Y-chromosomal STR variation in Kurds and Arabs population in Iraqi Kurdistan

Background: The Iraqi Kurdistan local population involves more than eight gatherings of tenants. The Muslim Kurds make up most of the population and after that the Yezidi Kurds. Alternate gatherings incorporate Armenians, Assyrian, Chaldea, Syriacs, and little minority of Arab and Turkmen individuals.Methods: A total of 36 unrelated males from the two population groups in Iraqi Kurdistan: Kurds and Arabs were analyzed for eight Y-chromosome STRs (DYS19, DYS392, DYS437, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4). Total DNA from blood cells was extracted using DNA extraction Kit.Results: A number of genetic parameters such as mean number of alleles, allele frequency, gene diversity, polymorphic information content (PIC), and genetic distance were calculated using Power Marker V3.25 software. The DYS458 had the highest diversity (GD: 0.883), while loci DYS456 and Y-GATA-H4 had the lowest (GD: 0.574). The Dendrogram separated the populations into two main clades, the Kurd group and the Arab group except in one case only from the whole population.Conclusions: This study confirms the discriminating power of high-resolution Y-STR typing and provides first primary dataset on Iraqi Kurdistan samples. The comparison of Kurdish and Arab datasets reveals an interesting overall picture of isolation of Kurdish group. The primers DYS19, DYS448, DYS458, and DYS635 can be considered the best for their high PIC power.

Las pruebas de ADN en el contexto forense parte II. Interpretación estadística / Basic concepts of DNA testing in the forensic context part II. Statistical interpretation

Este artículo expone los conceptos básicos de las pruebas de ADN en el contexto forense. Describe como se establece la coincidencia entre el perfil genético de la muestra biológica encontrado en la escena del crimen con el perfil de un sospechoso o imputado; como se estima la probabilidad de que la coincidencia haya sido por azar evaluando la frecuencia del perfil genético en la población, es decir, la probabilidad de que el sospechoso en realidad no haya sido la fuente de la evidencia; y otros parámetros estadísticos importantes al momento de evaluar un análisis de ADN...(AU)

Comparison of gene frequencies of short tandem repeats loci on Y Chromosome between offenders with initiative-aggressive behavior and impulsive-aggressive behavior / 中华行为医学与脑科学杂志

Objective To explore the distributional differences of the gene frequencies of 22 short tandem repeats loci on Y Chromosome(Y?STRs) between offenders with Initiative?aggressive behavior and impulsive?aggressive behavior,and to probe into the genetic factors of initiative?aggressive behavior and im?pulsive?aggressive behavior. Methods Biological samples of 271 offenders with initiative?aggressive behav?ior and 271 offenders with impulsive?aggressive behavior were collected and PCR compound amplification was carried out with the aid of PowerPlex Y23 System. Then the PCR products were subjected to electrophoresis and gene detection with AB3500xL gene analysis system so as to calculate and compare the alleles and haplo?types of 22 Y?STRs gene frequency in the two groups. Results The distribution of allele frequency were sig?nificantly difference in locus DYS437(P=0.022) between two groups,not in the other 21 Y?STRs loci( all P>0.05) . Univarite analysis showed significant differences at allelle 14 in locus DYS437 between both groups ( initiative?aggressive behavior group:69. 37%;impulsive?aggressive behavior group:58. 67%; P=0. 009 ) . Conclusion Loci DYS437 may be associated with aggressive behavior. In the group of aggressive behavior, allelle 14 on locus DYS437 may be the susceptible factor of initiative?aggressive behavior and the resistant factor of impulsive?aggressive.

Genomic instability at the 13q31 locus and somatic mtDNA mutation in the D-loop site correlate with tumor aggressiveness in sporadic Brazilian breast cancer cases

OBJECTIVE: Genomic instability is a hallmark of malignant tissues. In this work, we aimed to characterize nuclear and mitochondrial instabilities by determining short tandem repeats and somatic mitochondrial mutations, respectively, in a cohort of Brazilian sporadic breast cancer cases. Furthermore, we performed an association analysis of the molecular findings and the clinical pathological data. METHODS: We analyzed 64 matched pairs of breast cancer and adjacent non-cancerous breast samples by genotyping 13 nuclear short tandem repeat loci (namely, D2S123, TPOX, D3S1358, D3S1611, FGA, D7S820, TH01, D13S317, D13S790, D16S539, D17S796, intron 12 BRCA1 and intron 1 TP53) that were amplified with the fluorescent AmpFlSTR Identifiler Genotyping system (Applied Biosystems, USA) and by silver nitrate staining following 6% denaturing polyacrylamide gel electrophoresis. Somatic mtDNA mutations in the D-loop site were assessed with direct sequencing of the hypervariable HVI and HVII mitochondrial regions. RESULTS: Half of the cancer tissues presented some nuclear instability. Interestingly, the D13S790 locus was the most frequently affected (36%), while the D2S123 locus presented no alterations. Forty-two percent of the cases showed somatic mitochondrial mutations, the majority at region 303-315 poly-C. We identified associations between Elston grade III, instabilities at 13q31 region (p = 0.0264) and mtDNA mutations (p = 0.0041). Furthermore, instabilities at 13q31 region were also associated with TP53 mutations in the invasive ductal carcinoma cases (p= 0.0207). CONCLUSION: Instabilities at 13q31 region and the presence of somatic mtDNA mutations in a D-loop site correlated with tumor aggressiveness.

Molecular typing of Mycobacterium leprae strains from northern India using short tandem repeats.

Background & objectives: Due to the inability to cultivate Mycobacterium leprae in vitro and most cases being paucibacillary, it has been difficult to apply classical genotyping methods to this organism. The objective of this study was therefore, to analyze the diversity among M. leprae strains from Uttar Pradesh, north India, by targeting ten short tandem repeats (STRs) as molecular markers. Methods: Ninety specimens including 20 biopsies and 70 slit scrappings were collected in TE buffer from leprosy patients, who attended the OPD of National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, and from villages of Model Rural Health Research Unit (MRHRU) at Ghatampur, Kanpur, Uttar Pradesh. DNA was extracted from these specimens and ten STRs loci were amplified by using published and in-house designed primers. The copy numbers were determined by electrophoretic mobility as well as sequence analysis. Phylogenetic analysis was done on variable number of tandem repeats (VNTRs) data sets using start software. Results: Diversity was observed in the cross-sectional survey of isolates obtained from 90 patients. Allelic index for different loci was found to vary from 0.7 to 0.8 except for rpoT for which allelic index was 0.186. Similarity in fingerprinting profiles observed in specimens from the cases from same house or nearby locations indicated a possible common source of infection. Such analysis was also found to be useful in discriminating the relapse from possible reinfection. Interpretation & conclusions: This study led to identification of STRs eliciting polymorphism in north Indian strains of M. leprae. The data suggest that these STRs can be used to study the sources and transmission chain in leprosy, which could be very important in monitoring of the disease dynamics in high endemic foci.

Association study between the genetic polymorphism of 15 STR loci and the crime of rape / 中华行为医学与脑科学杂志

Objective To investigate the relationship between rapists and related allele genes based on the analysis of 15 short tandem repeats (STRs) loci genetic polymorphism. Methods The method of Genome-wide scan was being used. Buccal swab samples of 129 rapists and 156 random populations were collected and PCR compound amplification was carried out with the aid of AmpFISTR Identifiler system. Then the products were subjected to electrophoresis and gene detection with AB13100 type gene analysis system so as to calculate and compare the alleles of 15 STRs gene frequency in the two groups. Results All the 15 STRs loci allele gene frequency in rapists and random population was found to coincide with Hardy-Weinberg law(P>0. 05). Allele 28 of D21S11 (rapists: 1.55% ,control group:5. 13%) ,allele22 of FGA(rapists:24.03% ,control group:16.99%),allele23 of FGA(rapists: 17.05% ,control group:26.28%) ,allele 10 of TH01(rapists:1.16% ,control group:4.17%) ,allele 8 of TPOX(rapists:55.77% ,control group:63.77%),allele 12 of TPOX(rapists:4.26% ,control group: 1.28%) were different between the two groups (P< 0.05) .while it is no differ significantly in other STRs loci allele gene(P >0.05). Conclusion Allele 28 of D21 S11,allele 22 and 23 of FGA, allele 10 of TH01, allele 8 and 12 of TPOX may be associated with the violent crime of rape. It is suggested that there are existing sensitive or resistance genes about the violent crime of rape in chromosome 2,4,11,21.

Analysis of paternal lineages in Brazilian and African populations

The present-day Brazilian population is a consequence of the admixture of various peoples of very different origins, namely, Amerindians, Europeans and Africans. The proportion of each genetic contribution is known to be very heterogeneous throughout the country. The aim of the present study was to compare the male lineages present in two distinct Brazilian populations, as well as to evaluate the African contribution to their male genetic substrate. Thus, two Brazilian population samples from Manaus (State of Amazon) and Ribeirão Preto (State of São Paulo) and three African samples from Guinea Bissau, Angola and Mozambique were typed for a set of nine Y chromosome specific STRs. The data were compared with those from African, Amerindian and European populations. By using Y-STR haplotype information, low genetic distances were found between the Manaus and Ribeirão Preto populations, as well as between these and others from Iberia. Likewise, no significant distances were observed between any of the African samples from Angola, Mozambique and Guinea Bissau. Highly significant Rst values were found between both Brazilian samples and all the African and Amerindian populations. The absence of a significant Sub-Saharan African male component resulting from the slave trade, and the low frequency in Amerindian ancestry Y-lineages in the Manaus and Ribeirão Preto population samples are in accordance with the accentuated gender asymmetry in admixture processes that has been systematically reported in colonial South American populations.

Análisis de la estructura genética en una muestra poblacional de Bucaramanga, departamento de Santander / An assessment of genetic structure in a Bucaramanga, department of Santander, population sample

Introducción: El fenómeno de sub-estructura en las poblaciones ha tenido desde hace varios años un abordaje amplio, que se enfocó, entre otros, en la identificación y cuantificación de la mezcla étnica presente en estudios de mapeo asociativo, para comprobar la asociación de marcadores polimórficos en el desarrollo de enfermedades comunes complejas, como responsable de falsos positivos. No obstante el reconocimiento de este problema, no se tiene suficiente información genética en el contexto nacional ni local que permita determinar la posible diferenciación de subgrupos poblacionales en cada región en particular. Objetivo: Determinar la estructura genética en una muestra poblacional de la ciudad de Bucaramanga, a partir del análisis de 19 marcadores microsatélites autosómicos en distintos subgrupos poblacionales. Metodología: De la base de datos del Laboratorio de Genética Humana de la Universidad Industrial de Santander, se seleccionaron aleatoriamente 350 muestras de ADN, y se amplificaron 19 marcadores autosómicos Short Tandem Repeat mediante los "kits Powerplex® 16 y FFFL (Promega)".Resultados: En el análisis de equilibrio Hardy Weinberg, no se obtuvieron diferencias estadísticamente significativas en 18 de 19 marcadores Short Tandem Repeat autosómicos analizados en la población de Bucaramanga. El único marcador que mostró no estar en equilibrio Hardy Weinberg en la población de Bucaramanga fue el F13B (valor de significancia de p=0.00264, después de aplicar la corrección de Bonferroni). Discusión: Las poblaciones representadas en los seis estratos socioeconómicos mostraron alta diversidad genética intragrupos, que ratificó una alta variabilidad entre los individuos de la ciudad de Bucaramanga, acorde con el bajo valor de FST entre distintos grupos, determinado en el análisis molecular de varianza con base en frecuencias alélicas observadas para los 19 Short Tandem Repeat analizados.

Introduction: The phenomenon of substructure in the populations has been greatly analyzed for several years, and it has been focused especially on the identification and quantification of ethnic mixture present in studies of associative mapping to verify the association of polymorphic markers in the development of complex and common diseases responsible for false positives. Nevertheless, despite the recognition of this issue, there is insufficient genetic information within the national or local contexts that allow assessing the possible differentiation of population sub-groups in each particular region. Objective: To determine the genetic structure in the city of Bucaramanga through the analysis of 19 autosomal microsatellite markers in different subgroups of the population. Methodology: A total of 350 DNA samples were randomly selected from the database of the Human Genetic Laboratory at Universidad Industrial de Santander by using Epi Info version 6.04 2001. Also, 19 Short Tandem Repeat markers were amplified using "kits Powerplex® 16 and FFFL (Promega)". Results: In the Hardy Weinberg equilibrium analysis (100 steps in Markov chain and 1000 dememorization steps), no statistically significant differences in 18 out of the 19 analyzed STRs markers in the population of Bucaramanga were obtained. A unique marker that proved not present in HWE in the population of Bucaramanga was the F13B (for a significance value of p=0.00264, after applying the Bonferroni correction). Discussion: The populations represented in the six socioeconomic levels presented high genetic diversity intragroups, which ratified the high variability among the individuals in this city according to the low value of FST for different groups, determined via the molecular analysis of variance based on the allelic frequencies observed for the 19 analyzed Short Tandem Repeats.

Microsatellite diversity among the primitive tribes of India.

The present study was undertaken to determine the extent of diversity at 12 microsatellite short tandem repeat (STR) loci in seven primitive tribal populations of India with diverse linguistic and geographic backgrounds. DNA samples of 160 unrelated individuals were analyzed for 12 STR loci by multiplex polymerase chain reaction (PCR). Gene diversity analysis suggested that the average heterozygosity was uniformly high ( >0.7) in these groups and varied from 0.705 to 0.794. The Hardy-Weinberg equilibrium analysis revealed that these populations were in genetic equilibrium at almost all the loci. The overall GST value was high (GST = 0.051; range between 0.026 and 0.098 among the loci), reflecting the degree of differentiation/heterogeneity of seven populations studied for these loci. The cluster analysis and multidimensional scaling of genetic distances reveal two broad clusters of populations, besides Moolu Kurumba maintaining their distinct genetic identity vis-à-vis other populations. The genetic affinity for the three tribes of the Indo-European family could be explained based on geography and Language but not for the four Dravidian tribes as reflected by the NJT and MDS plots. For the overall data, the insignificant MANTEL correlations between genetic, linguistic and geographic distances suggest that the genetic variation among these tribes is not patterned along geographic and/or linguistic lines.

Analysis of 31 STR loci in the genetic isolate of Carloforte (Sardinia, Italy)

The genotypes of 31 autosomal short tandem repeat loci in the population of Carloforte were analyzed, these representing a linguistic and genetic isolate located on the island of Sardinia (Italy). The markers span the entire length of chromosomes 19, 20, 21 and 22. Allele frequencies and statistical parameters were presented for all loci. Observed heterozygosity ranged from 0.279 to 0.884, and polymorphism information content from 0.552 to 0.886. All but two loci showed Hardy-Weinberg equilibrium after Bonferroni correction. The 31 short tandem repeat loci examined in the present work provide additional data on the genetic structure of the Carloforte population.

Haplotype Analysis of 9 STR_S Loci on Human Y Chromosome in Han Ethnic Group of Kunming City / 医学研究杂志

Objective To study the haplotype diversity of DYS390、DYS393、DYS437、DYS438、DYS439、DYS447、DYS448、DYS460、H4 loci in 216 unrelated individuals in Han ethnic group of Kunming city,Yunnan province.Methods The DNA were extracted with Chloroform,phenol methods or Chelex-100 method.STR-PCR,Non-denaturing polyacylaminde gel electrophoresis and Sliver staining and ABI377 sequencer were carried out for study.216 undividuals were collected from Han ethnic group in Kunming city.Results 216 types of haplotype were detected from 9 STRS.Every haplotype frequence was detected at 0.0046,GD=1.00005934437,The lowest arrangement of the repeat units was detected at 0.0046.S E=1.25?10-9。Conclution The 9 Y-STRs loci of Kunming people are highly polymorphic and are powerful means in determination of identify and paternity for forensic practice.

Population Study of Y-chromosome STR Haplotypes in Koreans / 대한법의학회지

The Y-chromosome short tandem repeat (STR) systems including DYS391, DYS389I/II, DYS439, DYS438, DYS437, DYS19, DYS392, DYS393, DYS390 and DYS385 (PowerPlex Y System, Promega) were investigated in 569 Korean males (the Central region). A total of 473 haplotypes were observed in the 569 individuals studied, of which 426 (90.06%) were unique. The overall haplotype diversity for the 12 Y-STR loci was 0.9985, and the discrimination capacity was 0.8313. The gene diversity varied from 0.2586 at DYS391 to 0.9558 at DYS385. We scrutinized for the presence of non-standard (intermediate and duplicated) alleles among Y chromosome STR haplotypes. Three mutations were identified in three short tandem repeat (STR) loci DYS439, DYS19 and DYS385. In DYS439, we found a new mutant allele that added an A at upstream of the first GATA motif of the repeat region. The allele was designated 11.1 according to the sequence structure. We also detected a duplicate allele in DYS19 and a triplicate allele at DYS385 locus.

Comparación de tres métodos de extracción de ADN a partir de restos óseos / Comparison of three methods for DNA extraction from bone remains

Extraction of amplifiable DNA is a frequent problem when working with degraded specimens like bone samples. The possibility of obtaining as much information as possible from these samples has a particular significance in many forensic investigations. The present investigation was aimed to assess the efficiency of three organic extraction methods for purifying amplifiable DNA from bone samples. The amount of nucleic acids obtained, the success rate in the amplification of DNA microsatellite (STR) markers and amelogenin by PCR, the influence of PCR inhibitors and environmental conditions, and where the samples were found before their processing in the laboratory, were all evaluated in this investigation for the three methods. Results showed that method A (a modification of FBI method for DNA extraction) performed better in producing not a higher amount but a better quality amplifiable DNA, in comparison with the other two methods evaluated. It was also demonstrated that the quality of the DNA to be amplified by PCR was influenced by the presence of inhibitors and/or contaminants and the environmental conditions where the bone sample was taken from. The worst conditions were observed from aquatic environments. The results suggest that the implementation of some specific modifications in the method A (use of purification columns, reliable quantification methods and different dilutions) would help to obtain better DNA extracts intended to be used in different molecular identification tests.

Analysis of Mitochondrial and Y-chromosomal DNA from 350-Year-Old Mummified Human Tissue / 대한법의학회지

This paper describes the successful DNA extraction and amplification, and analysis of mitochondrial and Y-chromosomal DNA from an approximately 350-year-old mummy exhumed from Gyunggi-do, South Korea in 2001. Sample tissue was obtained from internal organs such as lung, liver, and muscle of the mummy. Mummy tissue was rehydrated in trisodium phosphate solution, and protein was digested by proteinase K. Sample DNA was extracted using phenol-chloroform-isoamyl alcohol and silica column. Every step of DNA extraction and PCR was cautiously carried out according to general guideline to prevent contamination of the sample DNA. PCR products of mitochondial DNA (mtDNA) were observed with good yield, and sequence analysis of the mtDNA was successfully accomplished in the control regions (HV1, HV2, and HV3). In addition, minimal haplotype Y-STRs were tried to analysis. However, DYS19, DYS389l, DYS390, DYS391, DYS392 and DYS393 were only amplified and clearly genotyped. Sequence analysis of mtDNA and YSTR genotyping were performed more than twice with time intervals, and the results were accepted only when they showed the even profile for authenticating mummy DNA. There are some difficulties in the analysis of DNA from ancient mummified human remains has wellknown problems, such as low template quantity, poor quality of DNA, and the presence of PCR inhibitors. This implies that the most critical factor for ancient DNA analysis is extraction of DNA. In order to overcome these troubles, we used DNA extraction using phenol-chloroform-isoamyl alcohol and silica column and optimized PCR condition. Therefore, the analysis of mtDNA and Y-STRs from mummy was successfully performed.