HLA Alleles and Risk of Cervical Intraepithelial Neoplasia Among Southwestern American Indian Women

An increase in cervical intraepithelial neoplasia (CIN) has been described in American Indian women in New Mexico. Differences in human leukocyte antigen (HLA) alleles have been reported in cervical intraepithelial neoplasia (CIN) compared with controls in other populations. We investigated HLA alleles and CIN in Southwest American Indian women. The case control study included 89 women with biopsy-proven CIN II/III (diagnosed November 1994 through October 1997) and 271 similar women with normal cervical epithelium from the same clinics. DRB1, DQB1, and DPB1 alleles were determined using DNA typing techniques. DQA1 and HLA-A allele typing was included for some subjects (randomly chosen n = 37 and n = 163 cases and controls, respectively). We found a decreased risk of CIN with DRB1*1402 (OR 0.5, 95% CI 0.3-0.9) and an increased risk with DRB1*1501 (OR 2.7, 95% CI 0.9-7.3). Additionally, DQA1*0102 was associated with increased risk (OR 4.5, 95% CI 1.3-5.3) and HLA-A*02 with decreased risk (OR 0.4, CI 0.2-0.9). Our findings are discussed along with studies in other populations.

HLA alleles and haplotypes among the lakota sioux: report of the ASHI minority workshops, part III

Human leukocyte antigen (HLA) class I and II alleles were defined for 302 Lakota Sioux American Indians as part of the American Society for Histocompatibility and Immunogenetics coordinated studies on minority populations. The study group was comprised of adult volunteers from the Cheyenne River and Ogala Sioux tribes residing, respectively, on the Cheyenne River and Pine Ridge Reservations in South Dakota. Of the participants, 263 (87%) claimed full American Indian ancestry through both maternal and paternal grandparents. The study group included 25 nuclear families that were informative for genotyping. HLA phenotypes from 202 adults with no other known first-degree relative included in the study were used for calculation of allele and haplotype frequencies by maximum likelihood estimation. HLA-A, -B, and -Cw alleles were found to be in Hardy Weinberg equilibrium. Deviation from equilibrium was observed for DRB1 alleles (p=0.01), but could be attributed to the sample size and the occurrence of some genotypes with low expected frequencies. Polymorphism among the Sioux was limited with four to seven alleles comprising >80% of those observed at each locus. Several alleles were found at high frequency (0.05-0.30) among the Sioux that are also prevalent in other Native Americans and Alaska Natives, including: A*2402, *3101, and *0206; B*3501,*3901, *5101, and *2705; Cw*0702, *0404, and *03041; DRB1*0407, *0404, *1402, and *16021; and DQB1*0301, *0302, and *0402. DRB1*0811, which has been only previously described in Navajo and Tlingit Indians, was found to occur at a frequency of 0.119 among the Sioux. Two new alleles were defined among the Sioux: Cw*0204 and DRB1*040703, which were found in two and four individuals, respectively. In the haplotype analyses, significant linkage disequilibrium (p<0.00001) was seen in all pairwise comparisons of loci and numerous two and three locus haplotypes were found to have strong, positive linkage disequilibrium values. The two most common extended haplotypes among the Sioux, determined by maximum likelihood estimation and genotyping were: A*31012, B*3501, Cw*0404, DRB1*0407; and A*24021, B*3501, Cw*0404, DRB1*0404.

Genetic structure of seven Mexican indigenous populations based on five polymarker loci

This descriptive study investigates the genetic structure of seven Mexican indigenous populations (Mixteca Alta, Mixteca Baja, Otomies, Purepecha, Nahuas-Guerrero, Nahuas-Xochimilco, and Tzeltales) on the basis of five PCR-based polymorphic DNA loci: LDLR, GYPA, HBGG, D7S8, and GC. Genetic distance and diversity analyses indicate that these Mexican indigenous are similar and that more than 96% of the total gene diversity (H(T)) can be attributed to individual variation within populations. Mixteca-Alta, Mixteca-Baja, and Nahuas-Xochimilco show indications of higher admixture with European-derived persons. The demonstration of a relative genetic homogeneity of Mexican Indians for the markers studied suggests that this population is suitable for studying disease-marker associations in the search for candidate genes of complex diseases.

On the genetic uniqueness of the Ami aborigines of Formosa

In the attempt to reconstruct the prehistory of Pacific and Indian Ocean populations, Taiwan's aborigines appear to be of particular interest. Linguistic and archeological evidence indicates that the dispersal of Austronesian speakers throughout the islands of Oceania and Southeast Asia may have originated from Taiwan about 5,000 years ago. The Ami are Taiwan's largest aboriginal group. Here, we report on six polymorphic point mutation loci in Ami individuals and compare allelic frequencies to worldwide populations. In order to examine the genetic characteristics and relationships of the Ami aborigines, we used the allelic frequency data to generate expected heterozygosities, power of discrimination values, maximum likelihood phylogenetic trees, principal component maps, and centroid gene flow plots. These analyses argue for the genetic isolation and uniqueness of the Ami people. Data supportive of limited gene flow and/or small population size, as well as genetic similarities to Native Americans, were observed.

Genetic population history relationships of the population of Bogotá, Colombia, by using the D1S80, VWA, and TH01 molecular markers

The genetic relationships of the population of Bogotá, Colombia, was comparatively studied with regard to other populations from America, Europe, and Asia, by using the D1S80, VWA, and TH01 molecular loci. From a population history point of view, the population of Bogotá seems to be more related to a European origin, with several differential contributions coming from Amerindians rather than from African and Asian populations, when the D1S80 and TH01 markers were employed. However, the contribution was greater from African populations for the VWA marker. Several explanations are offered to resolve the genetic affiliation of this population.

Distribution of the HLA-DQA1 and polymarker alleles in the Basque population of Spain

HLA-DQA1 and polymarker (LDLR, GYPA, HBGG, D7S8, and GC) genotypic and allelic frequencies are determined for a population sample of 102 unrelated Basque individuals using PCR-based methodology. All six loci met Hardy-Weinberg expectations in at least two of the three analyses performed (HLA-DQA1 failed to meet Hardy-Weinberg requirements in the heterozygote deficiency test). Three linkage analysis programs (GDA, GENEPOP and LINKDOS) detected possible linkage disequilibrium between LDLR and HBGG and results from one (GDA) indicated a possible non-random association between HBGG and HLA-DQA1 as well. Allelic data for the six loci are compared to that previously established for other populations (18 for polymarker alone, 16 for polymarker plus HLA-DQA1) to determine homogeneity between the Basque sample and these groups. According to the results of G-tests based on these loci, the Tadjik, a nomadic Caucasian group from western Asia, and the Basque residents are the only sample populations surveyed that are homogenous with the Basque sample. Phylogenetic analysis places the Basque sample correctly within the Caucasian cluster.

Human phylogenetic relationships according to the D1S80 locus

By analyzing the allelic frequencies at the D1S80 locus in 43 human populations, we show that the locus is polymorphic globally and that it can be used to discriminate between major racial groups and subpopulations through phylogenetic analysis. Although the use of informative multiple loci generally provides more accurate phylogenetic relationships, in instances where time and/or target DNA availability is limited, D1S80 could provide useful data to discriminate between human groups. Also, knowledge of which loci independently provide accurate phylogenetic relationships, such as the D1S80, can be used to design more accurate multi-locus combinations. In addition, allele frequencies at the locus are reported, for the first time, for Bahamian individuals of African origin and for Chimila, Bari, and Navajo (Cañoncito Valley) native Americans. Allelic data was obtained using standard polymerase chain reaction (PCR) techniques. In the four new populations, 65 genotypes and 20 segregating alleles were observed. All populations conformed to Hardy-Weinberg expectations except the Chimila.