Population data of five STRs in three regions from Portugal

Allele and haplotype frequencies of five chromosome STR loci (CD4, TPO, FES, TH01 and VWA) were determined for unrelated males throughout Portugal. This report presents STR data for three separate regions of Portugal, being the first time that data on the south of the country is presented. This study reveals that the three regions from Portugal are not genetically homogeneous. The north of Portugal presents significant differences in the CD4 locus, when compared with the other two populations. When compared with Madeira and A?ores, the three regions show a different behavior at TPO and VWA loci.     

Evaluation of population variation at 17 autosomal STR and 16 Y-STR haplotype loci in Croatians

Seventeen autosomal STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA, Penta E and Penta D) and 16 Y-STR haplotype loci (DYS19, DYS385, DYS389I, DYS398II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1) were analyzed in the sample of 200 unrelated Croatians. The agreement with HWE was confirmed for all autosomal STR loci. The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 17 autosomal STR loci were 0.999999999999999999682299331476 and 0.99999995, respectively. Penta E proved to be the most informative autosomal STR locus. Among 200 Croatian males, 197 Y-STR haplotypes were identified and haplotype diversity was estimated at 0.9998 ± 0.0005.     

Allelic frequencies of 13 STR loci in autochthonous Basques from the province of Vizcaya (Spain)

Allelic frequencies of 13 STR loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D16S539, TH01, TPOX, CSF1PO, and D7S820) were estimated from a sample of 73 unrelated healthy donors natives of the Spanish Basque province of Vizcaya. These STR loci constitute the core of polymerase chain reaction (PCR)-based DNA genetic markers in the US Combined DNA Index System (CODIS). All STR loci analysed met Hardy-Weinberg expectations. Based upon the allelic frequencies, forensically important parameters including gene diversity (GD), polymorphism information content (PIC) and power of discrimination (PD) were calculated.     

Allele sequences of six new Y-STR loci and haplotypes in the Chinese Han population

Human chromosome Y-specific short tandem repeat (Y-specific STR) markers have useful properties for forensic applications. However, there is a need to develop more Y-specific STR markers, because the discriminating power of each STR locus is limited. In the present study, we describe our results on six new Y-specific STR markers that were initially located using sequence database information by Ayub et al. and were named DYS434, DYS435, DYS436, DYS437, DYS438 and DYS439. Our studies focused on the analysis of the DNA sequence for each allele at all six Y-specific STR loci in order to understand their structures in the human genome and to construct human allelic ladders, which are necessary for forensic DNA typing. In addition, the haplotype distribution for all six analyzed loci was studied in a Chinese Han population sample. The results indicate that DYS434, DYS435, DYS436, DYS437, DYS438 and DYS439 are useful Y-specific STR markers for forensic sciences.     

A DNA microarray system for forensic SNP analysis

Forensic DNA analysis is routinely performed using polymorphic short tandem repeat (STR) markers. However, for degraded or minute DNA samples, analysis of autosomal single nucleotide polymorphisms (SNPs) in short fragments might be more successful. Furthermore, sequencing of mitochondrial DNA (mtDNA) is often performed on highly degraded or scarce samples due to the high copy number of mtDNA in each cell. Due to the increasing number of complete mtDNA genome sequences available, the limited discrimination power of an mtDNA analysis, may be increased by analysis of coding region polymorphisms in addition to the non-coding variation. Since sequence analysis of the coding region would require more material than generally present in forensic samples, an alternative SNP analysis approach is required. We have developed a one-colour microarray-based SNP detection system for limited forensic materials. The method is based on minisequencing in solution prior to hybridisation to universal tag-arrays. In a first outline of a forensic chip, a combination of 12 nuclear and 21 mitochondrial SNP markers are analysed simultaneously. The mitochondrial markers on the chip are polymorphisms within the hypervariable region as well as in the coding region. Even though the number of markers in the current system is limited, it can easily be extended to yield a greater power of discrimination. When fully developed, microarray analysis provides a promising system for efficient sensitive SNP analysis of forensic samples in the future.     

Distribution of Y chromosome lineages in Jerba island population

We have analysed Y chromosome polymorphism on six STR markers (DYS19, DYS389I, DYS390, DYS391, DYS392, and DYS393) and eight classical UEP markers (SRY10831a, YAP, SRY4064, M2, 92R7, M9, SRY2627 and 12f2) in three distinct ethnical, linguistic and cultural groups of Jerba island (Berbers, Arabs and a Jerban group of Sub-Saharan origin). Fst genetic distance and principal co-ordinate analysis based on STR haplotype frequencies, showed a genetic differentiation between the three Jerban groups and a genetic relationship between Jerban Berbers and Mozabites (a well defined Berber group in Algeria). Compound use of UEP and STR markers have increased discriminatory capacity. The detection of the most common haplotype (H9) in both Berbers and Mozabites may be useful in forensic special cases.     

Zimbabwe black population data on the six short tandem repeat loci – CSF1PO, TPOX, THO1, D3S1358, VWA and FGA

Allele frequencies for six tetrameric short tandem repeat (STR) loci CSF1PO, TPOX, THO1, D3S1358, VWA, and FGA were determined in a Black African sample population from Zimbabwe. All loci are highly polymorphic and meet Hardy-Weinberg expectations. An inter-class correlation test analysis detected only one departure from independence out of 15 pair-wise comparisons of the six loci (i.e., CSF1PO/VWA loci, P=0.026). The allele frequency data at four of the six STR loci in the Black African sample population are similar to African American data.     

Two loci ‘exclusion’ of true paternity is due to genetic disorder in a child

We describe a paternity case with three genetic incompatibilities between a three-year-old boy and his putative father.STR analysis of 2 out of 25 markers revealed the absence of paternal alleles and presence of two maternal alleles at D2S441 and D2S1338 loci in the child. The rest 23 STR markers served to confirm paternity. In addition, we analyzed Y-STRs and determined the same haplotype in the child and his putative father.With massive parallel sequencing on HID Ion GeneStudio S5 System using Precision ID GlobalFiler NGS STR Panel v2 (Applied Biosystems) we confirmed the presence of two alleles of maternal origin at D2S441, D2S1338 loci and identified two maternal alleles at additional locus D2S1776 located on chromosome 2 in the child.Finally, we confirm paternity. Three loci ‘exclusion’ was due to maternal uniparental disomy of chromosome 2 in the child.     

STR基因座单倍型的推断方法初探

本文参考Browning SR等提出的以SNP等位基因频率为基础,通过统计学模型推断SNP单倍型的方法,初步探讨亲权鉴定中STR基因座单倍型的推断方法。以两个处于连锁不平衡状态的X-STR基因座的女性分型结果为例进行说明。本方法为STR单倍型的推断提供了一个思路,有助于更科学准确地进行STR分型结果的解释。     

Population genetic study in two Transylvanian populations using forensically informative autosomal and Y-chromosomal STR markers

Our study provides population genetic data on two population samples collected in a Hungarian speaking region of Transylvania, Romania. Allele frequency and profile databases were generated on 17 autosomal STR loci (D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, VWA, FGA, TH01, TPOX, CSF1PO, Penta E and Penta D) as well as at the 12 European Y-STR extended haplotype loci (DYS19, DYS389-I/II, DYS390, DYS391, DYS392, DYS393, DYS385 loci, DYS437, DYS438 and DYS439). Data were compared to a Central Hungarian (Budapest region) population sample [B. Egyed, S. Füredi, M. Angyal, L. Boutrand, A. Vandenberghe, J. Woller, Z. Padar, Analysis of eight STR loci in two Hungarian populations, Forensic Sci. Int. 113 (2000) 25-27] that was used as a reference group of the Hungarian population. Calculating the F(ST) indices and with the pairwise comparisons of interpopulation molecular variance (AMOVA) the two populations from Transylvania could be fit into the Hungarian population data showing less substructuring effects as compared to the previous findings in Hungary [B. Egyed, S. Füredi, M. Angyal, L. Boutrand, A. Vandenberghe, J. Woller, Z. Padar, Analysis of eight STR loci in two Hungarian populations, Forensic Sci. Int. 113 (2000) 25-27; B. Egyed, S. Füredi, M. Angyal, I. Balogh, L. Kalmar, Z. Padar, Analysis of the population heterogeneity in Hungary using fifteen forensically informative STR markers, Forensic Sci. Int. 158 (2005) 244-249].     

Portuguese population data on the six short tandem repeat loci — CSF1PO,TPOX, THO1, D3S1358, VWA and FGA

Allele frequencies for six tetrameric short tandem repeat (STR) loci CSF1PO, TPOX, THO1, D3S1358, VWA and FGA were determined in a Caucasian population sample from Portugal. All loci are highly polymorphic and meet Hardy-Weinberg expectations. There is little evidence for association of alleles among the six loci. The three loci D3S1358, VWA and FGA are more polymorphic and, hence, are more informative than the loci CSF1PO, TPOX, and THO1. However, all six loci would be useful for human identification applications. The STR allelic frequency data are similar to other Caucasian data.     

Validation of the STR DXS7424 and the linkage situation on the X-chromosome

X-linked microsatellite markers have proven to be powerful tools for parentage testing, mainly in deficiency paternity cases when the disputed child is female. However, only a small number of X-linked short tandem repeats (STRs) have been comprehensively described for forensic applications to date.We present sequence and population genetic data of the DXS7424 STR (GDB-G00-577-633) which is a trinucleotide repeat polymorphism representing 12 alleles of 147-180 bp in length. DXS7424 is located at Xq22 and closely linked to DXS101, corresponding to a genetic localisation of 104.9-121 cM from Xp-tel.PCR fragment length measurements and sequencing were carried out using the automatic gene analyser ABI 310 (Applied Biosystems).The population of 764 unrelated Germans checked for this STR exhibited the following features: polymorphism information content (PIC) = 0.780; heterozygosity (Het) = 0.843; mean exclusion chance (MEC = 0.766. Kinship tests revealed a typical X-linked inheritance. In 300 meioses under investigation, mutations were not found. Significant deviations from the Hardy-Weinberg equilibrium (HWE) were not established.Linkage studies confirmed closely linkage to DXS101. Additional we found linkage disequilibrium between DXS7424 and DXS101. This requires to use the established haplotype frequencies in kinship testing.     

Allele frequencies for 15 autosomal STR loci and admixture estimates in Puerto Rican Americans

Allelic frequencies of 15 short tandem repeats (STR) markers (CSF1PO, FGA, THO1, TPOX, VWA, D3S11358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, D19S433 and D2S1338) were determined using the AmpFl STR Identifiler PCR Amplification Kit in Puerto Rican American individuals (N=205) from Massachusetts. The FGA, D18S51 and D2S1338 loci had a high power of discrimination (PD) with values of 0.967, 0.965 and 0.961, respectively. Significant deviations from the Hardy-Weinberg (HW) equilibrium were not detected. An important genetic contribution of Caucasian European (76.4%) was detected in Puerto Rican Americans. However, comparative analysis between Puerto Rican American and other neighboring populations from United States mainly with African and Caucasian Americans, revealed significant differences in the distribution of STR markers. Our results are important for future comparative genetic studies of different American ethnic groups, in particular a cultural group called Hispanic-Americans and should be helpful for forensic and paternity testing.     

体位性窒息对脑血管损伤的实验观察

目的 观察体位性窒息对脑血管损伤的影响。方法 家兔20只,致其中10只体位性窒息,另10只断颈处死进行对照。用兔抗人白蛋白抗体和兔抗人(von Willebrand Factor,vWF)抗体进行LSAB免疫组化法显色。结果抗人白蛋白抗体及抗人vWW、检测均显示出阳性;对照组显示不明显。秩和检验显示,两组间具有显著性差异。结论　在体位性窒息时,呼吸障碍所引起的缺氧,可损害脑血管的正常结构。     

豫鄂汉族人群9个STR基因座频率调查

调查了河南、湖北两省D3S1358、vWA、FGA、D8S1179、D21S11、D18S5l、D5S818、D13S317、D7S820等9个STR基因座在汉族人群中的频率分布,对696份汉族无关个体的血样检测结果进行了统计分析,9个STR基因座分别观察到8个等位基因和20、27、70、36、49、63、28、28、26种基因型;统计学计算结果显示两群体9个STR基因座基因频率无显著性差异,9个STR基因座组成的复合扩增系统应用于法医学个体识别及亲权鉴定有很高的实用价值.     

Allele frequencies for 70 autosomal SNP loci with U.S. Caucasian, African-American, and Hispanic samples

189 samples from 3 different U.S. sample groups Caucasian (74), African American (71) and Hispanic (44) were typed for 70 autosomal genetic markers. These 70 markers are bi-allelic (C/T) short nucleotide polymorphisms (SNPs). For each sample, the 70 SNP markers were typed in 11 unique 6-plexes and a single 4-plex PCR. A total of 10 of the 210 tests (70 loci x 3 populations) for Hardy-Weinberg equilibrium indicated a statistically significant result. In order to evaluate the minimum number of SNP loci needed to distinguish all 189 samples from one another, we ranked the loci according to their levels of observed heterozygosity and p-values obtained upon testing for Hardy-Weinberg equilibrium. The top 12 loci according to these ranking criteria were tabulated along with the number of unique genotypes observed when combining subsequent SNP markers. The 12 selected SNPs possessed an observed heterozygosity of >0.45 in all three populations examined and thus would be expected to exhibit more differences between samples. All of the 189 samples in this study were individualized with a subset of 12 SNP loci. However, it is likely that the addition of more than 12 SNP loci will be required to resolve larger sets of unrelated individuals from one another. By way of comparison, in these same 189 individuals all but one pair is resolved from one another with three of the traditional short tandem repeat (STR) loci possessing the highest heterozygosity values (D2S1338, D18S51, and FGA) run with the Identifiler kit. The final pair of unrelated samples could be resolved with the combination of 4 STR loci: D2S1338, D18S51, FGA, and VWA.     

Potential forensic application of closely linked autosomal STR haplotype in complex kinship testing

It has been noticed that the most commonly used commercial STR kits and mtDNA may not be able to solve some special kinship cases, such as alleged aunt, uncle, niece, nephew or half-siblings. Due to its unique hereditary pattern, the haplotype of genetic markers could be a solution of these questioned family relationships. In this study, we investigated the genetic features of an autosomal STR cluster by employing confirmed family samples. To evaluate the forensic practical value of autosomal STR haplotype, 5 closely linked STR loci, D1S2127-D1S2138-D1S3460-D1S1643-D1S518, which were arranged in about 2 cM region (from 186.29 cM to 188.02 cM; 1 cM represents 1% average recombination between two loci) on chromosome one, were selected to compose haplotype. Genotyping of 60 samples from 8 trios (father–mother–children), 8 duos (father or mother–children), and 4 three-generation pedigrees were performed using PAGE. Haplotypes were identified in the child by determining alleles for all 5 loci transmitted from each parent. Total 73 haplotypes were detected in all samples and 34 haplotypes were observed to be passed down as a whole and was corresponding with the inherited characteristics of haplotype. In all family members, 34 unrelated individuals contributed 65 haplotypes, of which 62 haplotypes appeared only once and the rest 3 haplotypes appeared twice. No recombination was observed in 4 three-generation pedigrees. In conclusion, the haplotype consisting of 5 closely linked autosomal STRs could pass down steadily as a whole. The family specificity of most haplotypes may provide a unique advantage in forensic complex kinship testing.     

D18S51及其侧翼区3个SNP组成的SNP-STR在亲子鉴定中的应用

目的将一个单倍型区块内的遗传标记单核苷酸多态性(SNP)和短串联重复序列(STR)组成SNPSTR单倍型,调查其在成都汉族人群中的分布,并探讨其在特殊亲子鉴定案例中的应用价值。方法选取DNA联合索引系统(combined DNA index system,CODIS)中突变率较高的基因座D18S51,与其侧翼区的3个SNP位点(rs8089331、rs8094489、rs7236090)组成SNP-STR,通过巢式等位基因特异性PCR的方法获得SNP-STR单倍型,调查该单倍型在75名成都汉族人群中的分布,并应用于两例D18S51基因座不符合遗传规律的二联体亲子鉴定案件。结果成功建立SNP-STR分型方法,在成都汉族人群中共发现43种单倍型,多态性为0.948 6,并成功解决了两例二联体亲子鉴定案件。结论 SNP-STR具有良好的多态性,有望应用于特殊的亲缘关系鉴定。     

Haplotypic blocks of X-linked STRs for forensic cases: study of recombination and mutation rates

In complex kinship cases, markers situated in haplotypic blocks may provide additional clues to other unlinked markers. We have established a protocol to amplify six X-chromosome microsatellites, located in two haplotype blocks, using PCR with fluorochrome-labeled primers and capillary electrophoresis. The segregation stability was explored in 92 unrelated families with individuals from three generations. Sixty-one different haplotypes were found in the DXS10079-DXS10074-DXS10075 block in the grandfathers and 96 in the mothers, with estimated haplotype diversities of 0.9828 and 0.9842, respectively. Fifty and 73 different haplotypes were found in the DXS6801-DXS6809-DXS6789 block in the grandfathers and the mothers, with estimated haplotype diversities of 0.9711 and 0.9742, respectively. We observed 10 between-cluster and one within-cluster recombinations in 99 female meioses. The overall per-locus mutation rate was 0.0034. This protocol allows for the characterization of the alleles of two sets of linked markers of the X-chromosome that can be useful in complex forensic cases.     

Swiss Caucasian population data for the STR loci D2S1338 and D19S433 using the AmpFISTR SGM plus PCR amplification kit

Allele and genotype frequencies for the ten STR loci D3S1358, VWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01, FGA were determined in a Swiss Caucasian population sample (n=206) using the AmpFISTR SGM Plus Amplification kit. Electrophoresis was carried out on an ABI PRISM CE 310 Genetic Analyzer instrument. Previously, allele frequencies were published for the 13 STR loci D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, THO1, TPOX, CSF1PO and D16S539 for the same samples (n=206) amplified with the AmpFISTR Profiler Plus and Cofiler PCR Amplification kits. Since the results for the eight loci D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, THO1, D16S539 shared between the AmpFISTR SGM Plus, Profiler Plus and Cofiler PCR Amplification kits already are published, only the allele frequencies for the two STR loci D2S1338 and D19S433 are reported in this paper. The two loci meet Hardy-Weinberg expectations. In addition, there is little evidence for association of alleles among the 15 loci (amplified with the Profiler, Cofiler, and SGM Plus amplification kits). The allelic frequency data can be used in forensic analyses to estimate the frequency of a multiple STR locus DNA profile in the Swiss population.