Determination of HLA class II alleles by genotyping in a Manchu population in the northern part of China and its relationship with Han and Japanese populations

Incorporation of a Novel CD4+ Helper Epitope Identified from Aquifex aeolicus Enhances Humoral Responses Induced by DNA and Protein Vaccinations

CD4+ T cells play an important role in the maturation of the antibody responses. Conjugation of identified CD4+ T cell helper epitope to the target antigen has been developed as a strategy to enhance vaccine-induced humoral immunity. In this work, we reported the identification of a novel HLA-IAb helper epitope LS-3 from Aquifex aeolicus. In silico analysis predicted this epitope to have high binding affinity to common human HLA alleles and have complementary binding coverage to the established PADRE epitope. Introduction of HLA-IAb knockout mutations to the LS-3 epitope significantly attenuated humoral responses induced by a vaccine containing this epitope. Finally, engineered fusion of the epitope to a model antigen, influenza hemagglutinin, significantly improved both binding and hemagglutination inhibition antibody responses in mice receiving DNA or protein vaccines. In summary, LS-3 and additional identified CD4+ helper epitopes may be further explored to improve vaccine responses in translational studies.

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Identification of a novel CD4+ helper epitope, LS-3, from Aquifex aeolicus

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In silico analysis predicts high binding affinity of LS-3 to human HLA-DR alleles

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Fusing LS-3 to antigen enhances humoral response by vaccinations

Development of a humanized HLA-A2.1/DP4 transgenic mouse model and the use of this model to map HLA-DP4-restricted epitopes of HBV envelope protein

A new homozygous humanized transgenic mouse strain, HLA-A2.1(+/+)HLA-DP4(+/+) hCD4(+/+)mCD4(-/-)IAβ(-/-)β2m(-/-) (HLA-A2/DP4), was obtained by crossing the previously characterized HLA-A2(+/+)β2m(-/-) (A2) mouse and our previously created HLA-DP4(+/+) hCD4(+/+)mCD4(-/-)IAβ(-/-) (DP4) mouse. We confirmed that the transgenes (HLA-A2, HLA-DP4, hCD4) inherited from the parental A2 and DP4 mice are functional in the HLA-A2/DP4 mice. After immunizing HLA-A2/DP4 mice with a hepatitis B DNA vaccine, hepatitis B virus-specific antibodies, HLA-A2-restricted and HLA-DP4-restricted responses were observed to be similar to those in naturally infected humans. Therefore, the present study demonstrated that HLA-A2/DP4 transgenic mice can faithfully mimic human cellular responses. Furthermore, we reported four new HLA-DP4-restricted epitopes derived from HBsAg that were identified in both vaccinated HLA-A2/DP4 mice and HLA-DP4-positive human individuals. The HLA-A2/DP4 mouse model is a promising preclinical animal model carrying alleles present to more than a quarter of the human population. This model should facilitate the identification of novel HLA-A2- and HLA-DP4-restricted epitopes and vaccine development as well as the characterization of HLA-DP4-restricted responses against infection in humans.

HLA Genes in Mayos Population from Northeast Mexico

HLA class I and class II alleles have been studied in 60 unrelated people belonging to Mayos ethnic group, which lives in the Mexican Pacific Sinaloa State. Mayos HLA profile was compared to other Amerindians and worldwide populations’ profile. A total of 14,896 chromosomes were used for comparisons. Genetic distances between populations, Neigbour-Joining dendrograms and correspondence analyses were performed to determine the genetic relationship among population. The new specific Mayo HLA haplotypes found are: HLA-A*02-B*35-DRB1*1406-DQB1*0301; HLA-A*02-B*48-DRB1*0404-DQB1*0302; HLA-A*24-B*51-DRB1*0407-DQB1*0302 and HLA-A*02-B*08-DRB1*0407-DQB1*0302. However, the typical Meso American HLADRB1*0407 represents a 40% of all DRB1 alleles. While common HLA characteristics are found in Amerindian distant ethnic groups, still new group specific HLA haplotypes are being found, suggesting that a common founder effect (i.e. high DRB1*0407) is noticed. Moreover, new HLA haplotypes are almost certainly appearing along time probably due to specific pathogen (?) selection for diversity. Mayo language is close to the Tarahumara one (another geographically close group); notwithstanding both groups are not genetically close according to our results, showing again the different evolution of genes and languages, which do not correlate. Finally, Sinaloa is one of the Mexican States in which more European genes are found. However, the results presented in this paper, where no European HLA genes are seen in Mayos, should have a bearing in establishing transplant programs and in HLA and disease studies.

HLA genes in Wayu Amerindians from Colombia

Amerindians origins and prehistory are still debated. HLA profile is different to all other World populations, although they have particular alleles in common with Asians, Australians and Pacific Islanders. In the present work, HLA-A, -B, -DRB1, -DQB1 alleles have been studied in Wayu Amerindians from Colombia. HLA alleles haplotypes, genetic distances and NJ dendrograms were calculated by Arlequin and DISPAN software. Only a few both class I and class II alleles have been observed. Most common extended haplotypes include: A*24-B*51-DRB1*0403-DQB1*0302, A*2-B*15-DRB1*1602-DQB1*0301, A*2-B*35-DRB1*0407-DQB1*0302, but also A*68-B*15-DRB1*0403-DQB1*0302. No trace of Caucasoid or Negroid admixture is detected. The Wayu HLA profile is typical from Amerindians and shows how languages and genes do not correlated particularly in this case (i.e., Wayu closest HLA genetic group is North Argentinian Guarani group). Results obtained in this work may be useful for future transplant programs and also for HLA linked diseases and individualized pharmacogenetics.

HLA genes in Uros from Titikaka Lake, Peru: origin and relationship with other Amerindians and worldwide populations

Uros population from the Titikaka Lake live in about 42 floating reed ('totora') islands in front of Puno City (Peru) at a 4000 m high altiplano. They present both an mtDNA and a human leucocyte antigen (HLA) profile different from the surrounding populations: mtDNA A2 haplogroup is common to Uros and Amazon forest lowland Amerindians. HLA genetic distances between populations have been calculated and neighbour-joining dendrograms and correspondence analyses were carried out. Approximately 15 006 HLA chromosomes from worldwide populations have been used for comparisons. Only eight HLA-A alleles have been found, three of them accounting for most of the frequencies. The same phenomenon is seen for HLA-B, HLA-DRB1 and HLA-DQB1 alleles: a few alleles (3, 4 and 3, respectively) are present in most individuals. The presence of HLA-B*4801 and HLA-DRB1*0901 alleles in a relatively high frequency (although not the most frequent alleles found) is a characteristic shared with Asians and some populations from the Andean altiplano. Three specific Uros haplotypes have been found among the most frequent ones: HLA-A*680102-B*3505-DRB1*0403-DQB1*0302; HLA-A*2402-B*1504-DRB1*1402-DQB1*0301; and HLA-A*2402-B*4801-DRB1*0403-DQB1*0302. The present study suggests that Uros may have been one of the first populations from the shores of the Titikaka Lake coming from the Amazonian forest, which might have given rise to other later differentiated ethnic group (i.e. Aymaras). Uros HLA profile is also useful to study genetic epidemiology of diseases linked to HLA and to construct a future transplant waiting list by adding up regional lists in order to get a bigger pool for transplanting with better HLA matching.

Origin of Bolivian Quechua Amerindians: their relationship with other American Indians and Asians according to HLA genes

The Incas were Quechua-speaking people who settled down near Cuzco (Peru). They had an empire ranging from Ecuador to Chile, when Spanish conquerors seized their kingdom around 1532 AD. Nowadays, Quechua-speaking people inhabits Colombia, Ecuador, Bolivia, Peru and Argentina; however, Quechua language was imposed by both Incas and Spaniards to many non-Quechua speaking communities. We have taken a sample of Quechuan Bolivian blood donors from La Paz (Titicaca Lake region) where Inca-Quechuas themselves believed that came from. This group was compared with 6892 individuals from 68 different world populations regarding HLA/DNA allele frequencies distribution. Genetic distances, dendrograms and correspondence analyses were carried out in order to establish relationships among populations. The main conclusions are: (1) DRB1 and -DQB1 haplotypes shared with Asians are found in Quechuas and are not observed in other (Mesoamerican) Amerindians. (2) Aymara-speaking people from the same Titicaca Lake (La Paz) area shows close genetic distances with Quechuas in one dimension results (genetic distances); however, their HLA gene frequency distribution differs according to Neighbor-Joining (NJ) trees and correspondence analysis (multidimensional and more reliable analyses). Also, the common high frequency Asian and Athabascan HLA-DRB1*0901 allele is found in Quechuas in a significant frequency. Quechuas are clearly included within the Amerindian group.

Polymorphism of HLA-DRB1, -DQB1 and -DPB1 genes in Bai ethnic group in southwestern China

In this work, polymorphism of human leukocyte antigen (HLA)-DRB1, -DQB1 and -DPB1 genes was detected using polymerase chain reaction-sequence-based typing method in 128 healthy unrelated volunteers from the Bai ethnic group of Yunnan province of southwest China. Among all the 28 alleles detected for the DRB1 gene, the most common allele was DRB1*120201 with a frequency of 16.41%, followed by DRB1*090102, DRB1*080302, DRB1*1404, DRB1*150101, DRB1*140101 and DRB1*160201, with frequencies of 10.16%, 9.77%, 9.38%, 8.98%, 8.59% and 8.21%, respectively. Among 19 DQB1 alleles detected, the most frequent allele was DQB1*030101/0309 (35.94%), followed by DQB1*050201 (11.33%), DQB1*060101/060103 (10.54%) and DQB1*0401 (10.16%). For the DPB1 locus, the most common alleles were DPB1*0501 (42.19%), DPB1*1301 (13.28%), DPB1*020102 (10.93%) and DPB1*040101 (9.77%). The comparison of HLA class II allele frequencies of Bais with those of other Chinese populations suggested that the Bai ethnic group belonged to the southern group of Chinese.

Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies

This paper presents a meta-analysis of high-resolution human leukocyte antigen (HLA) allele frequency data describing 497 population samples. Most of the datasets were compiled from studies published in eight journals from 1990 to 2007; additional datasets came from the International Histocompatibility Workshops and from the AlleleFrequencies.net database. In all, these data represent approximately 66,800 individuals from throughout the world, providing an opportunity to observe trends that may not have been evident at the time the data were originally analyzed, especially with regard to the relative importance of balancing selection among the HLA loci. Population genetic measures of allele frequency distributions were summarized across populations by locus and geographic region. A role for balancing selection maintaining much of HLA variation was confirmed. Further, the breadth of this meta-analysis allowed the ranking of the HLA loci, with DQA1 and HLA-C showing the strongest balancing selection and DPB1 being compatible with neutrality. Comparisons of the allelic spectra reported by studies since 1990 indicate that most of the HLA alleles identified since 2000 are very-low-frequency alleles. The literature-based allele-count data, as well as maps summarizing the geographic distributions for each allele, are available online.

HLA class I (A, B, C) and class II (DRB1, DQA1, DQB1, DPB1) alleles and haplotypes in the Han from southern China

In this study, polymerase chain reaction-sequence-specific oligonucleotide prode (SSOP) typing results for the human leukocyte antigen (HLA) class I (A, B, and C) and class II (DRB1, DQA1, DQB1, and DPB1) loci in 264 individuals of the Han ethnic group from the Canton region of southern China are presented. The data are examined at the allele, genotype, and haplotype level. Common alleles at each of the loci are in keeping with those observed in similar populations, while the high-resolution typing methods used give additional details about allele frequency distributions not shown in previous studies. Twenty distinct alleles are seen at HLA-A in this population. The locus is dominated by the A*1101 allele, which is found here at a frequency of 0.266. The next three most common alleles, A*2402, A*3303, and A*0203, are each seen at frequencies of greater than 10%, and together, these four alleles account for roughly two-thirds of the total for HLA-A in this population. Fifty alleles are observed for HLA-B, 21 of which are singleton copies. The most common HLA-B alleles are B*4001 (f= 0.144), B*4601 (f= 0.119), B*5801 (f= 0.089), B*1301 (f= 0.068), B*1502 (f= 0.073), and B*3802 (f= 0.070). At the HLA-C locus, there are a total of 20 alleles. Four alleles (Cw*0702, Cw*0102, Cw*0801, and Cw*0304) are found at frequencies of greater than 10%, and together, these alleles comprise over 60% of the total. Overall, the class II loci are somewhat less diverse than class I. Twenty-eight distinct alleles are seen at DRB1, and the most common three, DRB1*0901, *1202, and *1501, are each seen at frequencies of greater than 10%. The DR4 lineage also shows extensive expansion in this population, with seven subtypes, representing one quarter of the diversity at this locus. Eight alleles are observed at DQA1; DQA1*0301 and 0102 are the most common alleles, with frequencies over 20%. The DQB1 locus is dominated by four alleles of the 03 lineage, which make up nearly half of the total. The two most common DQB1 alleles in this population are DQB1*0301 (f= 0.242) and DQB1*0303 (f= 0.15). Eighteen alleles are observed at DPB1; DPB1*0501 is the most common allele, with a frequency of 37%. The class I allele frequency distributions, expressed in terms of Watterson's (homozygosity) F-statistic, are all within expectations under neutrality, while there is evidence for balancing selection at DRB1, DQA1, and DQB1. Departures from Hardy-Weinberg expectations are observed for HLA-C and DRB1 in this population. Strong individual haplotypic associations are seen for all pairs of loci, and many of these occur at frequencies greater than 5%. In the class I region, several examples of HLA-B and -C loci in complete or near complete linkage disequilibrium (LD) are present, and the two most common, B*4601-Cw*0102 and B*5801-Cw*0302 account for more than 20% of the B-C haplotypes. Similarly, at class II, nearly all of the most common DR-DQ haplotypes are in nearly complete LD. The most common DRB1-DQB1 haplotypes are DRB1*0901-DQB1*0303 (f= 0.144) and DRB1*1202-DQB1*0301 (f= 0.131). The most common four locus class I and class II combined haplotypes are A*3303-B*5801-DRB1*0301-DPB1*0401 (f= 0.028) and A*0207-B*4601-DRB1*0901-DPB1*0501 (f= 0.026). The presentation of complete DNA typing for the class I loci and haplotype analysis in a large sample such as this can provide insights into the population history of the region and give useful data for HLA matching in transplantation and disease association studies in the Chinese population.

HLA genes of Aleutian Islanders living between Alaska (USA) and Kamchatka (Russia) suggest a possible southern Siberia origin

Aleuts HLA profile has been compared with that of neighboring and worldwide populations. Thirteen thousand one hundred and sixty-four chromosomes have been used for this study. Computer programs have obtained HLA allele frequencies, genetic distances between populations, NJ relatedness dendrograms, correspondence analysis and most frequent HLA extended haplotypes. Aleuts have inhabited Aleutian Islands since about 9000 years BP according to fossil and genetic (mtDNA) records. They are genetically different to Eskimo, Amerindian and Na-Dene speakers according to their HLA profile; this correlates with cultural and anthropological Aleut distinctiveness. No typical Amerindian HLA alleles have been found in a significant frequency. Their HLA relatedness to Saami (or Lapps, northern Scandinavians), Finns and Pomors (North-West Russia) indicates an ancient possible origin from the Baikal Lake Area (southern Siberia) around the present day Buryat peopling area; other origins are not discarded. Aleuts characteristic HLA profile may influence future transplantation programs in the region and be useful to study diseases linked to HLA epidemiology.

HLA class I polymorphism in Mongolian and Hui ethnic groups from Northern China

HLA-A, -B, and -C alleles were genotyped by sequencing-based typing (SBT) in 102 unrelated ethnic Mongolian individuals living in Inner Mongolia and 110 Hui individuals inhabiting the Qihai plateau in Northern China. In all, 28 HLA-A, 49 HLA-B, and 27 HLA-C alleles in Mongolians and 29 HLA-A, 41 HLA-B, and 27 HLA-C alleles in Hui were detected in this study. A*24G1, A*110101/1121N and A*02G1 are the three most frequent HLA-A alleles both in Mongolians and Hui. At the HLA-B locus, only B*51G1 was found with a frequency of more than 10% in Hui. Cw*070201G1 is the most common HLA-C allele both in Mongolian and Hui. The most frequent HLA-A:C:B, HLA-A:C, and HLA-C:B haplotypes are A*330301-Cw*030201/030202-B*5801, A*330301-Cw*030201/030202, and Cw*030201/030202-B*5801 in Mongolian and A*0207/0215N-Cw*010201/010202-B*4601, A*02G1-Cw*070201G1, and Cw*010201/010202-B*4601 in Hui, respectively. The genetic distance (GD) estimated according to HLA-A, -B, and -C allele frequency indicates that Mongolian and Hui have the closest relationship, and both are closer to Northern Han rather than Southern Han, suggesting that the two ethnicities might have been subjected to intensive gene exchange with Northern Han in history. The dendrogram based on the GD measurements further demonstrates that Mongolian and Hui cluster as a branch with Northern Han Chinese and Northeast Asians. Our results may lead to better understanding of the origins and relationships of Chinese ethnic groups and provide the genetic background for disease association studies.

HLA genes in Cubans and the detection of Amerindian alleles

Caribbean Islands including Cuba were first inhabited by Meso-American and later by Arawak-speaking Amerindians from nowadays Venezuela. Spanish invaders brought to almost extinction to the Amerindian population after 1492. Black slaves from West Africa were taken into Cuba by Europeans. The degree of admixture among populations is approached. HLA alleles were studied by DNA techniques. Comparison with other worldwide populations (a total of 14.094 chromosomes) included genetic distances, Neighbour-Joining dendrograms, correspondence analyses and calculation of extended haplotypes. While African-European HLA features were clearly found, Amerindian HLA characteristics are less evident, indicating that Amerindian devastation was particularly marked after 1492 AD. However, typical Amerindian alleles have been found in our Cuban sample, i.e. DRB1*0403, DRB1*0404, DRB1*0407, DRB1*0411, DRB1*0802 and DRB1*1602. The presence of Amerindian alleles in Cubans [corrected] may have a bear in the making up of transplantation registries (both for bone marrow and solid organ transplantation) at the regional level and also be important for epidemiological studies of diseases linked to HLA.

Sequencing-based analysis of the HLA-DPB1 polymorphism in Nu ethnic group of south-west China

In the present study, DNA typing for HLA-DPB1 was performed using polymerase chain reaction-sequencing-based typing method in 72 randomly selected Nu ethnic individuals inhabiting the Yunnan province of south-west China. Among the 12 detected DPB1 alleles, the most frequent was DPB1*1301, with the percentage of 20.83%, followed by DPB1*0501 (19.44%), DPB1*040101 (16.67%) and DPB1*2801 (9.72%). The allele DPB1*1501 was found for the first time in the Chinese population. Neighbour-joining showed that the Nu ethnic minority belonged to East Asian cluster and was most closely related to Lisu, being consistent with the historical records. In addition, the results obtained in this study will also provide useful information on organ transplantation, forensic investigations and disease association studies.

Polymorphism of HLA class II genes in Miao and Yao nationalities of Southwest China

In the present study, the polymorphism of human leucocyte antigen class II genes was investigated by the sequence-based typing method in two Chinese populations: the Miaos (n = 85) from Guizhou province and the Yaos (n = 66) from Yunnan province. These two populations exhibited certain similarity in their allelic distributions. Among 24 DRB1 alleles detected, DRB1*150101, DRB1*140101, DRB1*160201 and DRB1*090102 in Miao and DRB1*120201, DRB1*140101, DRB1*150101 and DRB1*090102 in Yao were highly predominant. Sixteen DQB1 alleles in total were found in these two populations among which DQB1*050201, DQB1*060101/060103 and DQB1*030101/0309 in both Miao and Yao and DQB1*050301 in Yao were commonly observed. In the 13 DPB1 alleles detected, the most frequent allele was DPB1*0501 in Miao and Yao followed by DPB1*02 and DPB1*1301. Frequent comparisons with other Chinese populations suggested the southern Chinese feature for both the Miao and Yao nationalities.

Polymorphism of the DPB1 locus in Hani ethnic group of south-western China

Polymorphism of HLA-DPB1 was revealed with a sequencing-based typing (SBT) method in 47 unrelated healthy individuals from Yunnan Hani ethnic minority. The alleles DPB1*5901 and DPB1*7001 were detected for the first time in Chinese populations. A dendrogram showed that the Hani ethnic group belongs to the southern group of Chinese.

Origin of Aymaras from Bolivia and their relationship with other Amerindians according to HLA genes

Aymara Amerindians from the Titicaca Lake Andean highlands are studied for HLA-A, HLA-B, HLA-DRB1 and HLA-DQB1 gene frequencies. Genetic distances, neighbour-joining and correspondence analyses are performed by using other Amerindian and worldwide populations (15384 chromosomes are studied). The HLA genetic profile of Aymaras is different from neighbouring and language-related Quechuas (Incas). Both Quechuas and Aymaras seem to present an HLA-DRB1*0901 high frequency, which is present in a very low frequency or absent in Mesoamericans (Mazatecans, Mayans) and most studied Amerindians. Moreover, it is observed a closer relatedness of Aymaras with Amerindians from the Amazon Basin and Chaco lowlands, compared to Quechuans.

Polymorphism of human leukocyte antigen-DRB1, -DQB1, and -DPB1 genes of Shandong Han population in China

In the present study, polymerase chain reaction-sequence-based typing (PCR-SBT) was used to analyze human leukocyte antigen (HLA)-DRB1, -DQB1, and -DPB1 alleles of 98 unrelated healthy Shandong Han individuals. A total of 60 alleles, in which 28 in DRB1, 15 in DQB1 and 17 in DPB1 were found. Among the 28 detected DRB1 alleles, DRB1*150101, DRB1*070101, DRB1*090102, DRB1*120201, and DRB1*080302 were commonly observed, with frequencies of 16.3%, 11.2%, 10.2%, 8.2%, and 5.6%, respectively. The most predominant DQB1 allele was DQB1*030101/0309 with the frequency of 20.4%, followed by DQB1*0201/0202 (14.8%), DQB1*0602 (14.3%), DQB1*030302 (12.2%), and DQB1*060101/060103 (10.7%). Of the 17 detected DPB1 alleles, DPB1*0501 was the most frequent allele with the frequency of 37.2%. DPB1*020102 (18.4%), DPB1*040101 (11.2%), DPB1*0402 (7.1%), and DPB1*1701 (6.6%) were also very frequent alleles. A total of 53 estimated DRB1-DQB1 two-locus haplotypes were observed in Shandong Han population, of which DRB1*150101-DQB1*0602 was the most predominant, followed by DRB1*090102-DQB1*030302, DRB1*070101-DQB1*0201/0202 DRB1*120201-DQB1*030101/0309, and DRB1*080302- DQB1*060101/060103. The distribution of the HLA class II alleles and haplotypes frequencies as well as the dendrogram showed that the Shandong Han population belongs to the northern group of Chinese. The data have implications for anthropological studies and disease associations.

Variation of HLA class II genes in the Nganasan and Ket, two aboriginal Siberian populations

Allelic frequencies at the three most polymorphic loci of the HLA class II region (DRB1, DQA1 and DQB1) were determined in the Nganasan and Ket, the remnants of the two most ancient groups in the Lower Yenisey River/Taimyr Peninsula region in northern Siberia. By single-stranded conformational polymorphism typing, verified by sequencing, 19 HLA-DRB1-DQA1-DQB1 haplotypes and 15 HLA-DRB1, seven DQA1 and 11 DQB1 alleles were found. The most frequent alleles were DRB1*1301 (23.5%), DQA1*0103 (29.4%), *0501/03/05 (29.4%), and DQB1*0301/09 (32.4%) in the Ket, and DRB1*0901 (25%), DQA1*0301 (39.6%), and DQB1*0301/09 (37.5%) in the Nganasan. The distribution patterns and comprehensive phylogenic analysis based on the haplotype frequencies of 17 Siberian populations suggest that the founders of both the Ket and the Nganasan came from Palaeolithic populations in the Altai-Sayan Upland.

Geographic patterns of functional categories of HLA-DRB1 alleles: a new approach to analyse associations between HLA-DRB1 and disease

Because specific amino acids found within the peptide-binding cleft of human leukocyte antigen (HLA) molecules have been implicated in HLA/disease associations, an approach which consists in grouping the alleles according to their functional properties at the protein level may enable us to better understand HLA associations than the conventional allelic classification. In this study, we applied this methodology to investigate the associations between HLA-DRB1 and rheumatoid arthritis. The alleles were first classified into seven functional categories [restrictive supertype patterns (RSPs)], among which three were known to be significantly associated with susceptibility (one category) or resistance (two categories) to rheumatoid arthritis. The frequencies of these categories were then estimated in 104 population samples previously tested for HLA-DRB1, and their variability was analysed spatially on a worldwide scale by applying an original methodology for detecting discontinuities in geographically patterned data. RSP frequencies were also compared to known values of rheumatoid arthritis prevalence in some populations. The results indicated that the three RSP frequency distributions were geographically structured, and that these patterns could generally be explained by the history of human migrations. However, the peculiar pattern observed for RSP 'A' (conferring susceptibility to rheumatoid arthritis) indicated a possible association with some latitude-dependent disease. Furthermore, the very high correlation coefficient found between RSP 'A' frequencies and rheumatoid arthritis prevalence confirmed the significant disease association of this functional category. In contrast, the putative protective effect of the other RSPs ('De' and 'Q') was not detectable at the worldwide level, but may be significant in specific geographic areas. This study shows that population genetic diversity analyses based on a functional grouping of HLA alleles provide an efficient way to explore the mutual influence of HLA genetic variation and disease.

Molecular analyses of HLA-DRB1, -DPB1, and -DQB1 in Jing ethnic minority of Southwest China

In the present study, DNA typing for HLA-DRB1, DQB1 and DPB1 was performed using polymerase chain reaction-sequencing based typing (PCR-SBT) method in 144 random selected Jing ethnic individuals inhabiting in South China. Allele frequencies and two-locus haplotypes (DRB1-DQB1) were statistically analyzed and 20 DPB1 alleles, 27 DRB1 and 20 DQB1 were detected. The most frequent DPB1 allele was DPB1*0501 with the percentage of 36.9% followed by DPB1*1301 (15.7%), DPB1*0401 (11.0%) and DPB1*020102 (9.8%). Among the 27 detected DRB1 alleles, DRB1*120201 (13.8%) was most commonly observed followed by DRB1*150201, *030101 and *090102 alleles with the frequencies of 9.4%, 9.1% and 8.3%, respectively. Among the 20 detected DQB1 alleles the most predominant one was DQB1*030101/0309 (19.9%). DQB1*050201 (19.1%), DQB1*0201/0202 (16.1%) and DQB1*050101 (12.3%) were also frequently observed in Jing population. Statistical analysis of two-locus haplotypes showed that DRB1*120201-DQB1*030101/DRB1*120201-DQB1*0309 (HF = 9.4%, D = 6.65x10(-2)) was most predominant followed by DRB1*030101-DQB1*0201/DRB1*030101-DQB1*0202 (HF = 8.1%, D = 6.66 x 10(-2)). The comparison of HLA class II allele and haplotype frequencies in Jing with those in other populations all over the world and a dendrogram based on the DRB1, DQB1 and DPB1 genes suggested that Jing ethnic population has an origin of Southeast Asia and is belonged to the southern group of Chinese populations.

HLA-DRB1, DQB1 and DPB1 polymorphism in the Naxi ethnic group of South-western China

Polymorphism of HLA-DRB1, DQB1 and DPB1 was revealed with a sequencing-based typing (SBT) method in unrelated healthy volunteers from the Naxi ethnic group. Among the 43 DRB1 alleles detected, the most common allele was DRB1*12021 with a frequency of 17%, followed by DRB1*08032, DRB1*09012 and DRB1*1404 with frequencies of 8.5%, 7.4% and 7.4%, respectively. Among 23 DQB1 alleles detected, the most frequent DQB1 allele was DQB1*03011/0309 (21.9%), followed by DQB1*0502 (16.4%) and DQB1*05031 (9.6%). For the DPB1 locus, the most common alleles were DPB1*0501 (25.5%), DPB1*0402 (14.6%) and DPB1*02012 (12.0%). The most common DRB1-DQB1-DPB1 haplotype was DRB1*1404-DQB1*05031-DPB1*0402 with a frequency of 5.26%, followed by the DRB1*08032-DQB1*06011-DPB1*1301 (3.51%). The distribution characteristics of the HLA class II alleles revealed that the Naxi ethnic group belonged to the Southern group of Chinese.

HLA-DRB1 and DQB1 allele distribution in the Muong population exposed to malaria in Vietnam

The distribution of 30 HLA-DRB1 alleles in 85 individuals and of 10 HLA-DQB1 alleles in 91 individuals of the Viet Muong population was studied and compared with those of nine other Asian populations, including 103 Viet Kinh belonging to the major ethnic group in Vietnam. In terms of genetic distance, our data are consistent with a close ethnogeographic relationship between Viet Muong, Buyi and Dai Lue, two Southern Chinese ethnic groups. Conversely, these three populations are distant from the Northern Chinese population. The Viet Kinh belong to an intermediate group, together with North-eastern Thais, Thais and present day Thais. The striking presence of the HLA-DQ1*0502 allele (48% frequency) in the Viet Muongs is possibly anthropological or environmental in origin: the Viet Muongs have been submitted to endemic malaria for centuries, and the survivors carry the protective trait of glucose-6-phosphate dehydrogenase deficiency. This raises the hypothesis of a possible resistance to lethal or severe forms of the disease, where the association with a specific HLA-DQB1 allele may play a role.

HLA-DPB1 allelic frequency of the Pumi ethnic group in south-west China and evolutionary relationship of Pumi with other populations

A sequencing-based typing of the HLA-DPB1 gene was carried out in 51 unrelated healthy individuals from the Yunnan Pumi ethnic minority. A total of 18 DPB1 alleles, in which DPB1*0501 (52.0%) and DPB1*0402 (15.7%) greatly predominated, were found, of which alleles DPB1*20011, 2201, 3601, 3701, 3801, 4901, 5001 and 8001 were recorded for the first time in the Chinese population. This may be because the typing methods used in previous genotyping of Chinese populations were of lower sensitivity than that used in our study. A dendrogram constructed by the maximum likelihood method showed that the Pumi ethnic minority belongs to the Asian/Australasian cluster and has the closest relationship to Trobriander, implying an unusual relationship between Australasian and South China populations. However, the Yi ethnic minority, which also comes from the ancient Qiang, did not show a very close relationship with the Pumi. This is probably because the Pumi were historically assimilated by local south-west China populations.

Sequence-Based analysis of the HLA-DRB1 polymorphism in Metalsa Berber and Chaouya Arabic-speaking groups from Morocco

To examine the genetic diversity in Morocco, the polymorphism at the HLA-DRB1 locus was investigated in two populations: the Metalsa group consisting of Berbers from north Morocco (who speak the Tarifit language and live in the Nador area), and the Chaouya group who are Arabic-speaking people from west Morocco (Atlantic coast) living in the Settat area. The DRB1 alleles of 197 healthy unrelated individuals were identified by direct DNA sequencing of exon 2 using fluorescently-labeled primers. A total of 28 and 29 alleles at DRB1 locus were identified in the Metalsa and Chaouya groups, respectively. The most frequent alleles in the Metalsa group are DRB1*03011 (20.2%), DRB1*0701 (12.12%), and DRB1*1302 (11.11%). In the Chaouya group, DRB1*0701 (16.33%), DRB1*15011 (12.76%), and DRB1*03011 (11.73%) are most common. Each population exhibits some specific variants and some uncommon alleles. The frequency of the DRB1*03011 allele differs significantly between the two populations (p = 0.0311). The DRB1 frequency distributions in the two groups suggest the effects of balancing selection. The interpopulation analysis highlighted a strong relatedness, based on genetic distances, between the two Moroccan groups and the other north Africans (the Moroccans from El Jadida area, Moroccan Souss Berbers, Algerians, and Tunisians), and to a lesser extent with the Iberians, French, and Ethiopians.

African diversity from the HLA point of view: influence of genetic drift, geography, linguistics, and natural selection

This study investigates the influence of different evolutionary factors on the patterns of human leukocyte antigen (HLA) genetic diversity within sub-Saharan Africa, and between Africa, Europe, and East Asia. This is done by comparing the significance of several statistics computed on equivalent population data sets tested for two HLA class II loci, DRB1 and DPB1, which strongly differ from each other by the shape of their allelic distributions. Similar results are found for the two loci concerning highly significant correlations between geographic and genetic distances at the world scale, high levels of genetic diversity within sub-Saharan Africa and East Asia, and low within Europe, and low genetic differentiations among the three broad continental areas, with no special divergence of Africa. On the other hand, DPB1 behaves as a neutral polymorphism, although a significant excess of heterozygotes is often observed for DRB1. Whereas the pattern observed for DPB1 is explained by geographic differentiations and genetic drift in isolated populations, balancing selection is likely to have prevented genetic differentiations among populations at the DRB1 locus. However, this selective effect did not disrupt the high correlation found between DRB1 and geography at the world scale, nor between DRB1 and linguistic differentiations at the African level.

HLA genes in Mexican Mazatecans, the peopling of the Americas and the uniqueness of Amerindians

The HLA allele frequency distribution of the Mexican Mazatecan Indians (Olmec culture) has been studied and compared with those of other First American Natives and worldwide populations (a total of 12,100 chromosomes; 6,050 individuals from 59 different populations). The main conclusions are: 1) An indirect evidence of Olmec and Mayan relatedness is suggested, further supporting the notion that Olmecs may have been the precursors of Mayans; 2) Language and genetics do not completely correlate in microenvironmental studies; and 3) Peopling of the Americas was probably more complex than postulated by Greenberg and others (three peopling waves). Significant genetic input from outside is not noticed in Meso and South American Amerindians according to the phylogenetic analyses; while all world populations (including Africans, Europeans, Asians, Australians, Polynesians, North American Na-Dene Indians and Eskimos) are genetically related. Meso and South American Amerindians tend to remain isolated in the Neighbor-Joining, correspondence and plane genetic distance analyses.

HLA-DRB1, -DQA1, and -DQB1 genotypes in patients with nasal polyposis

OBJECTIVES/HYPOTHESIS

Genetic etiology is suspected in the development of nasal polyposis on the basis of familial aggregation. This study investigated whether there is an association between HLA-DRB1, -DQA1, and -DQB1 alleles and developing nasal polyposis.

STUDY DESIGN

Data from 50 polypectomized patients were compared with data from 50 healthy randomly selected controls. Polyp score, possible asthma, aspirin sensitivity, and ASA triad were also recorded.

METHODS

Genotyping of HLA-DRB1 alleles was carried out with the Dynal RELI SSO HLA-DRB, a direct DNA probe test that utilizes a polymerase chain reaction (PCR) and nucleic acid hybridization for the differentiation of 70 HLA-DRB alleles and 9 supertypes. For DQA1* genotyping PCR-RFLP (restriction fragment length polymorphism) was used, differentiating eight alleles. The DQB1* typing was carried out using a INNO-LiPA DQB PCR-reverse hybridization kit, allowing the discrimination of 30 alleles.

RESULTS

People carrying the HLA-DR7-DQA1*0201, and -DQB1*0202 haplotype were found to have a two to three times higher odds ratios (ORs) for developing the disease, compared with controls. Patients with ASA triad carried the above-mentioned DR7 allele with the linked alleles significantly more often (P < .001). Subjects carrying HLA-DR5 allele and the linked alleles had lower odds ratio values.

CONCLUSION

These results underline that allergy is not conditional for the formation of nasal polyps as thought before. Nasal polyposis associated with asthma and aspirin sensitivity is probably a unique form of nasal polyps. The authors plan further investigations in this field.

T cell responses to 53-kDa outer membrane protein of Porphyromonas gingivalis in humans with early-onset periodontitis

Patients with early-onset periodontitis (EOP) are susceptible to infection with periodontopathic bacteria, such as Porphyromonas gingivalis. Ag53, 53-kDa outer membrane protein of P. gingivalis, evokes strong humoral immune responses in EOP patients. In a first step to clarify how host immune cells recognize Ag53, we established Ag53-specific short-term T cell lines from 22 subjects including 6 EOP patients and 16 healthy donors, using overlapping peptides based on Ag53 amino acid sequences. All T cell lines from active EOP patients recognized a common region (p141-181, especially p141-161) on Ag53, while those from healthy donors showed heterogeneous specificity. p141-181 was not recognized by T cell lines established from EOP patients following therapy. A monoclonal antibody to HLA-DRB 1 inhibited Ag53-induced proliferation of most of the T cell lines. Our observations suggest that, although antigen-presenting molecules are common in EOP patients and in healthy individuals, p141-161 includes a major T cell epitope(s) on Ag53 for active EOP patients but not for healthy individuals or inactive EOP patients.

HLA class II allele and haplotype frequencies in Ethiopian Amhara and Oromo populations

HLA class II alleles were identified in 181 healthy unrelated Ethiopian children of both sexes and in 350 European controls from the South of France. The Ethiopian individuals belonged to the two major ethnic groups of the country: Oromo (N=83) and Amhara (N=98). In both panels, genetic polymorphism of HLA class II alleles was analysed for the first time by molecular typing of DRB1, DQA1 and DQB1 loci. Allelic and phenotypic frequencies were compared with those of European controls and other African populations. Construction of HLA class II three-locus haplotypes was also performed. The study revealed some differences between the two groups. Characteristic features of Central and North African populations appeared on the Ethiopian HLA genotypes. Surprisingly, DRB1*11 presented one of the lowest gene frequencies in both Ethiopian ethnic groups in contrast to Europeans and West Africans. Furthermore, this decrease was more marked than those observed using serological techniques in other geographically close East African countries. Oromo and Amhara only showed minor differences in spite of their different origins and histories. One significant difference consisted of a lower DRB1*01 gene frequency in Oromo as reported in most West African people. Some new or rare haplotypes were also observed in the Oromo group. Our results underline the distinctive features of the Ethiopian populations among the few HLA genotyping data available for East African groups and emphasise the major interest of such investigations in this region of Africa.

Major histocompatibility complex class II alleles in an Uygur population in the Silk Route of Northwest China

HLA class II (DRB1, DQA1, DQB1 and DPB1) genotyping was performed in 57 unrelated Uygur individuals inhabiting the northwestern China area by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Among 98 DRB1 alleles tested, 23 alleles were detected, and DRB1*0701 (16.7%) and DRB1*0301 (14.0%) were the most and the second most common alleles, respectively. In 8 DQA1 alleles detected, DQA1*05 (26.3%), DQA1*03 (21.9%) and DQA1*0201 (21.1%) were very frequent. Of 21 DQB1 alleles tested, 13 were observed. Among them, DQB1*02 was highly predominant with the gene frequency of 32.5%. Of 46 DPB1 alleles tested, 15 were detected, among which DPB1*0401 (31.6%) was the most frequent. Two haplotypes predominate clearly; DRB1*0701-DQA1*0201-DQB1*02 (15.5%) and DRB1*0301-DQA1*05-DQB1*02 (12.6%). The dendrogram constructed by the neighbour-joining (NJ) method based on the allele frequencies of the DRB1, DQA1, DQB1 and DPB1 genes of 13 representative populations all over the world suggested that Uygur belonged to the Asian group and lay at the closest genetic distance to a Kazak population inhabiting the same area.

Major histocompatibility complex class II alleles in Kazak and Han populations in the Silk Route of northwestern China

Genetic polymorphism of the HLA class II loci including the DRB1, DQA1, DQB1 and DPB1 genes was investigated by the polymerase chain reaction-restriction fragment-length polymorphism (PCR-RFLP) method in a Kazak population inhabiting the most northwestern part of China, Urümqi in the Xinjiang Uygur Zizhiqu as well as in a Han population in the same area. Forty-two Kazak and 59 Han unrelated volunteers were enrolled in this study. Among 51 DRB1 alleles tested, 29 alleles were detected, and DRB1*0301 (13.1%) and DRB1*07 (10.7%) in Kazak and DRB1*0901 (11.9%), DRB1*1501 (11.0%) and DRB1*07 (11.0%) in northwestern Han were highly predominant. In 8 DQA1 alleles detected, DQA1*0501 (29.8%) and DQA1*0301 (23.8%) in Kazak, and DQA1*0301 (28.8%) and DQA1*0102 (19.5%) in northwestern Han were the most and the second most common alleles, respectively. Of 18 DQB1 alleles tested, 14 were observed, among which DQB1*0201 and DQB1*0301 were very frequent both in Kazak (23.8% and 21.4%, respectively) and northwestern Han (18.6% and 16.9%, respectively) populations. Of 37 DPB1 alleles tested, 14 were detected. Among them, the frequencies of DPB1*0401 (21.4%), DPB1*0501 (20.2%), DPB1*0402 (19.0%) and DPB1*0201 (16.7%) in Kazak, and those of DPB1*0501 (38.1%) and DPB1*0201 (16.1%) in northwestern Han were highly increased. Several three-locus haplotypes were recognized to predominate significantly, namely DRB1*0301-DQA1*0501-DQB1*0201 (13.1%) and DRB1*0701-DQA1*0201-DQB1*0201 (8.3%) in Kazak; and DRB1*0901-DQA1*0301-DQB1*0303 (11.9%) and DRB1*0701-DQA1*0201-DQB1*0201 (10.2%) in northwestern Han. The dendrogram constructed by the neighbor-joining (NJ) method based on the allele frequencies of the DRB1, DQA1, DQB1 and DPB1 genes of 12 representative populations all over the world including northern Han, southern Han, Manchu and Japanese suggested that Kazak and northwestern Han were the closest to each other, but Kazak was a little farther from the Asian ethnic groups than northwestern Han.

HLA class I and class II frequencies of a Hong Kong Chinese population based on bone marrow donor registry data

HLA-A, and -B antigen, gene and haplotype frequencies have been calculated from 18,774 southern Chinese donors on a Hong Kong-based bone marrow donor registry. Two hundred and fifty donors were also tested for HLA-DRB1, -DQA1, and -DQB1 alleles using the PCR-SSP technique. Forty-one HLA-A, -B combinations showed statistically significant positive linkage disequilibrium at the 0.05 level after adjustment for the number of haplotypes theoretically possible and 43 showed significant negative disequilibrium. Thirty-nine different DRB1-DQA1-DQB1 haplotypes were identified of which 20 occurred 5 or more times. The most prevalent was DRB1*0901-DQA1*0301-DQB1*0303 (haplotype frequency = 0.1620). This is the first paper to report the distribution of DQA1*0104, DQA1*05011 and DQA1*05012/13 alleles in Chinese. These data are important for phylogenetic, comparative and medico-legal studies and are of particular value in estimating the likelihood of obtaining appropriately matched donors for Chinese patients awaiting bone marrow transplantation.

Molecular analysis of HLA polymorphism in Khoton-Mongolians

We have investigated polymorphism of the HLA class I and class II genes in Mongolians for the first time using PCR-based techniques. A minor population of Khoton-Mongolians was studied and compared to the major Khalkh-Mongolian population. Eighty-five Khoton- and 41 Khalkh-Mongolian samples were analyzed for polymorphism in HLA-A, -B, -DRB1, -DRB3, -DRB5, -DQA1, -DQB1, -DPA1, and -DPB1 loci using PCR-SSOP and PCR-RFLP methods. Allele and haplotype frequencies were calculated. The results were then compared to those obtained from other human populations. In Khoton-Mongolians, the frequency of HLA-B38, DRB1*0301, DQA1*0502, DQB1*0201 and DPB1*0401 were significantly higher than those in other Mongoloid populations including Khalkh-Mongolians, Buryat, Chinese, Northern Han, Southern Han, Koreans and Japanese. In contrast, the frequency of HLA-A2, DQA1*0102, DPB1*0201 and DPB1*0501 were significantly lower in Khoton-Mongolians. Haplotype frequency analysis revealed that Khoton-Mongolians shared the same haplotypes specific to Mongoloids as well as to Caucasoids. On the other hand, several haplotypes were found to be specific for the Khoton. The phylogenetic tree analysis constructed by the NJ method based on allele frequencies of HLA-A, -B, -DRB1, -DQA1, and -DQB1 genes revealed that the Khoton belong to the Northeast Asian cluster and are most closely related to the Khalkh, Inner Mongolian, Uygur and Buryat populations. These data suggest a unique genetic background for Khoton-Mongolians. Furthermore, they are closely related genetically to both Mongoloids and Caucasoids.