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

Fort, Marylise; Stefano, G. F. De; Cambon‐Thomsen, Anne; Giraldo‐Alvarez, P.; Jm, Dugoujon; Ohayon, E; Scano, Giuseppina; Abbal, M.

doi:10.1111/j.1399-0039.1998.tb02971.x

Cited by 34 publications

(26 citation statements)

References 26 publications

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“…The present study and a previous one [29] also showed that the frequencies of HLA-DQB1*02 (a risk allele for podoconiosis) and HLA-DRB1*13 (a protective allele against podoconiosis) in the Ethiopian population were among the highest in Sub-Saharan Africa. HLA-DQB1*02 had the third highest frequency in the Ethiopian ethnic groups following Burkina Faso’s Fulani (DQB1*0201, 36.0%) and Central African Republic’s Aka Pygmy group (DQB1*0201, 36.9%).…”

Section: Discussionsupporting

confidence: 85%

“…Finally, we compared HLA allele frequency distributions between the population group in our dataset and unrelated and apparently healthy children of Oromo (n = 83) and Amhara (n = 98) ethnicity from central Ethiopia (http://www.allelefrequencies.net/). The mean age of the Oromo and Amhara subjects was 8.2 years, and ranges between 4 and 12 years [29], [44].…”

Section: Methodsmentioning

confidence: 99%

“…Next, we compared HLA-DRB1 and HLA-DQB1 allele frequencies in a combined dataset (n = 197) comprising Wolaita ethnic individuals in the prediction set (n = 109) and previously HLA typed controls free of podoconiosis in the training set (n = 88) with those previously reported in apparently healthy children of Oromo (n = 83) and Amhara (n = 98) ethnicity from semi-urban parts of Asela town, Arsi, central Ethiopia (http://www.allelefrequencies.net/) [29], [44]. Individuals with podoconiosis (an HLA associated disease [42]) were excluded to minimize bias in allele frequency.…”

Section: Methodsmentioning

confidence: 99%

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Prediction of HLA Class II Alleles Using SNPs in an African Population

et al. 2012

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BackgroundDespite the importance of the human leukocyte antigen (HLA) gene locus in research and clinical practice, direct HLA typing is laborious and expensive. Furthermore, the analysis requires specialized software and expertise which are unavailable in most developing country settings. Recently, in silico methods have been developed for predicting HLA alleles using single nucleotide polymorphisms (SNPs). However, the utility of these methods in African populations has not been systematically evaluated.Methodology/Principal FindingsIn the present study, we investigate prediction of HLA class II (HLA-DRB1 and HLA-DQB1) alleles using SNPs in the Wolaita population, southern Ethiopia. The subjects comprised 297 Ethiopians with genome-wide SNP data, of whom 188 had also been HLA typed and were used for training and testing the model. The 109 subjects with SNP data alone were used for empirical prediction using the multi-allelic gene prediction method. We evaluated accuracy of the prediction, agreement between predicted and HLA typed alleles, and discriminative ability of the prediction probability supplied by the model. We found that the model predicted intermediate (two-digit) resolution for HLA-DRB1 and HLA-DQB1 alleles at accuracy levels of 96% and 87%, respectively. All measures of performance showed high accuracy and reliability for prediction. The distribution of the majority of HLA alleles in the study was similar to that previously reported for the Oromo and Amhara ethnic groups from Ethiopia.Conclusions/SignificanceWe demonstrate that HLA class II alleles can be predicted from SNP genotype data with a high level of accuracy at intermediate (two-digit) resolution in an African population. This finding offers new opportunities for HLA studies of disease epidemiology and population genetics in developing countries.

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Section: Discussionsupporting

confidence: 85%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Prediction of HLA Class II Alleles Using SNPs in an African Population

et al. 2012

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“…The most frequent three‐locus haplotype DRB1*0701‐DQA1*0201‐DQB1*0201 (~13%) of north Indian Hindus was found in all the Caucasian populations ranging from 4.90% in Greeks (Fort et al ., 1998) to 20.1% among US Caucasians (Sanchez‐Velasco et al ., 2003). However, this haplotype cannot be defined as a true Caucasian haplotype as various African populations like Ethiopians Amharas — 19.20% (Fort et al ., 1998), Algerians — 9.9% (Djoulah et al ., 1994) and Moroccans — 20% (Gomez‐Casado et al ., 2000) and populations from East Asia like Chinese (10.20%) have also shown high frequency of this haplotype. We suggest that DRB1*0701‐DQA1*0201‐DQB1*0201 is one of the founder haplotypes and is universally present in all global populations.…”

Section: Discussionmentioning

confidence: 99%

Human genetic variation studies and HLA class II loci

Agrawal

Khan

Bharadwaj

2007

Int J Immunogenetics

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Human leucocyte antigen (HLA) loci widely known for their role in generation of immune responses by encoding cell-surface heterodimers are often considered to be effective for the purpose of reconstructing human phylogenies due to high degree of polymorphism and less recombination. In the present study, we have made an attempt to study HLA class II loci (DRB1, DQA1 and DQB1) in inferring phylogenetic relationship based on both phylogenetic and haplotype approach. In the phylogenetic approach, the compiled database of 19 populations got segregated and finely resolved in three basal clusters with very high bootstrap values corresponding to four geo-ethnic groups of Africans, Orientals, Americans and Caucasians. Maximum- likelihood phylogram has placed North Indian Hindus alongside other Caucasian populations. Haplotype analysis revealed high range of haplotype diversity with nearly 144 observed haplotypes. The haplotype distribution suggested that numbers of Caucasian-specific haplotypes are frequently found among north Indian Hindus. Our results indicate that if the property of less recombination is explored to assign extended haplotypes, followed by strong interpretation based on more logistic statistical model, then there is a high possibility that HLA class II loci can infer exact and accurate phylogenetic assessments as revealed by mtDNA and Y-chromosome markers.

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“…To have a broader picture of the genetic relationship between Fulani and other sub-Saharan African populations, we also included in the analysis data retrieved from the HLA Database (frequencies available at www.allelefrequencies.net), including Aka Pygmies from the Central African Republic (CAR) [35], Bantu from the Democratic Republic of Congo (DRC) [35], Banzabi from Gabon [36], Bubi from Equatorial Guinea [37], Amhara and Oromo from Ethiopia [38], Venda from South-Africa [39], and Shona from Zimbabwe [40]. When necessary, correspondent serologic specificities were used, and high-resolution molecular alleles were pooled to allow comparison across the 15 populations, based on current HLA nomenclature [41].…”

Section: Interpopulation Genetic Variationmentioning

confidence: 99%