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1.
In this study, we compared two recently released commercial Y-chromosomal short tandem repeat (Y-STR) kits: the PowerPlex Y23 System (PPY23) and Yfiler® Plus PCR amplification kit (YPlus). We performed validation studies, including sensitivity, tolerance to PCR inhibitors, and mixture analysis, and a population genetics study using 306 unrelated South Korean males. PPY23 and YPlus showed similar sensitivity, but PPY23 showed higher tolerance to humic acid than YPlus. Furthermore, the detection rate of unique minor alleles called from male/male mixtures was higher for PPY23 than for YPlus. Comparing the newly added loci, the mean values of gene diversity for PPY23 and YPlus were 0.6715 and 0.8158, respectively. The discrimination capacity in the 306 unrelated South Korean males for PPY23 was 0.9837, and that for YPlus was 0.9935. These results will inform the selection of suitable Y-STR kits based on the purpose of forensic DNA analysis. 相似文献
2.
Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) frequency distributions provide resources for assessment of male population stratification among world-wide populations. Currently, the Y-STR Haplotype Reference Database (YHRD) contains numerous Y-chromosome haplotype profiles from various populations and countries around the world. However, for many of the recently discovered and already phylogenetically mapped Y-SNPs, the population data are scarce. Herein, the typing of 27 Y-STRs (Yfiler Plus) and 143 Y-SNPs (self-designed Y-SNP panel) was performed on 1269 unrelated males from 11 Han Chinese populations. Haplogroup O-M175 was the most predominant haplogroup in our Han Chinese data, ranging from 67.34% (Henan Han) to 93.16% (Guangdong Han). The highest haplogroup diversity (0.967056) was observed in Heilongjiang Han, with a discrimination capacity (DC) value of 0.3723. The number of alleles at single-copy loci varied from 2 for DYS391 (Guangdong Han) to 16 for DYS518 (Henan Han). For the majority of the populations (8/11), both the haplotype diversity and DC values are 1.0000. Furthermore, genetic differentiations were observed between Northern and Southern Han Chinese. These genetic differences were mainly reflected in haplogroup distribution and frequency, and they were confirmed by statistical analysis. 相似文献
3.
With the advent of next-generation sequencing technology, SNP markers are being explored as a useful alternative to conventional capillary electrophoresis–based STR typing. Low mutation rate and short-sized amplicons are added advantages of SNP markers over the STRs. However, to achieve a sufficient level of discrimination among individuals, a higher number of SNPs need to be characterized simultaneously. Hence, the NGS technique is highly useful to analyze a sufficiently higher number of SNPs simultaneously. Though the technique is in its nascent stage, an attempt has been made to assess its usability in the central Indian population by analyzing 124 SNPs (90 autosomal and 34 Y-chromosome) in 95 individuals. Various quality parameters such as locus balance, locus strand balance, heterozygosity balance, and noise level showed a good quality sequence obtained from the Ion GeneStudio S5 instrument. Obtained frequency of SNP alleles ranged from 0.001 to 0.377 in autosomal SNPs. rs9951171 was found to be the most informative SNP in the studied population with the highest PD and lowest MP value. The cumulative MP of 90 SNPs was found to be 4.76698 × 10–37. Analysis of 34 Y-chromosome SNPs reveals 11 unique haplogroups in 54 male samples with R1a1 as the most frequent haplogroup found in 22.22% of samples. Interpopulation comparison by FST analysis, PCA plot, and STRUCTURE analysis showed genetic stratification of the studied population suggesting the utility of SNP markers present in the Precision ID Identity Panel for forensic demands of the Indian population. 相似文献
4.
International Journal of Legal Medicine - Y-chromosome haplotypes of 527 non-related males (176 Han, 186 Tibetan, and 165 Yi) in the Tibetan-Yi corridor were analyzed using SureID® PathFinder... 相似文献
5.
The Y-specific STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS434, DYS437, DYS438, DYS439
and GATA A10 were studied in a northern Portuguese population. Haplotype and allele frequencies of these 14 Y-chromosome STRs
were estimated. In a sample of 212 individuals it was possible to define 196 different haplotypes of which 182 were found
only once, 12 were found in 2 samples and the 2 most frequent haplotypes were shared by only 3 individuals. The observed
haplotype diversity value was 0.9992. The usefulness of the inclusion of each of these new markers for forensic purposes is
discussed by comparing expected and observed increases in haplotype diversity. When combining the new markers (DYS434, DYS437,
DYS438, DYS439 and GATA A10) with the classical set (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393)
a 0.68% increase in haplotype diversity was obtained and the number of different haplotypes rose from 157 to 196. When DYS434
was not considered the haplotype diversity was not affected.
Received: 18 June 2001 / Accepted: 23 October 2001 相似文献
6.
We analyzed the variation of eighteen miniSTR loci in 411 randomly chosen individuals from Korea to increase the probability that a degraded sample can be typed, as well as to provide an expanded and reliable population database. Six multiplex PCR systems were developed (multiplex I: D1S1677, D2S441 and D4S2364; multiplex II: D10S1248, D14S1434 and D22S1045; multiplex III: D12S391, D16S3253 and D20S161; multiplex IV: D3S4529, D8S1115 and D18S853; multiplex V: D6S1017, D11S4463 and D17S1301; multiplex VI: D5S2500, D9S1122 and D21S1437). Allele frequencies and forensic parameters were calculated to evaluate the suitability and robustness of these non-CODIS miniSTR systems. No significant deviation from Hardy–Weinberg equilibrium expectations were observed, except for D4S2364, D5S2500 and D20S161 loci. A multidimensional scaling plot based on allele frequencies of the six miniSTR loci (D1S1677, D2S441, D4S2364, D10S1248, D14S1434 and D22S1045) showed that Koreans appeared to have most genetic affinity with Chinese and Japanese than to other Eurasian populations compared here. The combined probability of match calculated from the 18 miniSTR loci was 2.902 × 10 ?17, indicating a high degree of polymorphism. Thus, the 18 miniSTR loci can be suitable for recovering useful information for analyzing degraded forensic casework samples and for adding supplementary genetic information for a variety of analyses involving closely related individuals where there is a need for additional genetic information. 相似文献
7.
Nine miniSTR loci were analyzed in 191 unrelated individuals from Korea using three multiplex PCR systems (multiplex I: D1S1677, D2S441 and D4S2364; multiplex II: D10S1248, D14S1434 and D22S1045; multiplex III: D12S391, D16S3253 and D20S161). Due to the short PCR amplicons (<145 bp), miniSTR systems can effectively be used in forensic analysis with highly degraded DNAs. Allele frequencies and forensic parameters were calculated to evaluate their usefulness in forensic casework. The Exact Test demonstrated that all loci surveyed here were found to be no deviation from Hardy–Weinberg equilibrium, except two miniSTR markers (D4S2364 and D16S3253). When we compared the distribution of genetic variation of six miniSTR markers (D1S1677, D2S441, D4S2364, D10S1248, D14S1434 and D22S1045), the Exact Test revealed significant differences ( P < 0.05) between the Korean sample studied here and almost all of other samples of East Asian and European populations. The combined probability of match calculated from nine miniSTR loci was 1.28 × 10 −8, which is high degree of polymorphism. Thus, the miniSTR system, combined with other valuable miniSTR markers, may be suitable for recovering useful information in analyzing degraded DNA samples. 相似文献
8.
Genetic analyses of geographically and ethno-linguistically different populations are essential for understanding population stratification and genomic structure in medical Genome-Wide Association Studies (GWAS) and genetic variation and diversity related to forensic and population genetics studies. Here, we genotyped 30 autosomal insertion/deletion (Indel) markers from 502 Tai-Kadai-speaking Gelao individuals residing in the rugged topographical area in Southeastern China. In addition, two comprehensive population genetic comparisons of 15,327 individuals from 95 worldwide populations and of 6122 individuals from Asia and adjoining populations were conducted based on allele frequency data and raw genotype data, respectively. All studied markers were found to be in Hardy-Weinberg equilibrium. The combined power of discrimination in the Gelao minority group was 0.999999999975, and the combined probability of exclusion was 0.9879. Our results from the forensic statistical parameters indicated that this Indel panel can be independently used as a powerful tool in forensic individual identification but can only be used as a complementary tool in paternity cases involving East Asians. We also found significant allele frequency differences between the Gelao and other continental populations with respect to the markers grouped in clusters ∼Ⅳ, suggesting that these can be used as forensic ancestry informative Indel markers to distinguish the Gelao from other continental populations. Genetic ancestry analyses demonstrated that Tai-Kadai-speaking Gelao share a dominant ancestry component with Hmong-Mien-speaking Miao. Our population genetic results from multidimensional scaling plots, principal component analysis, neighboring-joining tree construction and hierarchical clustering also suggested that the Zunyi Gelao are genetically closer to their linguistically or geographically close populations, such as the Han Chinese, Guizhou Bouyei and the Hubei Tujia, than to Turkic and Tibeto-Burman speakers. 相似文献
9.
Short tandem repeat on the non-recombining part of chromosome Y with paternally inheritable capability is a valuable tool in the studies of forensic genetics, population genetics and anthropology. The mutation rate of Y-STR is an important parameter in the applications. A total of 629 haplotypes at 44 Y-STR markers were found in 629 unrelated males of our population. Mutation rates at 44 Y-STR loci ranged from 0 (CI: 0–5.70 × 10 −3) to 40.63 × 10 −3 (25.90 × 10 −3–57.2 × 10 −3) in our population. A higher mutation rate was noted at DYS612, DYS449, DYS547, DYS518, DYS576, DYS627, DYF403S1b, DYF387S1, DYS385a/b, DYS527a/b, DYF404S1, DYF403S1a and DYF399S1 in this population. The Y-STR set showed a higher discrimination capacity in forensic applications, and the present study provided reference data for the application of forensic and population genetics. 相似文献
10.
The Hui group is the second largest ethnic minority and one of the most widespread ethnic groups in China. However, the genetic architecture of the Hui population remains largely unexplored, particularly with respect to the male-specific region of the Y chromosome. Here, we studied nine Hui populations (Xinjiang, Qinghai, Gansu, Ningxia, Shaanxi, Henan, Shandong, Sichuan, Yunnan) using 157 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 27 short tandem repeats (Y-STRs) to unravel their genetic substructure and forensic characteristics. A total of 650 unrelated male samples from the Hui populations were genotyped by SNaPshot ®, a single base extension (SBE) assay. Finally, 95 terminal haplogroups and high haplotype diversity (0.9999) were observed in Hui populations. Frequency heat map matrices, genetic distance (F ST) and network analysis within Hui populations indicated that these nine Hui populations can be divided into three groups: Hui populations from the northwest (NWH), Hui populations from Sichuan and Shandong (SSH), and Hui populations from Yunnan (YNH). Our results suggested that we should use different databases for different Hui samples in forensic cases. Comparison with other populations that used different population genetic analysis revealed that the Hui populations had close relationships with East Asian populations, especially Chinese Han population. Overall, the high-resolution panel with Y-SNPs and Y-STRs gives new and complete insight into Hui populations, which can be used to interpret the genetic substructure of Hui populations and affect the utility of forensic databases. 相似文献
11.
Y-chromosomal short tandem repeats (Y-STRs) have been widely used in forensic analysis and population genetics. With low to moderate mutation rates, conventional Y-STR panels, including commercially available Y-STR kits, enable the identification of male pedigrees but typically fail to differentiate related male individuals. The introduction of rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) with higher mutation rates (μ > 10−2) has been demonstrated to increase the discrimination capacity of unrelated men and the differentiation rate of related men compared with standard Y-STRs. To date, several studies have been performed worldwide. Here, 260 father–son pairs from Chinese Yi population were investigated, and 18.8% of them were differentiated with the 13 RM Y-STR markers, which was close to the theoretical estimate of 19.5% based on the mutation rates of these markers. Among the 57 mutations observed, repeat gains were more common than repeat losses (1.48:1), and one-step mutations were more common than two-step mutations (27.5:1). Locus-specific mutation rates ranged from < 3.85 × 10−3 (95% CI 0.00–1.41 × 10−2) to 3.85 × 10−2 (95% CI 1.86 × 10−2–6.96 × 10−2), with an average mutation rate of 1.46 × 10−2 (95% CI 1.11 × 10−2–1.89 × 10−2). Furthermore, we combined the father–son pair data from the present study with the data from the previous studies, generating an overall mutation rate of 1.70 × 10−2. The high differentiation rate obtained in the present study indicates the suitability of RM Y-STRs to distinguish paternal lineages in Chinese Yi population. 相似文献
12.
Complete mitochondrial control region data were generated for 230 unrelated Pathans from North West Frontier Province and
Federally Administered Tribal Areas of Pakistan. To confirm data quality and to explore the genetic structure of Pathans,
mitochondrial DNA haplogroup affiliation was determined by shared haplogroup-specific polymorphisms in the control region
and by the analysis of diagnostic coding region single-nucleotide polymorphisms using a multiplex system for the assignment
of eight haplogroups: M, N1′5, W, R, R0, T, J, and U. Sequence comparison revealed that 193 haplotypes were defined by 215
variable sites when major insertions were ignored at nucleotide positions 16193, 309, and 573. From a phylogenetic perspective,
Pathans have a heterogeneous origin, displaying a high percentage of West Eurasian haplogroups followed by haplogroups native
to South Asia and a small fraction from East Asian lineages. In population comparisons, this ethnic group differed significantly
from several other ethnic groups from Pakistan and surrounding countries. These results suggest that frequency estimates for
mtDNA haplotypes should be determined for endogamous ethnic groups individually instead of pooling data for these subpopulations
into a single dataset for the Pakistani population. Data presented here may contribute to the accuracy of forensic mtDNA comparisons
in the Pathans of Pakistan. 相似文献
13.
Allele frequencies and forensic efficiency parameters of 11 non-standard autosomal STR loci, D21S1437, D22S683, D8S1110, D10S2325, D12S1090, D17S1294, D3S1744, D14S608, D20S470, D18S536 and D13S765 were evaluated in a sample of 102 unrelated Bangladeshi individuals. No significant deviation from Hardy–Weinberg equilibrium was observed in any of the loci studied. Statistical parameters of forensic importance, the power of discrimination (PD), observed and expected heterozygosity (H), polymorphism information content (PIC), matching probability (MP), power of exclusion (PE) and typical paternity index (TPI) were calculated for the loci. The most informative locus among the 11 STR loci was D10S2325 (PD = 0.958), while the least informative was D17S129 (PD = 0.876). The combined PD (1-PM) and MP was calculated to be 0.9999999999997 and 2.23 × 10 ?23, respectively. These parameters indicated the usefulness of the loci in forensic personal identification and parentage testing among Bangladeshi population. 相似文献
14.
Y-chromosomal 28 short tandem repeat (STR) loci were investigated in unrelated healthy individuals of the Ovambo population from Namibia ( n = 54). Sixteen Y-chromosome short tandem repeat (Y-STR) polymorphic loci (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385, DYS393, DYS391, DYS439, DYS635, DYS392, GATAH4, DYS437, DYS438, and DYS448) were analyzed using AmpF ISTR Yfiler Polymerase Chain Reaction (PCR) Amplification Kit. DYS441–445 and DYS446, DYS447, DYS449, DYS450, DYS459a/b, DYS463 and DYS464a/b/c/d were investigated using a multiplex PCR system. Fifty-one haplotypes were identified in 54 Ovambos. The STR diversity values for Y-STRs loci ranged from 0.036 (DYS392) to 0.900 (DYS 385). 相似文献
15.
Y-chromosomal polymorphic STRs are a powerful tool for forensic and evolutionary studies. Within the last decade, a series of Y-STR systems have been developed and demonstrated to be suitable for a variety of forensic applications including sexual assault cases and paternity testing. This review describes our recent studies on novel male-specific Y-STRs, involving identification, development of a multiplex-PCR system, population study and forensic application. 相似文献
16.
The polymorphism of the two hypervariable segments (HVI and HVII) of the control region of mtDNA was analyzed in a population of 154 unrelated individuals from south west Switzerland using a fluorescent based capillary electrophoresis sequencing method. In our population data of 154 random individuals, 137 mtDNA types were observed. Of these, 124 sequences were observed only in one individual whereas 10 sequences were observed in 2 individuals, 2 sequences in 3 individuals and 1 sequence in 4 individuals. The probability of two unrelated individuals having the same sequence was 0.84%. The results were compared with four other Caucasian populations. Furthermore, the usefulness of the mtDNA sequencing was tested, for exclusion and inclusion, in 18 forensic cases including 69 evidence samples and 44 reference samples. Despite the fact that 55% of the evidence samples yielded a negative result for the nuclear DNA with the human dot quantitation system, the success rate of the mtDNA sequencing was 71.0%. This validation study proves the great usefulness and sensitivity of the mtDNA sequencing technique using nested PCR and fluorescent capillary electrophoresis. 相似文献
17.
In the current study, 217 unrelated individuals of the Hazara population were genotyped for 15 autosomal short tandem repeats to generate parentage and forensic efficacy parameters. Hazaras belong to the Shi’a sect and are recognized by their Turko-Mogholi features. We found that D2S1338 was the most discriminatory locus with a maximum power of exclusion and high value of polymorphism information content. Whilst the Combined Power of Discrimination (CPD), Combined Matching Probability (CMP) and Combined Power of Exclusion (CPE) were 0.999999999999999, 2.76796338879E -17 and 0.999999040733479 respectively. Furthermore, the pattern of genetic affinity with genetically assumed related populations was demonstrated through Heat Map and Phylogenetic analysis, which revealed a great level of genetic closeness of Hazaras with Mongol population and descendants of Genghis Khan. The resulting data can be used for forensic applications and anthropological studies. 相似文献
18.
Insertion/deletion (InDel) polymorphism genetic marker is a powerful and prospective tool for human identification and population genetic studies. Considering that the genetic polymorphisms and ethnic background of the Shaanxi Han population have not been fully explored to this day, herein, the novel developed AGCU InDel 50 kit which included 47 autosomal InDels was applied in the 556 unrelated healthy Han individuals from Shaanxi province for the first time. There were no significant deviations from Hardy–Weinberg equilibrium and linkage equilibrium at the 47 InDels after Bonferroni correction. In the Shaanxi Han population, the values of combined discrimination power and cumulative exclusion probability for the 47 InDels were 0.999999999999999999891 and 0.99966, respectively. Furthermore, the interpopulation comparisons and population genetic structure analyses based on the 47 InDels were performed among the Shaanxi Han population and 43 reference populations, and the results showed that the Shaanxi Han population exhibited similar genetic structure and closer genetic affinities with the East Asian populations. 相似文献
19.
International Journal of Legal Medicine - Y chromosomal short tandem repeat (Y-STR) haplotype diversity of 180 genetically unrelated male individuals from Sheikh population of Punjab Pakistan was... 相似文献
20.
International Journal of Legal Medicine - A multiplex assay has been developed with newly designed primer sets comprising high mutation rate 12 RM Y-STR markers (DYS570, DYF399S1, DYS547, DYS612,... 相似文献
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