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1.
Journal of Forensic Medicine ; (6): 500-506, 2022.
Article in English | WPRIM | ID: wpr-984143

ABSTRACT

OBJECTIVES@#To study the genetic polymorphism and population genetic parameters of 16 X-STR loci in Xinjiang Uygur population.@*METHODS@#The Goldeneye® DNA identification system 17X was used to amplify 16 X-STR loci in 502 unrelated individuals (251 females and 251 males). The amplified products were detected by 3130xl genetic analyzer. Allele frequencies and population genetic parameters were analyzed statistically. The genetic distances between Uygur and other 8 populations were calculated. Multidimensional scaling and phylogenetic tree were constructed based on genetic distance.@*RESULTS@#In the 16 X-STR loci, a total of 67 alleles were detected in 502 Xinjiang Uygur unrelated individuals. The allele frequencies ranged from 0.001 3 to 0.572 4. PIC ranged from 0.568 8 to 0.855 3. The cumulative discrimination power in females and males were 0.999 999 999 999 999 and 0.999 999 999 743 071, respectively. The cumulative mean paternity exclusion chance in trios and in duos were 0.999 999 997 791 859 and 0.999 998 989 000 730, respectively. The genetic distance between Uygur population and Kazakh population was closer, and the genetic distance between Uygur and Han population was farther.@*CONCLUSIONS@#The 16 X-STR loci are highly polymorphic and suitable for identification in Uygur population, which can provide a powerful supplement for the study of individual identification, paternity identification and population genetics.


Subject(s)
Female , Humans , Male , DNA, Ribosomal , Ethnicity/genetics , Gene Frequency , Paternity , Phylogeny , Polymorphism, Genetic , Microsatellite Repeats , Chromosomes, Human, X/genetics
2.
Journal of Central South University(Medical Sciences) ; (12): 351-360, 2021.
Article in English | WPRIM | ID: wpr-880666

ABSTRACT

OBJECTIVES@#Due to the genetic feature of high diversity than other DNA markers, short tandem repeat (STR) plays key roles in forensic, anthropology, and population genetics. Newly introduced multiple STR kit is more valuable because of the greatly improved discriminatory power with the increase in the number of STR loci. The genetic polymorphic data are essential for the application and research in specific population. This study aims to investigate the genetic polymorphism of Han population residing in Yuncheng district, Shanxi Province, to evaluate the application of 23 STR loci in forensic personal identification and paternity test, and to explore the genetic relationship of Han population between Yuncheng and other populations.@*METHODS@#A total of 23 STR loci were amplified from 525 healthy unrelated individuals from the Han nationality in Yuncheng, Shanxi Province using the AGCU EX25 amplification kit. The products were detected and separated by ABI 3500 Genetic Analyzer. Alleles were genotyped by GeneMapper ID (Version 3.2) software, and corresponding frequencies and forensic parameters were calculated. We calculated the genetic distance and plotted the neighboring-joining tree with other 13 population.@*RESULTS@#The allele frequency of the 23 STRs ranged from 0.0010 to 0.5090. No deviation from Hardy-Weinberg equilibrium (@*CONCLUSIONS@#These 23 STRs are highly genetic polymorphic and informative in the Han population of Yuncheng, Shanxi Province, which can provide basic data for forensic personal identification, paternity testing, and population genetic research.


Subject(s)
Humans , Asian People/genetics , China , Ethnicity/genetics , Gene Frequency , Genetic Loci , Genetics, Population , Microsatellite Repeats/genetics , Polymorphism, Genetic
3.
Journal of Forensic Medicine ; (6): 382-387, 2021.
Article in English | WPRIM | ID: wpr-985229

ABSTRACT

Objective To evaluate the discrimination efficiency of the SeqType® P52 Human Ancestry Identification SNP Detection Kit based on a high-throughput sequencing platform in five Chinese ethnic groups. Methods Using the SeqType® P52 Human Ancestry Identification SNP Detection Kit based on a high-throughput sequencing platform, a total of 350 samples from Han, Tibetan, Mongolian, Uygur, and Yi populations in China were detected and population cluster analysis was performed. Results The effective sequencing depth of a single site in a single sample was ≥720×, and the average report rate was 96%. The mean values of allele frequency differences between the Tibetan, Mongolian, Uygur, Yi and Han population were 0.20, 0.05, 0.24 and 0.11, respectively. Using Structure 2.3.4 software under K=5 mode, independent ancestral component in Han, Tibetan and Uygur could be detected, which was consistent with the result observed from the principal component analysis (PCA). For the Yi population, two thirds of them had relatively independent ancestral component close to the Tibetan population and one third were similar to the Uygur population. The Mongolian population had similar ancestral origin component with Han population. Conclusion The composite detection system with 52 screened ancestry-informative SNP sites has been established in this study, which can effectively analyze the composition and individual genetic components of populations from Han, Tibetan and Uygur. The ability to discriminate among Han, Mongolian and Yi needs to be further improved. The SeqType® P52 Human Ancestry Identification SNP Detection Kit can be used to infer the origin of an individual's ancestors in some forensic DNA cases.


Subject(s)
Humans , Asian People/genetics , China , DNA , Ethnicity/genetics , Gene Frequency , Genetics, Population , High-Throughput Nucleotide Sequencing , Polymorphism, Single Nucleotide
4.
Journal of Forensic Medicine ; (6): 358-365, 2021.
Article in English | WPRIM | ID: wpr-985225

ABSTRACT

Objective To study the genetic polymorphism of whole mitochondrial DNA (mtDNA) genomes in She population in Zhejiang and to explore the maternal genetic structure of the She population. Methods Whole mtDNA genomes of 231 unrelated individuals from She population in Zhejiang Province were sequenced. The number of mutations and population genetics parameters such as, the haplotype diversity (HD), discrimination power (DP), and random match probabilities (RMP) were analyzed. The mtDNA haplogroups of Zhejiang She population were classified, and the maternal genetic relationships between She and nine other Chinese populations were estimated. Results In 231 Zhejiang She samples, 8 507 mutations (702 types) were observed and the samples were classified into 94 haplogroups. The HD, DP and RMP values were 0.998 6, 0.994 2 and 0.005 8, respectively. The lowest genetic differentiation degree (Fst=0.006 89) was detected between Zhejiang She population and southern Han population. Principal component analysis (PCA) and median-joining network analysis showed that the genetic distance of Zhejiang She population with Guangxi Yao, Yunnan Dai and Southern Han populations was relatively close, but the population still had some unique genetic characteristics. Conclusion The whole mtDNA genomes are highly polymorphic in Zhejiang She population. The Zhejiang She population contains complex and diverse genetic components and has a relatively close maternal genetic relationship with Guangxi Yao, Yunnan Dai and Southern Han populations. Meanwhile, Zhejiang She population has kept its unique maternal genetic components.


Subject(s)
Humans , Asian People/genetics , China , DNA, Mitochondrial/genetics , Ethnicity/genetics , Genetics, Population , Haplotypes , High-Throughput Nucleotide Sequencing , Polymorphism, Genetic
5.
Journal of Forensic Medicine ; (6): 817-824, 2021.
Article in English | WPRIM | ID: wpr-984080

ABSTRACT

OBJECTIVES@#To evaluate the ability of the ForenSeqTM DNA Signature Prep kit (ForenSeq kit) in analyzing the sequence information of STRs in Zhejiang She ethnic group and its forensic application efficacy.@*METHODS@#A total of 50 Zhejiang She ethnic group samples were sequenced with the ForenSeq kit on the MiSeq FGx platform. The data was analyzed using ForenSeqTM universal analysis software to obtain the motif structure and flank regions of the 58 STRs, then compared with PCR-CE typing results to test the consistency. At last, the allele frequency and population genetic parameters were calculated.@*RESULTS@#A total of 448 sequence polymorphic alleles were detected in 50 samples of Zhejiang She ethnic group. Compared with fragment length polymorphism detected by PCR-CE, 82 alleles were increased by MPS detection based on ForenSeq kit, and 7 SNPs variation were detected in the flanking regions of 6 loci. The 22 male individuals were genotyped, and total 19 haplotypes were detected in 24 Y chromosome STRs of these 22 males. The cumulative discrimination power of the 27 autosomal STRs was 1-8.87×10-30, the cumulative probability of exclusion of duo-testing was 0.999 999 962 640 657, the cumulative probability of exclusion of trios-testing was 0.999 999 999 999 633.@*CONCLUSIONS@#Based on MPS typing technology, using the ForenSeq kit greatly improves the detection efficiency. In addition, the 58 STRs have good genetic polymorphisms in Zhejiang She ethnic group, which are suitable for individual identification and paternity identification in forensic application.


Subject(s)
Humans , Male , DNA , DNA Fingerprinting/methods , Ethnicity/genetics , Gene Frequency , High-Throughput Nucleotide Sequencing/methods , Microsatellite Repeats , Polymorphism, Single Nucleotide , Sequence Analysis, DNA/methods
6.
Biol. Res ; 53: 15, 2020. tab, graf
Article in English | LILACS | ID: biblio-1100921

ABSTRACT

BACKGROUND: Current South American populations trace their origins mainly to three continental ancestries, i.e. European, Amerindian and African. Individual variation in relative proportions of each of these ancestries may be confounded with socio-economic factors due to population stratification. Therefore, ancestry is a potential confounder variable that should be considered in epidemiologic studies and in public health plans. However, there are few studies that have assessed the ancestry of the current admixed Chilean population. This is partly due to the high cost of genome-scale technologies commonly used to estimate ancestry. In this study we have designed a small panel of SNPs to accurately assess ancestry in the largest sampling to date of the Chilean mestizo population (n = 3349) from eight cities. Our panel is also able to distinguish between the two main Amerindian components of Chileans: Aymara from the north and Mapuche from the south. RESULTS: A panel of 150 ancestry-informative markers (AIMs) of SNP type was selected to maximize ancestry informativeness and genome coverage. Of these, 147 were successfully genotyped by KASPar assays in 2843 samples, with an average missing rate of 0.012, and a 0.95 concordance with microarray data. The ancestries estimated with the panel of AIMs had relative high correlations (0.88 for European, 0.91 for Amerindian, 0.70 for Aymara, and 0.68 for Mapuche components) with those obtained with AXIOM LAT1 array. The country's average ancestry was 0.53 ± 0.14 European, 0.04 ± 0.04 African, and 0.42 ± 0.14 Amerindian, disaggregated into 0.18 ± 0.15 Aymara and 0.25 ± 0.13 Mapuche. However, Mapuche ancestry was highest in the south (40.03%) and Aymara in the north (35.61%) as expected from the historical location of these ethnic groups. We make our results available through an online app and demonstrate how it can be used to adjust for ancestry when testing association between incidence of a disease and nongenetic risk factors. CONCLUSIONS: We have conducted the most extensive sampling, across many different cities, of current Chilean population. Ancestry varied significantly by latitude and human development. The panel of AIMs is available to the community for estimating ancestry at low cost in Chileans and other populations with similar ancestry.


Subject(s)
Humans , Male , Female , Ethnicity/genetics , Indians, South American/genetics , Polymorphism, Single Nucleotide/genetics , Population Groups/genetics , Genetics, Population/organization & administration , Saliva , Genetic Markers/genetics , Chile , Phylogeography , Genotyping Techniques , Gene Frequency/genetics , Genotype
7.
Journal of Forensic Medicine ; (6): 791-796, 2020.
Article in Chinese | WPRIM | ID: wpr-985176

ABSTRACT

Objective To investigate the frequency distribution features of 11 Y-SNP of Guizhou Shui ethnic group, explore its genetic relationship with other ethnic groups and evaluate its forensic application value. Methods Multiplex amplification of the 11 Y-SNP of samples of 180 unrelated male individuals from Guizhou Shui ethnic group was performed with microsequencing technique. The frequency of haplogroup was calculated by direct counting method, and principal component analysis (PCA) of Guizhou Shui ethnic group and reference ethnic groups was performed by using Multi-variate statistical package (MVSP). The Fst genetic distance between Guizhou Shui ethnic group and other ethnic groups was calculated with Arlequin v3.5. The phylogenetic tree was established with MEGA 4.0 software according to the Fst value. Results Six types of Y chromosome haplogroups were observed in total. Among which, the distribution frequency of O-M175 haplogroup was the highest (71.11%), followed by C-M130 (25.00%), and D-M174 (3.89%). O1b-M268 (31.11%) and O2a2-IMS-JST021354 (28.33%) had a relatively high distribution frequency in O haplogroup. The paternal relationship between Guizhou Shui ethnic group and Guizhou Gelao ethnic group in the same language group was the closest. Conclusion The distribution of Y-SNP haplogroup of the Shui ethnic group in Guizhou has certain specificity, which can provide basic data for forensic biogeographic inference.


Subject(s)
Humans , Male , Asian People/genetics , China , Chromosomes, Human, Y/genetics , Ethnicity/genetics , Genetics, Population , Haplotypes , Phylogeny , Polymorphism, Genetic , Polymorphism, Single Nucleotide
8.
Journal of Forensic Medicine ; (6): 531-537, 2020.
Article in English | WPRIM | ID: wpr-985149

ABSTRACT

Objective To investigate the population genetic data of 47 autosomal insertion/deletion (InDel) polymorphism genetic markers involved in AGCU InDel 50 kit in Guangdong Han, Guangxi Zhuang, Guangxi Yao, Guangxi Jing, and Guangxi Mulam, and to evaluate their application in forensic DNA identification. Methods Multiplex amplification of the 768 unrelated individuals from the 5 ethnic groups mentioned above was performed with the AGCU InDel 50 kit. Genotyping was carried out by 3500xL gene analyzer, population genetic parameters were gathered and polymorphism analysis was performed. Results No linkage disequilibrium was found among 47 autosomal InDel loci in the 5 ethnic groups. The distribution of genotype frequency of 47 autosomal InDel loci confirmed to the Hardy-Weinberg equilibrium in Guangdong Han and Guangxi Zhuang. Except for rs139934789, the other 46 loci confirmed to the Hardy-Weinberg equilibrium in Guangxi Yao, Guangxi Jing, and Guangxi Mulam. The results of genetic variation analysis among the populations showed that 1.12% of genetic variation was caused by ethnic group differences. The cumulative discrimination power of 47 autosomal InDel loci for the 5 ethnic groups were all above 0.999 999 999 999 999. The cumulative probability of exclusion for each ethnic group was less than 0.999 9. The two Y-InDels were identified in all male individuals and were absent in all female individuals. Conclusion Except for rs139934789, the other 46 InDel loci have a relatively good genetic polymorphism in the 5 Chinese ethnic groups, and can be used for forensic individual identification and as effective supplements for paternity testing.


Subject(s)
Female , Humans , Male , Asian People/genetics , China , Ethnicity/genetics , Gene Frequency , Genetic Loci , Genetics, Population , INDEL Mutation , Microsatellite Repeats , Polymorphism, Genetic
9.
Journal of Forensic Medicine ; (6): 497-501, 2020.
Article in English | WPRIM | ID: wpr-985143

ABSTRACT

Objective To explore the association of cardiac disease associated genetic variants and the high incidence of Yunnan sudden unexplained death (YNSUD) in Yi nationality. Methods The genomic DNA was extracted from peripheral blood samples collected from 205 Yi villagers from YNSUD aggregative villages (inpatient group) and 197 healthy Yi villagers from neighboring villages (control group). Fifty-two single nucleotide variants (SNVs) of 25 cardiac disease associated genes were genotyped using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The SPSS 17.0 was used to analyze data. The pathogenicities of variants with differences between the two groups that have statistical significance were predicted by protein function prediction software PolyPhen-2 and SIFT. All villagers from inpatient group were given electrocardiogram (ECG) examination using a 12-lead electrocardiograph. Results The allele frequency and the genotype frequency of missense mutation DSG2 (rs2278792, c.2318G>A, p.R773K) of pathogenic genes of arrhythmogenic right ventricular cardiomyopathy (ARVC) in inpatient group was higher than that in control group (P<0.05). Abnormal ECG changes were detected in 71 individuals (34.6%) in the inpatient group, among which 54 individuals carried R773K mutation, including clockwise (counterclockwise) rotation, left (right) axis deviation, ST segment and T wave alteration and heart-blocking. Conclusion Definite pathogenic mutations have not been found in the 52 cardiac disease genes associated SNVs detected in Yi nationality in regions with high incidence of YNSUD. The cause of high incidence of YNSUD in Yi nationality needs further study.


Subject(s)
Humans , Arrhythmogenic Right Ventricular Dysplasia , China/epidemiology , Death, Sudden/etiology , Death, Sudden, Cardiac/etiology , Ethnicity/genetics , Incidence , Mutation
10.
Journal of Forensic Medicine ; (6): 341-346, 2020.
Article in English | WPRIM | ID: wpr-985123

ABSTRACT

Objective To investigate the allele distribution, population genetics parameters and genetic analysis of neighboring populations of 19 autosomal STR loci in Sichuan Han population, and to evaluate their forensic application value. Methods The Goldeneye?? DNA ID system 20A was used to perform multiplex PCR amplification and allelic gene typing of 19 STR loci in 1 201 unrelated Han individuals from Sichuan Province. Allele frequencies and population genetics parameters were calculated. The Nei's genetic distances between Sichuan Han population and 12 previously reported populations were analyzed. Multidimensional scaling and principal component analysis were carried out and phylogenetic trees were also constructed. Results The heterozygosity of 19 STR loci ranged from 0.617 0 to 0.915 1, their discrimination power ranged from 0.777 4 to 0.986 5, matching probability ranged from 0.013 5 to 0.222 6, polymorphism information content ranged from 0.546 4 to 0.910 5, probability of exclusion ranged from 0.311 8 to 0.826 3 (triplet) and from 0.197 9 to 0.712 1 (biplet), and no significant deviations from Hardy-Weinberg equilibrium were observed. Based on the results of multidimensional scaling, principal component analysis and phylogenetic trees of the genetic distances between Sichuan Han population and the other 12 populations, Sichuan Han population was closest to Hubei Han population and was farthest to Xinjiang Uygur population. Conclusion The 19 autosomal STR loci showed a high polymorphism and discriminating ability in Sichuan Han population, which can provide a data foundation for personal identification, paternity test and population genetics study.


Subject(s)
Humans , Asian People/genetics , China , Ethnicity/genetics , Gene Frequency , Genetics, Population , Microsatellite Repeats , Phylogeny , Polymorphism, Genetic
11.
Journal of Zhejiang University. Science. B ; (12): 287-290, 2019.
Article in English | WPRIM | ID: wpr-1010459

ABSTRACT

To further enrich the genetic data of the Chinese Xinjiang Mongolian group, the genetic distribution and forensic parameters of 19 autosomal short tandem repeats (STRs) were investigated. Altogether, 249 alleles were observed in these 19 STRs. The mean values of the polymorphism information content (PIC), match probability (MP), discrimination power (DP), and probability of exclusion (PE) for these 19 STRs were 0.7775, 0.0699, 0.9301, and 0.6085, respectively. Additionally, the cumulative DP and PE values obtained in the Mongolian group were 0.999 999 999 999 999 999 999 995 67 and 0.999 999 992 163, respectively. Furthermore, population genetic analysis of the Mongolian group and 20 published populations was conducted based on the population data of 15 overlapping STRs. Genetic distances indicated that the Mongolian group had closer genetic similarities with the Uyghur, Xibe, and other Chinese populations rather than the other continental populations. Multidimensional scaling analysis further revealed that the Mongolian group possessed similar genetic distributions as most Chinese populations. To sum it all up, these STRs could be used as an extremely efficient tool for forensic applications in the Xinjiang Mongolian group.


Subject(s)
Humans , Alleles , Asian People/genetics , China , DNA Fingerprinting , Databases, Genetic , Ethnicity/genetics , Gene Frequency , Genetic Markers , Genetics, Population , Genome, Human , Linkage Disequilibrium , Microsatellite Repeats , Mongolia , Polymorphism, Genetic , Principal Component Analysis , Probability , Software
12.
Journal of Forensic Medicine ; (6): 560-566, 2019.
Article in English | WPRIM | ID: wpr-985046

ABSTRACT

Objective To evaluate the effect of 56 ancestry informative single nucleotide polymorphism (aiSNP) genetic markers in the ForenSeqTM DNA Signature Prep Kit on ancestry inference. Methods A total of 85 samples from five populations including Hebei Han population, Inner Mongolia autonomous region Mongolian population, Tibet autonomous region Tibetan population, Xinjiang Uygur autonomous region Uygur population and Nigerian population were collected. The library was constructed with the ForenSeqTM DNA Signature Prep Kit and sequencing was performed based on the MiSeq FGx Forensic Genomics System. Using universal analysis software (UAS) of ForenSeqTM, principal component analysis (PCA), Structure and likelihood ratio method was used on the genotyping data of 56 aiSNP markers, respectively, and the genetic relationships between populations and inference of the origin of ancestors were analyzed. Results Among the five populations tested, the four ethnic populations in China (Hebei Han population, Inner Mongolia autonomous region Mongolian population, Tibet autonomous region Tibetan population and Xinjiang Uygur autonomous region Uygur population) could be significantly distinguished from Nigerian population. Xinjiang Uygur autonomous region Uygur individuals were shown as having mixed origins of ancestors and could be distinguished from the other three Chinese populations. However, the other three populations in China (Hebei Han population, Inner Mongolia autonomous region Mongolian population and Tibet autonomous region Tibetan population) could not be effectively distinguished by the system. Conclusion The 56 aiSNP markers in the ForenSeqTM DNA Signature Prep Kit can make accurate ancestry inference from the intercontinental level, but it is not yet able to distinguish between Chinese subpopulations.


Subject(s)
Humans , Asian People/genetics , China , DNA , DNA Fingerprinting , Ethnicity/genetics , Forensic Genetics/methods , Genetics, Population , High-Throughput Nucleotide Sequencing/methods , Polymorphism, Single Nucleotide
13.
Biomédica (Bogotá) ; 37(4): 486-497, oct.-dic. 2017. tab
Article in Spanish | LILACS | ID: biblio-888493

ABSTRACT

Resumen Introducción. La composición genética del huésped determina, entre otros aspectos, el perfil clínico del dengue, lo cual se debería al efecto de variantes en los genes que codifican citocinas proinflamatorias. Objetivo. Evaluar la asociación entre las variantes de tres polimorfismos en los genes candidatos TNFA, IL6 e IFNG con la gravedad del dengue en una población colombiana. Materiales y métodos. Se evaluaron los polimorfismos rs1800750, rs2069843 y rs2069705 de los genes TNFA, IL6 e IFNG, respectivamente, en 226 pacientes con dengue. Los genotipos se tipificaron usando la reacción en cadena de la polimerasa (PCR) y los polimorfismos de la longitud de los fragmentos de restricción (Restriction Fragment Length Polymorphism, RFLP). Para determinar el riesgo de diferentes fenotipos del dengue, se compararon las frecuencias alélicas con la prueba de ji al cuadrado, y los genotipos y los haplotipos, con regresión logística. Por último, los análisis se ajustaron utilizando datos de autoidentificación o del componente genético ancestral. Resultados. El alelo A del rs2069843, ajustado por autoidentificación, se asoció con casos de dengue hemorrágico en afrocolombianos. En la muestra completa, dicho polimorfismo, ajustado por componente genético ancestral, fue reproducible. Además, hubo asociaciones significativas entre las combinaciones alélicas GGT y GAC de los rs1800750, rs2069843 y rs2069705 en pacientes con dengue hemorrágico, con ajuste por componente genético ancestral y sin él. Además, la combinación alélica AGC produjo 58,03 pg/ml más de interleucina 6 que la GGC, independientemente de los componentes genéticos europeo, amerindio y africano. Conclusión. Las variantes de los polimorfismos GGT y GAC de los rs1800750, rs2069843 y rs2069705 en los genes TNFA, IL6 e IFNG, respectivamente, se correlacionaron con la gravedad del dengue en esta muestra de población colombiana.


Abstract Introduction: The genetic makeup of the host contributes to the clinical profile of dengue. This could be due to the effect of variants in the genes encoding pro-inflammatory cytokines. Objective: To evaluate the association between the variants of three polymorphisms in TNFA, IL6 and IFNG candidate genes with dengue severity in a sample of Colombian population. Materials and methods: We evaluated the rs1800750, rs2069843, and rs2069705 polymorphisms in TNFA, IL6 and IFNG candidate genes, respectively, in 226 patients with dengue infection. The genotypes were typed using both polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP). To determine the risk of different dengue phenotypes, we compared allele frequencies with chisquare and genotypes and haplotypes using logistic regression. Finally, these analyzes were adjusted with data from self-identification or the ancestral genetic component. Results: The A allele in the rs2069843 polymorphism, adjusted by self-identification, was associated with dengue hemorrhagic fever cases in Afro-Colombians. In the entire sample, this polymorphism, adjusted by the ancestral genetic component, was reproducible. In addition, there were significant associations between GGT and GAC allelic combinations of rs1800750, rs2069843, and rs2069705 in dengue hemorrhagic fever patients, with and without adjustment by ancestral genetic component. Additionally, the AGC allelic combination produced 58.03 pg/ml of interleukin-6 more than the GGC combination, regardless of European, Amerindian and African genetic components. Conclusions: The variants of GGT and GAC polymorphisms of rs1800750, rs2069843, and rs2069705 in the TNFA, IL6 and IFNG genes, respectively, were correlated with the susceptibility to dengue severity in a sample of Colombian population.


Subject(s)
Adolescent , Adult , Child , Female , Humans , Male , Middle Aged , Young Adult , Interleukin-6/genetics , Interferon-gamma/genetics , Tumor Necrosis Factor-alpha/genetics , Polymorphism, Single Nucleotide , Dengue/genetics , Polymorphism, Restriction Fragment Length , DNA, Viral/genetics , Ethnicity/genetics , Polymerase Chain Reaction , Risk , Cross-Sectional Studies , Prospective Studies , Colombia/epidemiology , Genetic Predisposition to Disease , Dengue/epidemiology , Dengue Virus/classification , Dengue Virus/genetics , Alleles , Genetic Association Studies , Gene Frequency , Genotype
14.
Ciênc. Saúde Colet. (Impr.) ; 22(11): 3773-3780, Nov. 2017. tab
Article in Portuguese | LILACS | ID: biblio-890200

ABSTRACT

Resumo As hemoglobinas variantes (Hb) decorrem de mutações nos genes da globina. As variantes estruturais mais frequentes são HbS, HbC, HbD e HbE. O gene da hemoglobina S tem frequência elevada na América, enquanto que no Brasil é maior no Sudeste e Nordeste. O presente artigo tem por objetivo investigar a presença de hemoglobinas variantes em 15 comunidades quilombolas do estado do Piauí. Foram analisadas 1.239 amostras, nas quais as hemoglobinas foram triadas pela cromatografia líquida de alta eficiência (HPLC). Aplicou-se questionário referente a gênero, etnia e consanguinidade das populações. Das 1.239 amostras, 5,4% apresentaram o traço falciforme AS, as doenças falciformes SS e SC apareceram em 0,8% do total, nas hemoglobinas AC, AD e DD. Das 1.069 pessoas negras, 84 apresentaram alteração das hemoglobinas; destas, 34 eram do sexo masculino e 53 do feminino. Ocorreu a presença de 13 casamentos consanguíneos dentre as 84 alterações das hemoglobinas. O estudo das hemoglobinas variantes em 15 comunidades remanescentes de quilombos do Piauí contribui para sua educação em saúde frente aos aspectos da herança genética destas proteínas, relevante questão de saúde pública, proporcionando subsídios para a implantação do Programa Estadual da Doença Falciforme do Piauí.


Abstract Hemoglobin variants (Hb) result from mutations in globin genes, with amino acid substitution in the polypeptide chain. Among the most common structural variants are HbS, HbC, HbD and HbE. The S hemoglobin gene is a high frequency gene across America and Brazil, where it is more frequent in the Southeast and Northeast. The scope of this article is to investigate the presence of hemoglobin variants in 15 quilombos (fugitive slave communities) of Piaui. The sample was of 1,239 people and hemoglobin was screened by high-performance liquid chromatography (HPLC). A questionnaire was applied related to gender, ethnicity and consanguinity. Of the samples analyzed, 5.4% had AS sickle cell trait, while SS and SC sickle cell anemia showed a rate of 0.8%, with AC, AD and DD hemoglobin. Of the 1,069 Afro-descendants, 84 revealed hemoglobin abnormalities, 34 being male 53 being female. There were 13 consanguineous marriages among the 84 hemoglobin alterations. The study of hemoglobin variants in 15 former quilombo communities in the state of Piaui contributes to their education in health in the aspects of genetic inheritance of hemoglobin, a relevant public health issue, providing input for the implementation of the State Program of Sickle Cell Disease of Piaui.


Subject(s)
Humans , Male , Female , Sickle Cell Trait/epidemiology , Hemoglobins/genetics , Ethnicity/genetics , Anemia, Sickle Cell/epidemiology , Sickle Cell Trait/genetics , Genetic Variation , Brazil/epidemiology , Prevalence , Surveys and Questionnaires , Chromatography, High Pressure Liquid/methods , Consanguinity , Amino Acid Substitution/genetics , Black or African American/genetics , Gene Frequency , Anemia, Sickle Cell/genetics
15.
Salud pública Méx ; 59(5): 532-539, Sep.-Oct. 2017. tab, graf
Article in English | LILACS | ID: biblio-903800

ABSTRACT

Abstract: Objective: To determine the number of micronuclei and nuclear anomalies in Mexico's indigenous population. Materials and methods: One hundred twenty indigenous individuals were evaluated, including thirty from the ethnicities Cora, Huichol, Tarahumara and Tepehuano. The number of micronuclei (MN) and any nuclear abnormality (NA) in oral mucosa cells, including cells with nuclear buds, binucleated cells, cells with karyolysis, karyorrhetic, condensed chromatin and pyknotic cells were determined for each participant. Results: Tepehuano and Tarahumaras showed the greatest damage to DNA. The Tepehuano group presented the highest number of MN and NA, this being a significant difference (p < 0.05) compared with the rest of the studied groups. This group also presented the highest herbicide exposure (46.7%). In relation to the smoking and drinking habits, these were more frequent in the Tarahumara group (33.3 and 50% respectively). Conclusion: The ethnic diversity, habits and customs may influence the DNA nuclear integrity in the Amerindian groups.


Resumen: Objetivo: Determinar el número de micronúcleos y anomalías nucleares en la población indígena de México. Material y métodos: Se evaluó a ciento veinte indígenas, incluyendo treinta individuos de las etnias cora, huichol, tarahumara y tepehuana. A cada participante se le determinó el número de micronúcleos (MN) y de alguna anomalía nuclear (AN) en células de mucosa bucal, incluyendo células con brotes nucleares, binucleadas, cariolisis, cariorrexis, cromatina condensada y picnóticas. Resultados: Los tepehuanos y tarahumaras mostraron el mayor daño al ADN. El grupo tepehuano presentó el mayor número de MN y AN, con una diferencia significativa (p < 0.05) en comparación con el resto de los grupos estudiados; este grupo presentó también la mayor exposición a herbicidas (46.7%). En relación con los hábitos de fumar y beber, se presentaron con mayor frecuencia en el grupo tarahumara (33.3 y 50%, respectivamente). Conclusión. La diversidad étnica, hábitos y costumbres pueden influir la integridad del ADN en los grupos amerindios.


Subject(s)
Humans , Male , Female , Adolescent , Adult , Middle Aged , Young Adult , Indians, North American/genetics , Cell Nucleus/ultrastructure , Micronuclei, Chromosome-Defective , Alcohol Drinking/epidemiology , DNA/genetics , Ethnicity/genetics , Smoking/epidemiology , Diet , Feeding Behavior , Herbicides , Mexico , Mouth Mucosa/ultrastructure
16.
Journal of Forensic Medicine ; (6): 271-276, 2017.
Article in Chinese | WPRIM | ID: wpr-984891

ABSTRACT

OBJECTIVES@#To study the genetic polymorphisms of 30 insertion/deletion (InDel) loci and evaluate their forensic application in Ewenki ethnic group from Inner Mongolia.@*METHODS@#Peripheral blood samples were collected from 87 unrelated healthy individuals in Ewenki ethnic group. Genomic DNA were extracted, and 30 InDel loci of the samples were multiplex amplified and genotyped. Hardy-Weinberg balance tests were preformed for all loci and genetic parameters were calculated by modified PowerStats v1.2 software. The linkage disequilibrium between loci were tested by SNPAnalyzer v2.0 software. Based on the allele frequencies of 30 InDel loci, the genetic relationships between Ewenki ethnic group and other populations were evaluated by analysis of molecular variance, principal component analysis and phylogenetic reconstruction.@*RESULTS@#After correction, 30 InDel loci conformed to Hardy-Weinberg equilibrium. It was found that the pairwise InDel loci were in linkage equilibrium after Bonferroni correction. The results of population genetics indicated that Ewenki ethnic group had close genetic relationships with Henan Han and Beijing Han populations; whereas it was significantly different from several populations in Europe and Mexico.@*CONCLUSIONS@#There are relatively high genetic polymorphisms on 30 InDel loci of Ewenki ethnic group from Inner Mongolia, which can be used as a helpful supplement application for STR detection system.


Subject(s)
Humans , Asian People/genetics , Beijing , China/epidemiology , DNA , Ethnicity/genetics , Gene Frequency , Genetic Loci , Genetics, Population , Genotype , INDEL Mutation , Linkage Disequilibrium , Microsatellite Repeats , Phylogeny , Polymorphism, Genetic , Social Behavior
17.
São Paulo med. j ; 134(3): 205-210, tab
Article in English | LILACS | ID: lil-785810

ABSTRACT

CONTEXT AND OBJECTIVE: Dimethylarginine dimethylaminohydrolase enzymes (DDAH), which are encoded by the genes DDAH1 and DDAH2, play a fundamental role in maintaining endothelial function. We conducted a case-control study on a Chinese population that included three ethnic groups (Han, Kazakh and Uygur), to systemically investigate associations between variations in the genes DDAH1 and DDAH2 and hypertension. DESIGN AND SETTING: Experimental study at the Department of Internal Medicine and Genetic Diagnosis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology. METHODS: This case-control study included 1,224 patients with hypertension and 967 healthy unrelated individuals as controls. DDAH1 -396 4N (GCGT) del>ins, rs3087894, rs805304 and rs9267551 were genotyped using the TaqMan 5' nuclease assay. RESULTS: The G/C genotype of rs3087894 in DDAH1 was a risk factor for hypertension in the Kazakh group in the co-dominant model (G/C versus G/G) (OR 1.39; 95% CI: 1.02-1.88; P < 0.05), with the same result in the dominant model (G/C + C/C versus G/G) (OR 1.38; 95% CI: 1.03-1.84; P < 0.05). In contrast, the C/C genotype of rs3087894 seemed to be a protective factor against hypertension in the Uygur group in the recessive model (C/C versus G/G + G/C) (OR 0.62; 95% CI: 0.39- 0.97; P < 0.05). Similar findings for rs3087894 were also observed after adjusting the variable for the age covariate. CONCLUSION: Our results indicated that the C-allele of rs3087894 in DDAH1 was a risk factor for hypertension in the Kazakh group but a protective factor in the Uygur group.


RESUMO CONTEXTO E OBJETIVO: Enzimas dimetilarginina dimetilaminohidrolase (DDAH), codificadas por genes DDAH1 e DDAH2, desempenham papel fundamental na manutenção da função endotelial. Realizamos estudo tipo caso-controle na população chinesa, com três grupos étnicos (han, kazakh e uygur) para investigar sistematicamente a associação entre a variação de genes DDAH1 e DDAH2 e a hipertensão. DESENHO E LOCAL: Estudo tipo caso-controle no Departamento de Medicina Interna e Diagnóstico Genético, Hospital de Tongji, Tongji Medical College, Universidade de Ciência e Tecnologia de Huazhong. MÉTODOS: Este estudo incluiu 1.224 pacientes com hipertensão e 967 indivíduos saudáveis, sem parentesco, como controles. DDAH1 -396 4 N (GCGT) del > ins, rs3087894, rs805304 and rs9267551 foram genotipados usando o ensaio nuclease TaqMan 5'. RESULTADOS: O genótipo G/C de rs3087894 no DDAH1 foi um fator de risco para a hipertensão arterial no grupo kazakh em modelo codominante (G/C versus G/G; OR 1,39; IC 95%: 1,02-1,88; P < 0,05), com o mesmo resultado no modelo dominante (G/C + C/C versus G/G; OR 1,38; IC 95%: 1,03-1,84; P < 0,05). Em contraste, o genótipo C/C de rs3087894 parecia ser um fator de proteção para a hipertensão no grupo uygur no modelo recessivo (C/C versus G/G + G/C; OR 0,62; IC 95%: 0,39-0,97; P < 0,05). Achado semelhante para rs3087894 também foi observado depois de se ajustar a variante à covariante idade. CONCLUSÃO: Os nossos resultados indicaram que o C-alelo de rs3087894 no DDAH1 foi fator de risco para a hipertensão no grupo de kazakh, mas fator de proteção no grupo de uygur.


Subject(s)
Humans , Male , Female , Adult , Middle Aged , Aged , Genetic Variation , Asian People/genetics , Amidohydrolases/genetics , Hypertension/genetics , Base Sequence , Ethnicity/genetics , Case-Control Studies , China/ethnology , Risk Factors , Genotype , Hypertension/epidemiology
18.
Biomédica (Bogotá) ; 36(1): 91-100, ene.-mar. 2016. graf, tab
Article in Spanish | LILACS | ID: lil-779535

ABSTRACT

Introducción. La validación de los factores predictores de la sensibilidad a la warfarina es importante para evitar las hemorragias asociadas con la terapia anticoagulante. En los estudios previos hechos en Colombia con polimorfismos de los genes VKORC1 y CYP2C9 , se reportaban algoritmos con rendimientos diferentes para explicar la variación de las dosis, pero no se evaluaba la predicción de la sensibilidad a la warfarina. Objetivo. Determinar la exactitud del análisis farmacogenético de los polimorfismos *2 y *3 en el gen CYP2C9 y 1639G>A en el gen VKORC1 para predecir la sensibilidad a la warfarina en pacientes del Hospital Militar Central, un centro de referencia que atiende pacientes de diferentes lugares de Colombia. Materiales y métodos. Se recopilaron los datos demográficos y clínicos de 130 pacientes que habían recibido una dosis estable de warfarina durante más de dos meses. Se obtuvieron sus genotipos mediante un análisis de curvas de fusión , y, después de verificar el equilibrio de Hardy-Weinberg de los polimorfismos, se hizo un análisis estadístico con enfoque multivariado y predictivo. Resultados. Se construyó un modelo farmacogenético que explicó el 52,8 % de la variación de la dosis (p<0,001), solo 4 % por encima del rendimiento obtenido con los mismos datos usando el algoritmo del International Warfarin Pharmacogenetics Consortium . El modelo predictivo de sensibilidad logró 77,8 % de exactitud e incluyó como factores la edad (p=0,003), los polimorfismos *2 y *3 (p=0,002) y el polimorfismo 1639G>A (p<0,001). Conclusiones. Estos resultados en una población mestiza colombiana respaldan la validez de la predicción de la sensibilidad a la warfarina basada en los polimorfismos de los genes VKORC1 y CYP2C9.


Introduction: In the search to prevent hemorrhages associated with anticoagulant therapy, a major goal is to validate predictors of sensitivity to warfarin. However, previous studies in Colombia that included polymorphisms in the VKORC1 and CYP2C9 genes as predictors reported different algorithm performances to explain dose variations, and did not evaluate the prediction of sensitivity to warfarin. Objective: To determine the accuracy of the pharmacogenetic analysis, which includes the CYP2C9 *2 and *3 and VKORC1 1639G>A polymorphisms in predicting patients´ sensitivity to warfarin at the Hospital Militar Central , a reference center for patients born in different parts of Colombia. Materials and methods: Demographic and clinical data were obtained from 130 patients with stable doses of warfarin for more than two months. Next, their genotypes were obtained through a melting curve analysis. After verifying the Hardy-Weinberg equilibrium of the genotypes from the polymorphisms, a statistical analysis was done, which included multivariate and predictive approaches. Results: A pharmacogenetic model that explained 52.8% of dose variation (p<0.001) was built, which was only 4% above the performance resulting from the same data using the International Warfarin Pharmacogenetics Consortium algorithm. The model predicting the sensitivity achieved an accuracy of 77.8% and included age (p=0.003), polymorphisms *2 and *3 (p=0.002) and polymorphism 1639G>A (p<0.001) as predictors. Conclusions: These results in a mixed population support the prediction of sensitivity to warfarin based on polymorphisms in VKORC1 and CYP2C9 as a valid approach in Colombian patients.


Subject(s)
Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Warfarin/pharmacokinetics , Polymorphism, Single Nucleotide , Vitamin K Epoxide Reductases/genetics , Cytochrome P-450 CYP2C9/genetics , Anticoagulants/pharmacokinetics , Warfarin/administration & dosage , Warfarin/adverse effects , Algorithms , Ethnicity/genetics , Colombia , International Normalized Ratio , Dose-Response Relationship, Drug , Alleles , Genetic Association Studies , Geography, Medical , Hemorrhage/chemically induced , Hemorrhage/prevention & control , Anticoagulants/administration & dosage , Anticoagulants/adverse effects
19.
Biomédica (Bogotá) ; 35(3): 437-443, jul.-sep. 2015. tab
Article in English | LILACS | ID: lil-765472

ABSTRACT

Introduction: Fetal hemoglobin is an important factor in modulating the severity of sickle cell anemia. Its level in peripheral blood underlies strong genetic determination. Associated loci with increased levels of fetal hemoglobin display population-specific allele frequencies. Objective: We investigated the presence and effect of known common genetic variants promoting fetal hemoglobin persistence (rs11886868, rs9399137, rs4895441, and rs7482144) in 60 Colombian patients with sickle cell anemia. Materials and methods: Four single nucleotide polymorphisms (SNP) were genotyped by restriction fragment length polymorphisms (RFLP) and the use of the TaqMan procedure. Fetal hemoglobin (HbF) from these patients was quantified using the oxyhemoglobin alkaline denaturation technique. Genotype frequencies were compared with frequencies reported in global reference populations. Results: We detected genetic variants in the four SNPs, reported to be associated with higher HbF levels for all four SNPs in the Colombian patients. Genetic association between SNPs and HbF levels did not reach statistical significance. The frequency of these variants reflected the specific ethnic make-up of our patient population: A high prevalence of rs7482144-'A' reflects the West-African origin of the sickle cell mutation, while high frequencies of rs4895441-'G' and rs11886868-'C' point to a significant influence of an Amerindian ethnic background in the Colombian sickle cell disease population. Conclusion: These results showed that in the sickle cell disease population in Colombia there is not a unique genetic background, but two (African and Amerindian). This unique genetic situation will provide opportunities for a further study of these loci, such as fine-mapping and molecular-biological investigation. Colombian patients are expected to yield a distinctive insight into the effect of modifier loci in sickle cell disease.


Introducción. La hemoglobina fetal es un importante factor modulador de la gravedad de la anemia falciforme, cuya expresión está muy condicionada por el factor genético. Los loci asociados con el incremento de la hemoglobina fetal pueden presentar frecuencias alélicas específicas para cada población. Objetivo. Investigar la presencia y el efecto de las variantes genéticas rs11886868, rs9399137, rs4895441 y rs7482144 asociadas con la persistencia de hemoglobina fetal, en 60 pacientes colombianos con anemia falciforme. Materiales y métodos. Se hizo la genotipificación de los polimorfismos de nucleótido simple ( Single Nucleotide Polymorphisms, SNP) mediante la técnica de polimorfismos de longitud de fragmentos de restricción ( Restriction Fragment Length Polymorphisms, RFLP) y el procedimiento TaqMan. La hemoglobina fetal (HbF) se cuantificó utilizando la técnica de desnaturalización alcalina de la oxihemoglobina. Las frecuencias genotípicas se compararon con las reportadas en poblaciones de referencia global. Resultados. Se observaron variantes genéticas ya reportadas para aumento de HbF en los cuatro SNP. La asociación genética entre los SNP y el incremento de la HbF no alcanzó significancia estadística. La frecuencia de estos alelos reflejó la siguiente composición específica en esta muestra de pacientes colombianos: una gran prevalencia de rs7482144-'A', lo que indica que el origen de la mutación para la anemia falciforme es África occidental, y una gran frecuencia de rs4895441-'G' y rs11886868-'C', lo que denota la influencia significativa del origen genético amerindio. Conclusión. Los resultados evidenciaron que la población con anemia falciforme de Colombia no tiene un único origen genético, sino que existen dos (africano y amerindio). Esta situación genética única ofrece la oportunidad de llevar a cabo un estudio más amplio de estos loci a nivel molecular. Se espera que el estudio de pacientes colombianos permita una visión diferente del efecto de los loci modificadores en esta enfermedad.


Subject(s)
Adolescent , Adult , Child , Child, Preschool , Female , Humans , Male , Middle Aged , Young Adult , Fetal Hemoglobin/genetics , Nuclear Proteins/genetics , Ethnicity/genetics , Carrier Proteins/genetics , Polymorphism, Single Nucleotide , Quantitative Trait Loci/genetics , gamma-Globins/genetics , Anemia, Sickle Cell/genetics , Repressor Proteins , Senegal/ethnology , Sierra Leone/ethnology , Polymorphism, Restriction Fragment Length , Indians, South American/genetics , Colombia/epidemiology , Black or African American/genetics , Genotype , Anemia, Sickle Cell/blood , Anemia, Sickle Cell/ethnology
20.
Rio de Janeiro; s.n; 2015. 175 f p.
Thesis in Portuguese | LILACS | ID: lil-751065

ABSTRACT

O uso de marcadores do tipo STR e SNP tem se revelado de grande importância na discriminação entre indivíduos de uma mesma população, assim como para estudos evolutivos. A utilização de um conjunto de 17 STRs e 46 SNPs específicos de cromossomo Y permitiu a caracterização de um conjunto de amostras representativas das populações do Rio de Janeiro e do oeste africano, com uma avaliação mais ampla sobre a ancestralidade de origem paterna. Na primeira parte deste estudo foram analisados 605 indivíduos do sexo masculino do estado do Rio de Janeiro. Como resultado, não foram observadas diferenças significativas entre as populações do sudeste e do Rio de Janeiro, que apresentou uma alta diversidade de haplótipos (0,9999 ± 0,0001) e de haplogrupos (0,7589 ± 0,0171). A comparação da população miscigenada do Rio de Janeiro com diferentes grupos étnicos ou populacionais mostrou que a frequência de indivíduos com marcadores tipicamente Europeus é de 77%, africanos é de 14,87% e em ameríndios é de 2,31%. A segunda parte do estudo revelou uma grande diversidade haplotípica (1,0000 ± 0,0018) numa amostra do Oeste africano. Quanto ao valor da diversidade de haplogrupos (0,6895 ± 0,0200), este foi similar aos observados em populações de origem Bantu do oeste e centro africanos, principalmente de Benin, Nigéria e Costa do Marfim. A terceira parte deste estudo mostrou que não existem diferenças significativas entre o componente africano da amostra do Rio de Janeiro e as populações africanas do sudeste, oeste e centro oeste. Por outro lado, observamos diferenças significativas quando comparamos o componente africano do Rio de Janeiro e o oeste africano com populações de Uganda, Quênia e África do Sul. A ampliação de estudos genéticos nas populações da África se fazem necessários para o entendimento da diversidade genética no mundo...


he use of STR and SNP markers has proved to be of great importance to discriminate individuals of the same population as well as for evolutionary studies. The use of a set of 17 STRs and 46 SNPs specific from the Y chromosome allowed the characterization of a group of samples representative of the Rio de Janeiro and the West African populations, with a deep assessment of the paternal ancestry. The first part of this study focused in the analysis of 605 males of the state of Rio de Janeiro. The results showed no significant differences between the Brazilian southeastern populations and Rio de Janeiro, which showed high values of haplotype (0.9999 ± 0.0001) and haplogroup (0.7589 ± 0.0171) diversities. The second part of the study revealed a high haplotype diversity (1.0000 ± 0.0018) in a sample from West Africa. The value of haplogroup diversity (0.6895 ± 0.0200) was similar to those previously seen in the West and Center African Bantu populations, mainly from Benin, Nigeria and Ivory Coast. The third part of this study showed no significant differences between the African component of our sample from Rio de Janeiro and the Southeastern, Western and Midwestern African populations. On the other hand, significant differences were observed when comparing the samples of the African component in Rio de Janeiro and of West Africa with population samples from Uganda, Kenya and South Africa. The increase of genetic studies in African populations is important for a better understanding of world genetic diversity...


Subject(s)
Humans , Genetics, Population , Black People/genetics , Ethnicity/genetics , Africa/ethnology , Brazil/ethnology , Chromosomes, Human, Y , Polymorphism, Genetic , Population Dynamics
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