HLA in Jaidukama: an Amerindian secluded Colombian population with new haplotypes and Asian and Pacific-shared alleles

Prevalence of axial spondyloarthritis in Colombia: data from the National Health Registry 2017-2021

INTRODUCTION

Registries allow ascertaining the epidemiology of chronic diseases such as axial spondyloarthritis (axSpA). The Colombian Ministry of Health has implemented a National Health Registry (SISPRO) that collects data from each medical contact in the system, which provides close to universal coverage (around 98%).

OBJECTIVE

To establish the 5-year prevalence of axSpA in Colombia, and to describe its demographics, using data from January 1st, 2017, to December 31st, 2021.

METHODS

We performed an observational, cross-sectional study using the International Statistical Classification of Diseases and Related Health Problems as search terms related to ax-SpA, based on SISPRO data. We estimated the prevalence using three approaches: (1) ankylosing spondylitis (AS) diagnoses; (2) diagnoses compatible with axSpA; and (3) diagnoses compatible with axSpA, including sacroiliitis. We calculated prevalence per 100,000 inhabitants.

RESULTS

Based on our three approaches, patients with a primary diagnosis compatible with ax-SpA ranged between 12,684 and 117,648, with an estimated 5-year adjusted prevalence between 26.3 and 244 cases per 100,000 inhabitants (0.03-0.2%). The male-to-female ratio ranged between 1.2:1 and 0.4:1, which was markedly skewed towards a higher prevalence in women when we included the code for sacroiliitis. We found the highest frequency of cases in the 50-54 years group. A differential prevalence was observed between different regions in our country, particularly in regions known to have European ancestors.

CONCLUSION

This is the first study that describes demographic characteristics of ax-SpA in Colombia and offers valuable information for stakeholders. Key Points • Using the official country-level health database, the prevalence of axSpA in Colombia ranges between 26.3 and 244 cases per 100,000 inhabitants (0.03% - 0.2%) • The prevalence of axSpA peaked among the 50-54 years patient group, suggesting an increased survival • Nations with a substantial admixture, such as Colombia, may present a differential prevalence of axSpA among regions within the country • Including the ICD-10 code for sacroiliitis (M46.1) in epidemiological studies probably overestimates the frequency of axSpA.

HLA molecular study of patients in a public kidney transplant program in Guatemala

Guatemala is a country located in Central America, and while it is one of the most populated countries in the region, the genetic diversity of the population has been poorly analyzed. Currently, there are no analyses of the distribution of human leukocyte antigen (HLA) system alleles in mixed ancestry (i.e., ladino) populations in Guatemala. The HLA system exhibits the most extensive polymorphism in the human genome and has been extensively analyzed in a large number of studies related to disease association, transplantation, and population genetics (with particular importance in the understanding of diversity in the human population). Here, we present HLA typing data from 127 samples of unrelated individuals from the kidney transplant program of the San Juan de Dios General Hospital (Guatemala City) using a PCR-SSOP-based (PCR-sequence specific oligonucleotide probes) typing method. We found 16 haplotypes that accounted for 39.76 % of the total haplotype diversity, of which thirteen have been reported previously in Native American populations and three have been reported in European populations. The analyses showed no deviations from Hardy-Weinberg equilibrium, and admixture estimates calculated with k = 3 ancestral components showed that Native American was the most represented component, followed by the European component. The African component was less prominent in the Guatemala mixed ancestry sample in comparison to samples from other countries in Central America. The HLA-based admixture results for Central America showed a continuum in the distribution of Native American, European and African ancestries throughout the region, which is consistent with the complex demographic history of the region.

HLA-B Allele, Genotype, and Haplotype Frequencies in a Group of Healthy Individuals in Colombia

BACKGROUND

The sequencing of alleles of the HLA-B, a human leukocyte antigen (HLA) class I gene, was established as the most polymorphic of chromosome 6 and of the entire human genome. In this locus, the HLA-B*27 allele is highly polymorphic and has clinical relevance. Literature about the subtypes and singular frequency of these alleles in Colombia's healthy population is scarce.

OBJECTIVE

The aim of this study was to establish the HLA-B allele, genotype, and haplotype frequencies in a healthy Colombian population and analyze their association with the sex and geographical distribution of the individuals studied.

METHODS

This is a nonexperimental and descriptive study. The data from whole-blood samples whose HLA genes were genotyped by protocol with the Luminex 100/200 xMAP technology were evaluated. HLA-B*27 positivity was confirmed by the new-generation sequencing technology. The associations between the HLA-B alleles and demographic variables were evaluated by χ2 and Fisher exact tests.

RESULTS

Twenty-seven HLA-B genotypes were identified in 255 individuals, with the highest frequencies for HLA-B*35 (44.7%), B*40 (19.6%), and B*44 (16.8%). Additionally, 89 HLA-B alleles were found; the most common were HLA-B*35:01 (6.7%) and B*40:02 (6.5%). Nine individuals tested positive for the HLA-B*27 allele with genotype and allele frequencies of 3.5% and 1.8%, respectively; the HLA-B*27:05:02 subtype predominated.

CONCLUSIONS

Here, we report the most common HLA-B allele, genotype, and haplotype frequencies in a healthy Colombian population group and analyzed their association with the sex and geographical distribution of the individuals studied. Results for the HLA-B*27 allele confirm racial mixing in Colombia with a high degree of Caucasian influence, as well as the repopulation of Colombia's central region, attributed to the migration phenomena. Results agree with data published in Colombia that was obtained from cord blood samples.

The immunogenetic diversity of the HLA system in Mexico correlates with underlying population genetic structure

We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) allele groups and alleles by PCR-SSP based typing in a total of 15,318 mixed ancestry Mexicans from all the states of the country divided into 78 sample sets, providing information regarding allelic and haplotypic frequencies and their linkage disequilibrium, as well as admixture estimates and genetic substructure. We identified the presence of 4268 unique HLA extended haplotypes across Mexico and find that the ten most frequent (HF > 1%) HLA haplotypes with significant linkage disequilibrium (Δ'≥0.1) in Mexico (accounting for 20% of the haplotypic diversity of the country) are of primarily Native American ancestry (A*02~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*08~DQB1*04, A*68~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*14~DQB1*03:01, A*24~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*04~DQB1*03:02, A*02~B*40:02~DRB1*04~DQB1*03:02, A*68~B*35~DRB1*04~DQB1*03:02, A*02~B*15:01~DRB1*04~DQB1*03:02). Admixture estimates obtained by a maximum likelihood method using HLA-A/-B/-DRB1 as genetic estimators revealed that the main genetic components in Mexico as a whole are Native American (ranging from 37.8% in the northern part of the country to 81.5% in the southeastern region) and European (ranging from 11.5% in the southeast to 62.6% in northern Mexico). African admixture ranged from 0.0 to 12.7% not following any specific pattern. We were able to detect three major immunogenetic clusters correlating with genetic diversity and differential admixture within Mexico: North, Central and Southeast, which is in accordance with previous reports using genome-wide data. Our findings provide insights into the population immunogenetic substructure of the whole country and add to the knowledge of mixed ancestry Latin American population genetics, important for disease association studies, detection of demographic signatures on population variation and improved allocation of public health resources.

HLA-G in Amerindians: Epidemiology and Worldwide Population Comparison

Background:

HLA-G molecules are immunosuppressive and avoid fetal rejection by giving negative signals to maternal immune system from fetal trophoblast cell surface. HLA-G genes have been associated to different pathologies: Spontaneous abortions, autoimmunity, tumor progression, transplant rejection and infection. In addition, different World populations show remarkable different HLA-G allele frequencies in the allele that does not produce a full HLA-G molecule (HLA-G*05N); this allele is almost absent in studied Amerindians.

Objectives:

The aim is to study HLA-A.-B,-DRB1 and –G alleles and extended haplotypes in Amerindians for the first time. This may be useful to asses HLA-G epidemiology, association to disease and Preventive Medicine in Amerindians.

Methods:

HLA-A,-B and -DRB1 have been typed by using standard automatic protocols. HLA-G alleles have been detected by direct HLA-G exon 2, exon 3 and exon 4 DNA sequencing. Computer calculations have been done by specific standard methods.

Results:

HLA-A,-B,-DRB1 and –G extended haplotypes have been calculated in Amerindians for the first time. Also, their HLA-G frequencies have been compared with worldwide populations.

Conclusion:

Low frequencies of null HLA-G*01:05N allele are found in Amerindians. The extended haplotypes with this allele bear other typical Amerindian HLA-DRB1 alleles and its origin is discussed. HLA-G allele frequency profile is closer to that of Europeans than to that of Far East Asians. Our findings are useful to Preventive Medicine and Epidemiology associated to Fertility and HLA-G associated pathology and transplantation.

Ancestry of Amerindians and its Impact in Anthropology, Transplantation, HLA Pharmacogenomics and Epidemiology by HLA Study in Wiwa Colombian Population

Background:

HLA autosomic genes are unique because they conform the most polymorphic human system. Importance of this system is recognized in Medicine for Transplantation, Epidemiology (HLA and disease linkage), Pharmacogenomics (HLA linked to drug side effects) and for defining the origin of populations in both male and female lineages.

Objectives:

Studying HLA profile of a isolated Amerindian group from North Colombia (Wiwa) in order to draw conclusions about its Preventive Medicine, the genetic relationship with Worldwide populations and America peopling, since this last issue is hotly debated.

Methodology:

A total of 14,660 HLA chromosomes were included. Peripheral blood was obtained from volunteer blood donors belonging to Wiwa (also named Arsario) ethnic group. HLA-A, -B, -C, -DRB1 and -DQB1 genes were analyzed by standard methods. Wiwa Amerindians relationships with others were calculated by using Arlequin, Dispan and Vista software computer packages.

Results:

Extended HLA, -A, -B, -C, -DRB1 and -DQB1 haplotypes have been studied for the first time in this population. Classical Amerindian haplotypes have been found and also new Wiwa (Arsario) Amerindian haplotypes. New haplotypes are A*68:01 - B*15:01 - C*03:03 - DRB1*14:02 - DQB1*03:02, A*11:01 - B*07:02 - C*07:02 - DRB1*15:03 - DQB1*06:02 and A*68:01 - B*15:01 - C*03:04 - DRB1*14:02 - DQB1*03:01.

Conclusion:

They have been reached after exhaustive comparisons of Wiwa with other Amerindians and Worldwide populations by using genetic distances, Neighbor Joining trees, correspondence analysis and specific group of alleles which are common and frequent in both Amerindians and Pacific Islanders. They are: 1) The Americas First Inhabitants have been probably come through Bering Strait and also through Pacific (from Austronesia and Asia) and Atlantic (from Europe) routes. A bidirectional gene flow is not discarded. 2) Genetic HLA Amerindian profile is separated from that of other Worldwide populations. 3) Amerindians geographical proximity groups’ relatedness is not concordant with HLA genetic relatedness, neither with language. This may be explained by a substantial population decrease that occurred after Europeans invaded America in 1492 and carried new pathogens and epidemics. 4) Our results are also useful for Wiwa and other Amerindians future preventive medicine (HLA linked diseases), HLA pharmacogenomics and transplantation regional programs.

HLA genetic profile of Mapuche (Araucanian) Amerindians from Chile

Amerindian Mapuche (Araucanians) are now living in Chile and Argentina at both sides of Andean Mountains. They are anthropologically and genetically different from southernmost South America Patagonian Amerindians. Most of the HLA alleles found in our Mapuche sample are frequent or very frequent in North and South America Amerindians: (1) Class I: A*02:01, A*03:01, A*68:01, B*39:09, B*51:01, (2) Class II: DRB1*03:01, DRB1*04:03, DRB1*07:01, DRB1*08:02, DRB1*14:02, DRB1*16:02. One of the nine most frequent extended haplotypes seems to be from European origin, suggesting the existence of a degree of admixture with Europeans in our Mapuche sample. It has been calculated of about 11 % admixture. Three of the extended haplotypes are also found in other Amerindians and five of them are newly found in Mapuche Amerindians: A*68:01-B*39:09-DRB1*08:02-DQB1*04:02; A*68:01-B*51:01-DRB1*04:03-DQB1*03:02; A*29:01-B*08:01-DRB1*03:01-DQB1*02:01; A*02:01-B*15:01-DRB1*04:03-DQB1*03:02; A*33:01-B*14:02-DRB1*07:01-DQB1*03:03. The medical importance of calculating HLA profile is discussed on the diagnostic (HLA and disease) and therapeutical bases of HLA pharmacogenomics and on the construction of a virtual transplantation HLA list profile. Also, anthropological conclusions are drawn.