Honduras HIV cohort: HLA class I and CCR5-Δ32 profiles and their associations with HIV disease outcome.

IMPORTANCE: We identify both canonical and novel human leukocyte antigen (HLA)-HIV associations, providing a first step toward improved understanding of HIV immune control among the understudied Honduras Mestizo population. Our results are relevant to understanding the protective or detrimental effects of HLA subtypes in Latin America because their unique HLA diversity poses challenges for designing vaccines against HIV and interpreting results from such vaccine trials. Likewise, the description of the HLA profile in an understudied population that shows a unique HLA immunogenetic background is not only relevant for HIV immunology but also relevant in population genetics, molecular anthropology, susceptibility to other infections, autoimmune diseases, and allograft transplantation.

Allele Frequencies and Forensic Data of 25 STR Markers for Individuals in Northeast Brazil.

Identifying DNA markers such as Short Tandem Repeats (STR) can be used to investigate genetic diversity based on levels of heterozygosity within and between populations. Allele frequencies and forensic data for STRs were obtained from a sample of 384 unrelated individuals living in Bahia, Northeastern Brazil. Thus, the present study aimed to identify the allele frequency distribution, in addition to the forensic and genetic data, of 25 STR loci in the population of Bahia. Buccal swabs or fingertip punctures were utilized to amplify and detect 25 DNA markers. The most polymorphic loci were SE33 (43), D21S11, and FGA (21). The least polymorphic were TH01 (6), TPOX, and D3S1358 (7). Forensic and statistical data were obtained through data analysis, which revealed a large genetic diversity, with an average value of 0.813 for the analyzed population. The present study was more robust than previous STR marker studies and will contribute to future research on population genetics in Brazil and worldwide. The results of this study allowed the establishment of haplotypes found in the forensic samples of Bahia State to serve as a reference in the elucidation of criminal cases and paternity tests, as well as population and evolutionary investigations.

Frequencies of variants in genes associated with dyslipidemias identified in Costa Rican genomes.

Dyslipidemias are risk factors in diseases of significant importance to public health, such as atherosclerosis, a condition that contributes to the development of cardiovascular disease. Unhealthy lifestyles, the pre-existence of diseases, and the accumulation of genetic variants in some loci contribute to the development of dyslipidemia. The genetic causality behind these diseases has been studied primarily on populations with extensive European ancestry. Only some studies have explored this topic in Costa Rica, and none have focused on identifying variants that can alter blood lipid levels and quantifying their frequency. To fill this gap, this study focused on identifying variants in 69 genes involved in lipid metabolism using genomes from two studies in Costa Rica. We contrasted the allelic frequencies with those of groups reported in the 1000 Genomes Project and gnomAD and identified potential variants that could influence the development of dyslipidemias. In total, we detected 2,600 variants in the evaluated regions. However, after various filtering steps, we obtained 18 variants that have the potential to alter the function of 16 genes, nine variants have pharmacogenomic or protective implications, eight have high risk in Variant Effect Predictor, and eight were found in other Latin American genetic studies of lipid alterations and the development of dyslipidemia. Some of these variants have been linked to changes in blood lipid levels in other global studies and databases. In future studies, we propose to confirm at least 40 variants of interest from 23 genes in a larger cohort from Costa Rica and Latin American populations to determine their relevance regarding the genetic burden for dyslipidemia. Additionally, more complex studies should arise that include diverse clinical, environmental, and genetic data from patients and controls and functional validation of the variants.

Open-Access Worldwide Population STR Database Constructed Using High-Coverage Massively Parallel Sequencing Data Obtained from the 1000 Genomes Project.

Achieving accurate STR genotyping by using next-generation sequencing data has been challenging. To provide the forensic genetics community with a reliable open-access STR database, we conducted a comprehensive genotyping analysis of a set of STRs of broad forensic interest obtained from 1000 Genome populations. We analyzed 22 STR markers using files of the high-coverage dataset of Phase 3 of the 1000 Genomes Project. We used HipSTR to call genotypes from 2504 samples obtained from 26 populations. We were not able to detect the D21S11 marker. The Hardy-Weinberg equilibrium analysis coupled with a comprehensive analysis of allele frequencies revealed that HipSTR was not able to identify longer alleles, which resulted in heterozygote deficiency. Nevertheless, AMOVA, a clustering analysis that uses STRUCTURE, and a Principal Coordinates Analysis showed a clear-cut separation between the four major ancestries sampled by the 1000 Genomes Consortium. Except for larger Penta D and Penta E alleles, and two very small Penta D alleles (2.2 and 3.2) usually observed in African populations, our analyses revealed that allele frequencies and genotypes offered as an open-access database are consistent and reliable.

Population data for 21 STRs for the Salvadoran population using GlobalFiler Express and GlobalFiler STR Amplification Kits.

With the advent of expanded STR (short tandem repeats) typing kits, it was necessary to determine allele frequencies and other appropriate population data parameters for El Salvador. Samples were collected from the central, east, and west regions of the country and typed for 21 forensically relevant STR loci. The data indicate that all loci are highly polymorphic, the three regions are genetically similar, and the population data are similar to those of US Hispanics. The results of this study support that the allele frequency data described herein can be used for statistical calculations for human identity testing in El Salvador.

Allelic frequencies with 23 autosomic STRS in the Aymara population of Peru.

Population data of the Aymara in the province of Puno were established for 23 autosomal STR markers. DNA was obtained from unrelated individuals (n = 190) who reside in three areas of the Floating Islands of Lake Titicaca, residents on the border with Bolivia and residents who are not from the border with Bolivia. The PENTA E marker presented the highest PD (0.9738), PIC (0.8793), and PM (0.7847) values. The combined PD was greater than 0.99999999 and the combined PE was 0.99999994. The largest distance, based on Fst values, was between the Aymara population and the Ashaninca population (0.04022), and the smallest distance was with the populations of Bolivia (0.00136) and Peru (0.00525).

HLA allele and haplotype frequencies in the Panamanian population.

In this study, we report for the first time HLA allele and haplotype frequencies in the modern Panamanian population at a two-field (four digits) resolution level. Reported frequencies were calculated from genotype data for the HLA-A, -B, -C, -DPB1, -DQB1 and -DRB1 loci of 462 healthy unrelated Panamanian adults of Hispanic ethnicity. In addition to providing new insights on the allelic structure of the Panamanian population and its origin, these data are critical for better planning of healthcare strategies in the country and for future research exploring the association with certain chronic and infectious diseases.

Population genetic study of a Peruvian population using human identification STRs.

In this study, allele frequencies were determined in a Peruvian population for application to human identification. A population of 601 unrelated individuals was analyzed (400 individuals with the GlobalFiler Express kit and 201 individuals with the VeriFiler Express kit). The locus with the highest power of discrimination (PD) was SE33 (0.9851, 31 alleles), while the least polymorphic locus was D22S1045 (0.75810, 11 alleles). The PE in a similar fashion ranged from 0.2421 (D22S1045) to 0.7818 (SE33). Under the assumption of independence, the combined PD was > 0.9999999999 while the combined PE = 0.9999999933. When comparing the population studied with different populations of Latin America, the greatest Fst genetic distance was obtained with a Venezuelan population (0.052), and the shortest distance was with a Bolivian and Peruvian population (0.004).

Pro12Ala PPAR-γ2 and +294T/C PPAR-δ Polymorphisms and Association with Metabolic Traits in Teenagers from Northern Mexico.

Peroxisome proliferator-activated receptors (PPARs) play roles in glucose and lipid metabolism regulation. Pro12Ala PPAR-γ2 and +294T/C PPAR-δ have been associated with dyslipidemia, hyperglycemia and high body mass index (BMI). We compared metabolic traits and determined associations with Pro12Ala PPAR-γ2 or +294T/C PPAR-δ polymorphism among teenagers from different ethnicity. Four hundred and twelve samples with previous biochemical and biometric measurements were used. Genomic DNA from peripheral blood was extracted and analyzed by end-point PCR for Pro12Ala PPAR-γ2. The +294T/C PPAR-δ PCR product was also digested with Bsl I. Two genotype groups were formed: major allele homozygous and minor allele carriers. Pro12Ala PPAR-γ2 G minor allele frequencies were: 10% in Mestizo-1, 19% in Mestizo-2, 23% in Tarahumara, 12% in Mennonite, and 17% in the total studied population. The +294T/C PPAR-δ C minor allele frequencies were: 18% in Mestizo-1, 20% in Mestizo-2, 6% in Tarahumara, 13% in Mennonite, and 12% in the total studied population. Teenagers with PPAR-γ2 G allele showed a greater risk for either high waist/height ratio or low high-density lipoprotein; and, also had lower total cholesterol. Whereas, PPAR-γ2 G allele showed lower overweight/obesity phenotype (BMI Z-score) frequency, PPAR-δ C allele was a risk factor for it. Metabolic traits were associated with both PPAR polymorphisms.

Genetic diversity in oocyte donors used in in vitro bovine embryo production programs in Brazil / Diversidad genética en donadoras de ovocitos utilizadas en programas de producción de embriones bovinos in vitro en Brasil / Diversidade genética em doadoras de oócitos utilizadas em programas de produção de embriões bovinos in vitro no Brasil

Abstract Background: Current reproductive management of bovine elite populations involves the use of assisted reproductive technologies (ARTs), aiming to obtain the greatest genetic gain. However, inadequate use of ARTs may lead to loss of genetic diversity in the offspring. Objective: To assess the genetic diversity in elite female cattle populations used in commercial in vitro embryo production. Methods: Using genetic and ecological approaches for the study of populations based on microsatellite markers, we assessed the genetic diversity between and within populations of cows used in commercial in vitro embryo production programs in Brazil. Results: Endogamy within populations varied from zero to 9.1%, while heterozygosity between populations (FST) was <0.05 in the different population interactions. AMOVA showed 1% variation between populations, 8% between individuals and 91% within individuals. The dimensionality reduction method utilized indicated a lack of structure in the populations analyzed, identifying two main clusters in the three populations. Conclusions: Low genetic diversity between cow populations associated with commercial programs of in vitro embryo production in Brazil was evidenced. Variable levels of endogamy within the populations were observed. Approaches of population genetics as well as ecological diversity can be implemented to more thoroughly estimate genetic diversity in livestock populations.

Resumen Antecedentes: El actual manejo reproductivo en poblaciones de bovinos de élite incluye la utilización de tecnologías de reproducción asistida (ARTs) con el fin de obtener mayor ganancia genética. Sin embargo, el uso inadecuado de las ART puede llevar a la pérdida de diversidad genética en los descendientes. Objetivo: Evaluar la diversidad genética en poblaciones de vacas de élite utilizadas en la producción comercial de embriones bovinos in vitro. Métodos: Utilizando abordajes de la genética y ecología de poblaciones basados en marcadores microsatélites, evaluamos la diversidad genética entre y dentro de poblaciones de vacas participantes de programas comerciales de producción de embriones in vitro en Brasil. Resultados: La endogamia dentro de las poblaciones varió de cero a 9,1%, mientras que la heterocigosidad entre poblaciones (FST) fue <0,05 en las diferentes interacciones de la población. El AMOVA mostró variación del 1% entre poblaciones, 8% entre individuos y 91% dentro de individuos. El método de reducción de dimensionalidad utilizado indicó una falta de estructura en las poblaciones analizadas, identificando dos grupos principales en las tres poblaciones. Conclusiones: Se evidenció una baja diversidad genética entre las poblaciones de vacas asociadas a programas comerciales de producción de embriones in vitro en Brasil. Se evidenciaron niveles variables de endogamia entre las poblaciones. Abordajes de la genética poblacional, así como de diversidad ecológica pueden ser implementados para estimar de manera más amplia la diversidad genética en poblaciones animales de interés pecuario.

Resumo Antecedentes: O atual manejo reprodutivo das populações de elite em bovinos envolve o uso de tecnologias de reprodução assistida (ARTs), visando obter o maior ganho genético. No entanto, o uso inadequado de ARTs pode levar à perda de diversidade genética na prole. Objetivo: Avaliar a diversidade genética em populações de vacas de elite utilizadas na produção comercial de embriões bovinos in vitro. Métodos: Utilizando abordagens da genética e ecologia de populações baseadas em marcadores microssatélites, foi avaliada a diversidade genética entre e dentro das populações de vacas participantes de programas comercias de produção in vitro de embriões. Resultados: A endogamia dentro das populações variou de zero a 9,1%, enquanto a heterozigosidade entre populações (FST) foi <0,05 nas diferentes interações populacionais. AMOVA mostrou variação de 1% entre populações, 8% entre indivíduos e 91% dentro de indivíduos. O método de redução de dimensionalidade utilizado indicou uma falta de estrutura nas populações analisadas, identificando dois clusters principais nas três populações. Conclusões: Baixa diversidade genética entre populações de vacas associadas a programas de produção in vitro de embriões foi evidenciada. Níveis de endogamia variáveis dentro das populações foram observados. Abordagens da genética populacional assim como de diversidade ecológica podem ser implementadas na tentativa de estimar de maneira mais abrangente a diversidade genética em populações animais de interesse pecuário.

X-chromosome data for 12 STRs: Towards an Argentinian database of forensic haplotype frequencies.

The analysis of X-chromosome STRs is useful in certain kinship cases for which autosomal markers provide insufficient statistical power. Particularly, powerful results are achieved in paternity cases with a daughter, when the alleged father is not accessible for analysis, contrarily to his unquestioned mother or daughter. However, representative haplotype frequencies for this type of markers are not available for some populations, as is the case of Argentina, which prevents the quantification of the proof in routine forensic analyses. In this work we present haplotype frequencies for the 12 X-chromosome STRs included in the Investigator Argus X-12 kit, as well as segregation data, obtained from the analysis of the genetic profiles of 457 father-daughter duos, which gave us information on 914 (unrelated) haplotypes from residents of all Argentinian provinces.

Diversidad genética de palomas domésticas (Columba livia) en Ciénaga de Oro (Colombia), utilizando genes del plumaje / Genetic diversity of domestic pigeons (Columba livia) in Ciénaga de Oro, Colombia, using plumage genes / Diversidade genética de pombos domésticos (Columba livia) em Ciénaga de Oro (Colômbia), utilizando genes da plumagem

Resumen El objetivo de este trabajo fue evaluar la diversidad genética de las poblaciones de palomas domésticas (Columba livia) por medio del uso de genes que codifican la coloración y diseño del plumaje, en Ciénaga de Oro (Córdoba, Colombia). Se realizaron muestreos aleatorios en cinco colonias de Ciénaga de Oro, en el periodo comprendido entre junio y agosto de 2015. Mediante excursiones urbanas, observación directa y registros fotográficos, se estudiaron 325 palomas. Se utilizaron los marcadores autosómicos que codifican la coloración y diseño del plumaje: Grizzle (G), Spread (S), Checker (C) y el locus ligado al sexo Ash-Red (B). Los parámetros genéticos -frecuencia alélica, diversidad genética, equilibrio Hardy-Weinberg y estructura poblacional- fueron calculados con el programa PopGene 1.31. La estructura genética y la distancia genética se evaluaron mediante el programa FSTAT v. 2.9.3.2. La elaboración del dendrograma se realizó con el programa MEGA 5.2. El marcador de mayor frecuencia alélica fue Spread, mientras que el marcador Ash-Red presentó los valores más bajos. Se obtuvo escasa diferenciación genética entre las poblaciones y un elevado flujo génico. Se observó un exceso de heterocigotos; a esto se le suma la ausencia de equilibrio Hardy-Weinberg. Se evidenció posible selección natural para el marcador Spread.

Abstract This study aimed to evaluate the genetic diversity of domestic pigeon populations (Columba livia), using genes that are responsible for encoding plumage color and design, in Ciénaga de Oro (Córdoba, Colombia). Random samplings were performed in 5 colonies of Ciénaga de Oro from June to August 2015. By means of urban excursions, direct observation and photographic records, 325 pigeons were studied. Autosomal markers encoding plumage color and design were used: Grizzle (G), Spread (S), Checker (C), and the sex-linked Ash-Red locus (B). Genetic parameters-allele frequency, genetic diversity, Hardy-Weinberg equilibrium, and population structure-were calculated using the PopGene 1.31 program. Genetic structure and genetic distance were evaluated using the FSTAT v. 2.9.3.2 program. A dendrogram was elaborated using the MEGA 5.2 program. The marker with the highest allele frequency was Spread, while the Ash-Red marker showed the lowest values. Little genetic differentiation between populations and high gene flow were obtained. An excess of heterozygotes was observed, in addition to the absence of Hardy-Weinberg equilibrium. A possible natural selection for the Spread marker was evidenced.

Resumo O objetivo deste trabalho foi avaliar a diversidade genética das populações de pombos domésticos (Columba livia) por meio do uso de genes que codificam a coloração e desenho da plumagem, em Ciénaga de Oro (Córdoba, Colômbia). Se realizaram amostragens aleatórias em 5 colônias de Ciénaga de Oro, no periodo compreendido entre junho e agosto de 2015. Mediante excursões urbanas, observação direta e registros fotográficos, se estudaram 325 pombos. Se utilizaram os marcadores autossômicos que codificam a coloração e desenho da plumagem: Grizzle (G), Spread (S), Checker (C) e o locus ligado ao sexo Ash-Red (B). Os parâmetros genéticos - frequência alélica, diversidade gené tica, equilíbrio Hardy-Weinberg e estrutura populacional - foram calculados com o programa PopGene 1.31. A estrutura genética e a distância genética foram avaliadas mediante o programa FSTAT v. 2.9.3.2. A elaboração do dendrograma se realizou com o programa MEGA 5.2. O marcador de maior frequência alélica foi Spread, em quanto que o marcador Ash-Red apresentou os valores mais baixos. Obteve-se escassa diferenciação genética entre as populações e um elevado fluxo génico. Pôde-se observar um excesso de heterozigotos; a isto soma-se a ausência de equilíbrio Hardy-Weinberg. Constatou-se possível seleção natural para o marcador Spread.

Investigator® HDplex (Qiagen) reference population database for forensic use in Argentina.

Currently, autosomal Short Tandem Repeat (STR) markers represent the method of election in forensic human identification. Commercial kits of most common use nowadays -e.g. PowerPlex®Fusion, Promega Corp.; AmpFlSTR GlobalFiler, Thermofisher scientific; Investigator 24Plex QS,Qiagen-, allow the co-amplification of 23 highly polymorphic STR loci providing a high discrimination power in human identity testing. However, in complex kinship analysis and familial database searches involving distant relationships, additional DNA typing is often required in order to achieve well-founded conclusions. The recently developed kit Investigator® HDplex (Qiagen) co-amplify twelve autosomal STRs markers (D7S1517, D3S1744, D12S391, D2S1360, D6S474, D4S2366, D8S1132, D5S2500, D18S51, D21S2055, D10S2325, SE33), nine of which are not present in the above mentioned kits, providing a set of efficient supplementary markers for human identification purposes. In this study we genotyped a sample of 980 individuals from urban areas of ten Argentinean provinces using the Investigator® HDplex kit, aiming to provide forensic estimates for use in forensic casework and parentage testing in Argentina. We report reference allelic frequency databases for each of the provinces studied as well as for the combined samples. No deviation of Hardy-Weinberg equilibrium was observed. A reasonable discrimination capacity and power of exclusion was estimated which allowed predicting an acceptable forensic behavior of this kit, either to be used as the main STR panel for simple cases or as an auxiliary tool in complex cases. Additionally, population comparison tests showed that the studied samples are relatively homogeneous across the country for these STR set.

Genetic Variants of Cytochrome CYP2D6 in Two Mixed Chilean Populations.

OBJECTIVES: It is known that the interindividual and interethnic variability of the genetic polymorphisms of CYP2D6 plays an important role in the presentation of adverse drug reactions and concerning lack of therapeutic effects in humans. However, there are few data available from mixed populations of Latin America, including the Chilean. The aim of this study was therefore to estimate the frequencies of CYP2D6 variants in two samples of hospitals from the northern (Hospital San José, HSJ) and eastern (Clínica Las Condes, CLC) parts of Santiago, Chile, with different degrees of Amerindian admixture (HSJ: 34.5%; CLC: 15.9%). METHODS: We used polymerase chain reaction followed by restriction endonuclease digestion (PCR-RFLP) to genotype 7 CYP2D6 alleles in 250 healthy unrelated individuals of Chilean Mestizo background. The detection of allele CYP2D6*5 and the duplication of this gene was performed by long-PCR. RESULTS: The degrees of Amerindian admixture are reflected in the observed frequencies of the CYP2D6*1 (HSJ: 58.26%; CLC: 41.06%), CYP2D6*2 (HSJ: 28.10%; CLC: 40.65%), and CYP2D6*4 (HSJ: 8.26%; CLC: 12.60%) alleles; the frequencies of CYP2D6*1 (p = 0.0002) and CYP2D6*2 (p = 0.0036) are significantly different between the samples. Four individuals (CLC: 0.41%; HSJ: 1.24%) could not be assigned to a genotype. We identified 3.25% of the genotypes which predict a poor metabolizer phenotype in CLC and 1.65% in HSJ. CONCLUSION: Our data indicate ethnic group-dependent genetic differences in the vulnerability to treatment with the large variety of drugs metabolized by the enzyme CYP2D6.

Frequency of human platelet antigens (HPA)-1, -2, -5 and -15 in Brazilian blood donors and establishment of a panel of HPA-typed donors.

OBJECTIVES: The aim of this study is to keep a record of regular human platelet antigens (HPA)-typed blood donors and to compare their allele frequencies with those reported in other populations. BACKGROUND: HPA are polymorphisms expressed on platelet membrane glycoproteins. They can generate an immune response leading to platelet alloimmunisation that may show clinical manifestations, such as neonatal alloimmune thrombocytopenia, post-transfusion purpura and platelet refractoriness. Platelet alloimmunisation is not uncommon, therefore, for an optimum management, it is advantageous to establish a panel of typed platelets to help matched platelets selection in HPA-alloimmunised patients transfusion. METHODS: The polymerase chain reaction (PCR)-allele-specific primers and PCR-restriction fragment length polymorphism methods were used to determine the genotypes of HPA-1, -2, -5 and -15 systems of 337 blood donors. RESULTS: The three genotypes (AA, AB and BB) were found in all HPA systems analysed, and the most frequent genotypes were AA for HPA-1, -2 and -5 systems (mean: 0·732) and AB for HPA-15 system (mean: 0·523). Allele frequencies were 0·148, 0·155, 0·140 and 0·430 for HPA-1b, -2b, -5b and -15b, respectively, and they were similar to those found in Caucasian populations, especially for HPA-1. However, the B allele was more frequent in all HPA systems when compared with Amazon Indians, and the frequency of the B allele in our study was higher in HPA-1 and -15 systems and lower in HPA-2 and -5 systems in comparison with sub-Saharan African populations. CONCLUSIONS: A record of HPA-typed donors would enable rapid identification and selection of donors when HPA-compatible platelets are required for transfusion.

Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep.

THE AIM OF THIS STUDY WAS TO INVESTIGATE THE GENETIC DIVERSITY WITHIN AND AMONG THREE BREEDS OF SHEEP: Corriedale, Merino and Creole. Sheep from the three breeds (Merino n = 110, Corriedale n = 108 and Creole n = 10) were genotyped using the Illumina Ovine SNP50 beadchip(®). Genetic diversity was evaluated by comparing the minor allele frequency (MAF) among breeds. Population structure and genetic differentiation were assessed using STRUCTURE software, principal component analysis (PCA) and fixation index (FST). Fixed markers (MAF = 0) that were different among breeds were identified as specific breed markers. Using a subset of 18,181 single nucleotide polymorphisms (SNPs), PCA and STUCTURE analysis were able to explain population stratification within breeds. Merino and Corriedale divergent lines showed high levels of polymorphism (89.4% and 86% of polymorphic SNPs, respectively) and moderate genetic differentiation (FST = 0.08) between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (FST = 0.17 for both breeds). Hence, a subset of molecular markers present in the OvineSNP50 is informative enough for breed assignment and population structure analysis of commercial and Creole breeds.

New CODIS core loci allele frequencies for 96,400 Brazilian individuals.

We have reported the allele frequencies of 15 STR loci, including the original 13 CODIS core loci, in over 100,000 Brazilian individuals. A new CODIS core loci has been proposed, but the recently established Brazilian Integrated Network of DNA Databases made a decision in 2010 to postpone the implementation of this new set of loci due to the lack of allele frequency data for the Brazilian population. We aimed to report allele frequencies of 20 loci, estimated from 96,400 Brazilian individuals undergoing paternity testing during 2011-2013. The percentage of missing data was less than 0.6% for all loci, except for CSF1PO (3.15%) and D7S820 (2.5%). The dropout rates estimated by the MicroDrop software were 0.013 for CSF1PO, 0.000037 for D7S820 and less than 0.000001 for other loci. Small missing data percentages and dropout rates reflect the high quality of the data.

Allele and haplotype frequencies of HLA-DPA1 and -DPB1 in the population of Guadeloupe.

Genetic polymorphism of human leukocyte antigen (HLA)-DPA1 and -DPB1 loci was studied in 154 unrelated individuals from Guadeloupe, an archipelago of five islands located in the Carribean Sea. Thirty different DPB1 and eight different DPA1 alleles were observed with a heterozygosity index of 0.87 and 0.78, respectively. This high degree of heterozygosity corresponds with those found in African populations. The DPB1* 01:01:01 allele was most frequent (0.260), followed by 02:01:02 (0.143) and 04:01:01 (0.127). The DPA1 alleles 01:03 (0.380), 02:01 (0.302), 02:02 (0.175) and 03:01 (0.123) were identified in >35 individuals each, whereas 01:04, 01:05 and 04:01 were present only once. Haplotype estimations revealed the presence of 39 different haplotypes, with DPB1*01:01:01-DPA1*02:02 and DPB1*02:01:02-DPA1*01:03 as the most frequent (0.143 and 0.140, respectively). A striking difference was observed in DPB1/DPA1 associations between DPB1*04:02 and *105:01, that have identical exon 2 sequences. DPB1*04:02 was exclusively associated with DPA1*01:03, whereas DPB1*105:01 was present with DPA1*03:01, *03:02 or *04:01. This implies that the DP molecules are actually different, and this difference is relevant to consider in studies on the function of HLA-DP molecules in transplantation. Overall, HLA-DPA1 and DPB1 allele frequencies and haplotypes of the population of Guadeloupe were most similar to African populations, with characteristic alleles and haplotypes that bespeaks the admixture with other ethnicities.

Neutral and stable equilibria of genetic systems and the hardy-weinberg principle: limitations of the chi-square test and advantages of auto-correlation functions of allele frequencies.

Since the foundations of Population Genetics the notion of genetic equilibrium (in close analogy with Classical Mechanics) has been associated with the Hardy-Weinberg (HW) principle and the identification of equilibrium is currently assumed by stating that the HW axioms are valid if appropriate values of χ(2) (p < 0.05) are observed in experiments. Here we show by numerical experiments with the genetic system of one locus/two alleles that considering large ensembles of populations the χ(2)-test is not decisive and may lead to false negatives in random mating populations and false positives in non-random mating populations. This result confirms the logical statement that statistical tests cannot be used to deduce if the genetic population is under the HW conditions. Furthermore, we show that under the HW conditions populations of any size evolve in time according to what can be identified as neutral dynamics to which the very notion of equilibrium is unattainable for any practical purpose. Therefore, under the HW conditions the identification of equilibrium properties needs a different approach and the use of more appropriate concepts. We also show that by relaxing the condition of random mating the dynamics acquires all the characteristics of asymptotic stable equilibrium. As a consequence our results show that the question of equilibrium in genetic systems should be approached in close analogy to non-equilibrium statistical physics and its observability should be focused on dynamical quantities like the typical decay properties of the allelic auto-correlation function in time. In this perspective one should abandon the classical notion of genetic equilibrium and its relation to the HW proportions and open investigations in the direction of searching for unifying general principles of population genetic transformations capable to take in consideration these systems in their full complexity.

Análisis de marcadores STR sobre el cromosoma X en una población de Bogotá / STR markers analysis on X chromosome in a population from Bogotá

El análisis de marcadores del cromosoma X ha sido ampliamente usado en el área de la genética clínica, particularmente, para el análisis molecular de enfermedades ligadas al X. Recientemente, se han reconocido muchas repeticiones cortas en tándem (Short Tandem Repeats, STR) sobre este cromosoma, por su importancia en análisis forense y de paternidad. Los marcadores gonosómicos son especialmente eficientes para resolver casos difíciles, ya que las probabilidades de exclusión media son mayores que con los marcadores STR autosómicos. Objetivo. Determinar la frecuencia alélica y haplotípica de 10 marcadores STRs sobre el cromosoma X en 200 muestras de hombres no relacionados de la ciudad de Bogotá. Materiales y métodos. Se analizaron 200 muestras de sangre de hombres no emparentados nacidos en Bogotá. El ADN genómico fue extraído mediante la técnica Whatman FTA y amplificados por PCR. Los productos se analizaron en un secuenciador automático ABI Prism 310, con el software GeneMapper, versión 3.2. Resultados. Los sistemas evaluados indicaron la presencia de 6 a 11 alelos, con el mayor polimorfismo para los sistemas DXS6809 y DXS6789, seguido por el sistema DXS9902. Las frecuencias alélicas oscilaron entre 0,005 y 0,565, mientras que la frecuencia haplotípica fue de 0,005. Los parámetros forenses utilizados en este estudio reportaron que el sistema DXS7132 mostró una mayor diversidad y PD (0,832211 y 0,82805) respectivamente indicando que este sistema es altamente informativo; el sistema que presentó menor diversidad y PD fue el sistema DXS7133. Conclusión. Los diez marcadores analizados en este estudio permiten la genotipificación simultánea de los 10 STRs en solo una PCR, adicionalmente se evidenció que los marcadores analizados son ampliamente informativos y que su utilización puede ser de gran aporte en la práctica forense, particularmente en los casos de parentesco u otras deficiencias.

X chromosome markers analysis has been used widely in the clinical genetics area, particularly in molecular diseases X-linked analysis. Recently, many short tandem repeats (Short Tandem Repeats, STRs) on this chromosome has been recognized, by importance in forensic and paternity analysis. The gonosomal markers are particularly efficient resolve difficult cases, since the odds of half exclusion outweigh the STR autosomes markers. Objective. Determine the allelic frequency and haplotype frequency of 10 STRs markers located on the X chromosome, in 200 samples of unrelated men in the Bogotá city. Materials and methods. 200 blood samples were analyzed from unrelated males born in Bogotá. DNA extraction was performed using the Whatman FTA technique and PCR amplified. The products were analyzed in automatic sequencer ABI Prism 310, software GeneMapper, version 3.2. Results. The systems tested, showed of 6-11 alleles, with greater polymorphism DXS6809 and DXS6789 systems and this followed for DXS9902 system. The range of Allele frequencies from 0.005 to 0.565, while the haplotype frequency was 0.005. The forensic parameters used in this study, reported that the DXS7132 system showed greater diversity and PD (0.832211 and 0.82805) respectively, suggesting that this system is highly informative, the system had lower PD and diversity DXS7133 system. Conclusion. The ten analyzed markers in this study allow simultaneous genotyping of 10 STRs in only one PCR additionally revealed that informative markers are widely analyzed and their use can greatly contribute in forensics practice, particularly in cases of family or other deficiencies.