reaction and Dig-ddUTP labeled oligonucleotides we have investigated the DNA polymorphism for the DQB1 promoter region (QBP) and we have deduced four point haplotypes in 65 unrelated healthy individuals of the Dai minority population. A total of 8 QBP alleles were detected. The most frequent allele is QBP 5.11 with 87.7% allele frequency followed by QBP 3.21, 3.1, 5.12 with 33.8%, 23.1% and 15.4% allele frequency respectively. Four QBP alleles, 3.22, 3.32, 4.1 and 6.12 were absent in the Dai minority. The linkage disequilibrium of the QBP allele with certain DQB1 alleles was very strong. Complete positive association was found for QBP 2.1-DQB1^*0201, QBP3.1-DQB1^*0301, QBP6.11-DQB1^*0601. A total of 32 different four point haplotypes were deduced. Among them the most common haplotypes were DRB1^*1602, DQA1^*0102, QBP5.11; DQB1^*0502, DRB1^*1602-QBP5.11, DQA1^*0102, DQB1^*0502 (N = 19); DRB1^*09 DQA1^*03, QBP3.21, DQB1^*03032 (N = 5); DRB1^*1401, DQA1^*01, QBP5.11, DQB1^*0502 (N = 12) and DRB1^*1202, DQA1^*0601, QBP3.1, DQB1^*0301 (N = 10). We conclude from these data that a) there is a reduced class II polymorphism in the Dai minority population an b) the relationship between QBP and DQB1 alleles is not different from that observed in other populations.     

DQB1 Exon2 and promoter allele frequencies and haplotypes in native American Indians and a German Caucasoid population.

In order to investigate the distribution of the DQB1 promoter (QBP1) alleles and their linkage with the structural portion of the DQB1 gene, a comparative population-based study in native American Indians (Zapotecs) and a German Caucasoid population was carried out by PCR-SSO and -SSP typing. 215 healthy, unrelated German individuals and 66 healthy Zapotecs were analysed for the distribution and linkage of DQB1 and QBP1 alleles. Among the Zapotec population 9 out of 12 known QBP1 alleles were found. In 6 Zapotec individuals unsual hybridisation patterns suggestive of new QBP1 alleles were observed. In Zapotecs as well as in Germans a tight linkage between the promoter region and exon 2 of DQB1 was observed. Exceptions were seen for DQB1^*0501, ^*0603 and ^*0604 in Germans and ^*0501 in Zapotecs. Marked differences in allele frequencies between Germans and Zapotecs are seen mainly for DQB1^*0201, ^*0602, ^*04 and ^*0302. It is concluded that population-specific differences in haplotype frequencies exist, while linkage disequilibrium is maintained.     

HLA-encoded susceptibility to insulin-dependent diabetes mellitus is determined by DR and DQ genes as well as their linkage disequilibria in a Chinese population

HLA-DRB1 and -DQB1 genes were analyzed in 98 Chinese IDDM patients and 205 control subjects from Taiwan. The DRB1^*0301-DQB1^*0201 haplotype conferred strong susceptibility (RR = 7.7, p_c < 10−5). DRB1^*0405 also conferred susceptibility (RR = 3.1, p_c < 0.0005) whereas DRB1^*0403 (RR = 0.7) and DRB1^*0406 (RR = 0.2) conferred protection. Indeed, the relative risk for the DRB1^*0405-DQB1^*0302 haplotype (RR = 33.7, p_c < 0.002) was 48 and 168 times higher than those conferred by the DRB1^*0403-DQB1^*0302 and DRB1^*0406-DQB1^*0302 haplotypes, respectively, suggesting that the protection conferred by DRB1^*0403 and 0406 is dominant over DQB1^*0302. The strong linkage disequilibrium observed between DQB1^*0302 and DRB1^*0403(0406) can thus explain the surprising finding that the frequency of DQB1^*0302 was not significantly increased in the Chinese IDDM patients (RR = 0.9). Because the DRB1^*0405-DQB1^*0302 haplotype (RR = 33.7) conferred higher susceptibility than the DRB1^*0405-DQB1^*0401 (RR = 2.5) or DRB1^*0405-DQB1^*0301 (RR = 2.1) haplotypes, DQB 1^*0302 is indeed a susceptibility factor, while both DQB1^*0301 and DQB1^*0401 may confer protection against IDDM. The increased frequency of the protective DQB1^*0401 allele in patients compared to controls is due to linkage disequilibrium between DRB1^*0405 and DQB1^*0401. Interestingly, the previously demonstrated protective effect of DQB1^*0602 was not very strong in the Chinese (RR = 0.4). Our results suggested that HLA-encoded susceptibility to IDDM is determined by the combined effects of all DR and DQ molecules present in an individual. Therefore, the genotypic combinations of DR and DQ genes as well as their linkage disequilibria can influence IDDM susceptibility. At least four DR and DQ molecules conferring high susceptibility (DRB1^*0301, DRB1^*0405, and DQ/β0301/0201 and 0301/0302) occur at high frequency in the Chinese population. However, linkage disequilibria between highly susceptible DR and protective DQ or vice versa (e.g., DRB1^*0405-DQB1^*0301(0401] and DRB1^*0403[0406]-DQB1^*0302) are probably responsible for the lower incidence of IDDM in the Chinese.     

Polymorphism of the DQA1 promoter region (QAP) and DRB1, QAP, DQA1, DQB1 haplotypes in the Dai minority population in South-Western China

We have investigated the polymorphism of the DQA1 promoter region (QAP) and we have deduced four point (DRB1, QAP, DQA1, DQB1) haplotypes of 60 unrelated healthy Dai minority individuals using the polymerase chain reaction and Dig-ddUTP labeled oligonucleotides. A total of eight QAP alleles (QAP1.1, 1.2, 1.3, 1.4, 3.1, 3.2, 4.1 and 4.2) were detected and two QAP alleles, QAP1.5 and QAP2.1 were absent in this population. The most predominant allele was QAP1.2 with 80% allele frequency. We also found that QAP alleles are in strong linkage disequilibrium with certain alleles of the neighboring loci DQA1 and DQB1. Complete positive association was found for QAP4.1-DQA1^*05, QAP4.2-DQA1^*0601, QAP1.2-DR2 group, QAP3.2-DRB1^*09, QAP4.1-DRB1^*03. A total of 28 different four point (DRB1-QAP-DQA1-DQB1) haplotypes were deduced and the most frequent haplotypes were DRB1^*1602-QAP1.2-DQA1^*0102-DQB1^*0502 (N = 18, H.f. = 15%) and DRB1^*09-QAP3.2-DQA1^*03-DQB1^*03032 (N = 18, H.f. = 15%) followed by the haplotypes DRB1^*1401-QAP1.3-DQA1^*01-DQB1^*0502, DRB1^*1202-QAP4.2-DQA1^*0601-DQB1^*0301 and DRB1^*1502-QAP1.2-DQA1^*0101-DQB1^*0501 with H.f. 9.1%, 6.7% and 5.0% respectively. The other 23 haplotypes were all less than 5% (H.f. 0.8%-5%). The relationship between the QAP alleles and DQA1 in the Dai minority is the same as that in the Chinese and the Caucasoid population.     

The promotor QAP and QBP alleles in Czech population and rheumatoid arthritis multicase families

HLA promotor alleles of DQA1 and DQB1 genes were analyzed in a group of 65 Czech healthy individuals and 58 members of 14 RA multicase families by PCR and oligonucleotide hybridization. QAP4.1 and QBP3.1 were the most frequent alleles (gf=0.315, GF=0.254) due to the linkage disequilibrium with DQA1×0501 and DQB1×0301. The second most frequent allele QAP1.2 (gf=0.162) was found to be common for DR2 alleles. The analysis of RA multicase families showed promotor alleles and haplotypes similar to those reported in the healthy population. QBP3.21 was in a commplete positive association with DQB1×0302-DRB1×04, except DQB1×0302-DRB1×0408, where was detected QBP3.1, associated also with DQB1×0301-DRB1×0401. Promotor polymorphism may reflect a level of expression and function of HLA structural alleles.     

Distribution of HLA class II alleles and haplotypes in insulin-dependent moroccan diabetics

HLA class II polymorphism in Moroccan IDDM patients has not been investigated so far. In this study, HLA-DRB1, -DQA1, and -DQB1 allele and haplotype frequencies were analyzed in 125 unrelated Moroccan IDDM patients and 93 unrelated healthy controls, all originating from the Souss region and mostly of Berber origin. Some common features with other Caucasian groups were observed, in particular, a predisposing effect of the DRB1^*03-DQA1^*0501-DQB1^*0201 and DRB1^*04-DQA1^*0301-DQB1^*0302 alleles or allelic combinations. The Moroccan IDDM group also presented with more specific characteristics. Among DRB1^*04 subtypes, DRB1^*0405 was associated with susceptibility to and DRB1^*0406 with protection from the disease. The haplotype and the relative predispositional effect (RPE) analyses indicated that the DRB1^*08-DQA1^*0401DQB1 ^*0402 haplotype was also associated with susceptibility to IDDM. Interestingly, the DRB1^*09DQA1 ^*0301-DQB1^*0201 haplotype, completely absent from the control group and very rare in North African populations, was observed in 7.2% of the Moroccan diabetics. Conversely, the DRB1^*07-DQA1^*0201DQB1 ^*0201 and DRB1^*15-DQA1^*0102-DQB1^*0602 haplotypes were associated with protection from IDDM. Finally, we observed an age-dependent genetic heterogeneity of IDDM, the frequencies of predisposing alleles being higher and those of protective alleles lower in childhood- than in adult-onset diabetics. Our data on Moroccan diabetics, together with data on European and Northern Mediterranean patients, suggest a gradient of various HLA class II predisposing and protective markers that link these populations     

The frequency of QAP2.1 is increased in psoriasis vulgaris patients

The heritage of psoriasis has a polygenic mode, the most essential antigens being Cw6,DR7,DQA1^*0201 in many ethnic groups. We have found a strong association between the high risk HLA haplotypes carrying DQA1^*0201 and psoriasis. Thus, the aim of this study was to further examine if the flanking promotor genes, URRs of DQ (QAP and QBP) are involved in the susceptibility to this disease. The series consisted of 62 patients and 50 control subjects and the PCR-SSO method was used. The frequency of the promoter gene QAP2.1 was significantly increased in the psoriatics (P_c=1.5×10⁻², RR=4.6) and the frequency of QAP4.1 was decreased in the patients group (P_c=3.9×10⁻²). The psoriasis risk allele DQA1^*0201 was associated always with QAP2.1, except once with QAP3.1.

: The combination of QAP2.1 and DQA1^*0201 is associated to psoriasis. Promotor region could exert its influence by gene expression or functionally through different inducibility by cytokines.     

Distribution of TAP gene polymorphisms and extended MHC haplotypes in Mexican Mestizos and in Seri Indians from northwest Mexico

The study of the genetic structure is very useful for investigating the biological significance of polymorphism and may provide clues to understand population origins. We present TAP1/TAP2 gene analysis in the Seri indians from Sonora, and in Mestizos from the highlands of Mexico. Thirty-two Seri and 89 Mestizos were studied. TAP genes were typed using the ARMS-PCR technique. The most frequent alleles in Seri were: TAP1*0101/02, (68.8%); TAP1*02011/02012, (31.2%); TAP2*0201, (38.7%) and TAP2*0101, (29.0%). TAP1*0301, TAP1*0401, TAP2*0102 TAP2*0103 and TAP2H were absent in them. For Mestizos, the prevalent alleles were: TAP1*0101/02 (75.8%); TAP1*02011/12 (20.3%); TAP2*0101 (45.4%) and TAP2*0201 (29.3%). These results are similar to those found in Kaingang and Caucasians from Brazil, four Mediterranean, other Caucasians, two Oriental and one African group. In Seri, the extended prevalent haplotypes are typically Amerindian, such as TAP1*0101/2-TAP2*0201-QBP3.21-DQB1*0302-QAP*3.1-DQA1*03011-DRB1*0407-B*3501-A*0201 (HF = 16.6%). Thirty-two extended haplotypes were found in Seri, although TAP contributed scarcely to diversity. Mestizos show Amerindian and Caucasian combinations. No difference was detected in the distribution of amino acids in the individual variable sites, between both groups. These findings are the basis for further anthropological studies and to explore the contribution of TAP genes to disease expression in Mexicans.     

The genetic structure of Mexican Mestizos of different locations: tracking back their origins through MHC genes, blood group systems, and microsatellites.

Mexican Mestizos, who are the result of the admixture of Spanish, Indian, and Black genes, were analyzed for different systems. Three populations from geographical distinct areas were studied: the north (State of Nuevo Leon ), the center (State of Guanajuato), and the highlands (mainly Mexico City). Ten blood group systems (N = 229), STRs (N = 107), HLA-A*, B*, C* (N = 116-167), and DRB1, DQA1, and DQB1 (N = 40, 101, 160, respectively) were analyzed in the samples of the highlands. The three groups cluster together in the same branch: Mestizos from Venezuela, Mediterranean and Jews close to the cluster of Orientals, followed by Amerindians. All markers demonstrate that Indian genes are strongly represented in the highlands: Di(a), O, D(-)(+), s, A*0201, *0206, B*1539 (*1541), *3902, *3905, *3512, *3517, *4002, *4005, Cw*0801, *0304, *0401 among others. Cw*0501, *1203, *1204, and *1601 are of White ancestry. The most frequent haplotypes *0407-*03011-*0302 and *0802-*0401-*0402 are of Indian descent as well. The center and mainly the north show a more Caucasian and Semitic profile. The results demonstrate the high variability resulting from interethnic admixture, suggesting that this mechanism is the main factor responsible for the large diversity found in urban populations.     

The distribution of DR4 haplotypes in sardinia suggests a primary association of type I diabetes with DRB1 and DQB1 loci

The contribution of genetic variation at HLA class II loci to the susceptibility to and protection from IDDM was investigated by analyzing the distribution of HLA-DRB1^*04 haplotypes in 630 Sardinian newborns and 155 Sardinian IDDM patients. The different RRs and ARs of the various DR4-DQB 1^*0302 haplotypes, significantly ranging from the strongly associated DRB 1^*0405, DQB 1^*0302 to the protective DRB 1^*0403, DQB 1^*0302 haplotypes, provides clearcut evidence that the DRB 1 locus is crucial in conferring IDDM predisposition or protection. Also, the DQB1 locus influences IDDM predisposition or protection by restricting the disease-positive association to DRB 1^*0405 haplotypes carrying the susceptibility DQB 1^*0302 or DQB 1^*0201 alleles but not the protective DQB 1^*0301 allele. Haplotype analysis not only suggests that the DRB 1 and DQB1 loci influence IDDM risk in the same way, but also that the HLA-linked protection is “dominant” compared with “susceptibility.” These results, obtained from a population with one of the highest IDDM incidences in the world, define more clearly the contribution of the various HLA loci to IDDM protection or susceptibility and allow a more precise calculation of AR.     

Highly polymorphic promoter regions of HLA DQA1 and DQB1 genes do not help to further define disease susceptibility in insulin-dependent diabetes mellitus

HLA DQA1, HLA DQB1 genes confer susceptibility to insulin-dependent (type 1) diabetes mellitus (IDDM). Since variants of their upstream regulatory regions are linked to the exons, we investigated their promoter polymorphisms (QAP and QBP) by a combination of PCR-based typing protocols in 136 IDDM patients, 167 controls and 6 families with an IDDM proband to identify possible additional susceptibility markers. Of major interest for IDDM susceptibility are the promoter "splits" of HLA DQA1*0301 (QAP3.1 and QAP3.2) and HLA DQB1*0302 (QBP3.2 and QBP3.3). QAP 3.1 (96% in patients vs 98% in controls) and QBP3.2 (100% vs 99%) were found to be the most frequent promoter variants for HLA DQA1*0301 and DQB1*0302, respectively, whereas QAP3.2 and QBP3.3 were very rare. Furthermore the promoter "splits" were equally distributed on the respective exon alleles in all groups and cosegregated in families as expected. In conclusion, HLA DQ-mediated susceptibility and protection in IDDM is not restricted to the exon but extends to the promoter region without further defining the genetic risk.     

The HLA-DRB, -DQB polymorphism and anti-insulin antibody response in Slovenian patients with type 1 diabetes.

A combination of specific HLA class II antigens and the presence of type 1 diabetes (T1D)-related antibodies has a high positive predictive value for T1D but low sensitivity. The aim of the present study was to determine the frequencies of HLA-DRB-DQB deduced haplotypes associated with susceptibility and protection in Slovenian patients with established T1D, to evaluate the relationship between the HLA-DRB1-QBP-DQB1 haplotypes and the presence of insulin autoantibodies (IAA) and glutamic acid decarboxylase antibodies (GADA), and to access the possible impact of polymorphic QBP promoters on this relationship. A cohort of 135 patients with T1D (age 17.5 +/- 7.0 years, duration of T1D 9.14 +/- 6.3 years) was investigated. HLA-DRB1 and DQB1 alleles were typed using the polymerase chain reaction (PCR)-reverse line blot method. QBP promoter region alleles were determined using PCR-sequence-specific oligonucleotide hybridization (SSO) and PCR-sequence-specific primers (SSP). IAA and GADA antibodies were determined by enzyme-linked immunosorbent assay (ELISA). The chi-square test with Yates' correction was used for statistical analysis. Deduced haplotypes DRB1*0301-DQB1*0201 (P = 0.0001, OR = 3.4), DRB1*0401-DQB1*0302 (P = 0.0001, OR = 29.8), and DRB1*0402-DQB1*0302 (P = 0.008, OR = 4.7) were significantly more common, and DRB1*1501-DQB1*0602 (P = 0.0001, OR = 0.03) significantly less common in the investigated cohort than in a Slovenian control group. The highest risk and the strongest protective HLA-DR-DQ haplotypes found in Slovenian patients with T1D did not differ from those found in other Caucasian populations. While the DRB1*0301-QBP2.1-DQB1*0201 haplotype, where QBP2.1 did not help to further distinguish DQB1*0201-possessing haplotypes in IAA-positive and IAA-negative patients, was strongly associated with the presence of IAA, the DRB1*0101-QBP5.12-DQB1*0501 haplotype, although not protective compared to the control population, was associated with an absence of IAA in the investigated cohort. It is suggested that there may be a combined influence of the QBP5.12 promoter and the DQB1*0501 functional molecule on reduced IAA production.     

Haplotypic diversity of DQA1*03 and *05 subtypes differing at amino acid residue 160 encoded in the third exon in 2215 Japanese individuals

We analyzed the frequencies and haplotypes of DQA1*03 and *05 subtypes, DQA1*03011 or DQA1*0302 and DQA1 *0501 or DQA1*0503, respectively, differing only at codon 160 in the non-polymorphic third exon of the DQA1 gene. Of these, 1,862 and 337 individuals selected as DQA1*03- and DQA1**05-positive samples, respectively among 2,215 unrelated Japanese were typed for their nucleotide variation at residue 160 using PCR-SSP. As observed in other populations, all the samples carrying DQA1*03011 (Gene Frequency, GF: 7.8%) were found to share DQB1*0302, whereas those carrying DQA1*0302 (GF: 44.3%) were associated with a variety of DQB1 alleles including DQB1*0302. Both of the DQA1-DQB1 haplotypes with DQA1*03011 and DQA1*0302 carrying DRB1*0406, DQA1*03011-DQB1*0302 and DQA1*0302-DQB1*0302, showed a strong linkage disequilibrium with B62 (p< .0001, p< .005). These results suggested that DQA1*03011 was generated from a single amino acid change at residue 160 in the DQA1*0302-DQB1*0302 haplotype. However, none of the haplotypes with two different DQA1*03 subtypes carrying DRB1*0403, *0405, *0802 and *0901 showed a linkage disequilibrium with any common B-locus antigens, revealing extensive haplotypic diversity of the DQA1*03 group. For example, DRB1*0802 haplotypes showed linkage disequilibria with two different B-locus antigens, B35 and B61 depending on the presence of DQA1*03011 and DQA1*0302, respectively. The GFs of DQA1*0501 and *0503 were 5.1% and 2.7%, respectively. The DQA1*05 associated haplotypes in the DR52-antigen group with DQB1*0301 were divided into two groups, depending on the bimorphism at residue 160. Such a high degree of haplotypic diversity in association with DRB1 and B alleles observed in the DQA1*03 and *05 groups related to amino acid variation at residue 160, which may affect biological function such as the interaction between CD4 and HLA-DQ molecules, seems to reflect selective pressure in the evolutionary process of HLA antigens