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1.
This study developed a new multiplex PCR system that simultaneously amplifies 16 X‐STR loci in the same PCR reaction, and the polymorphism and mutation rates of these 16 X‐STR loci were explored in a Shanghai Han population from China. These loci included DXS10134, DXS10159, DXS6789, DXS6795, DXS6800, DXS6803, DXS6807, DXS6810, DXS7132, DXS7424, DXS8378, DXS9902, GATA165B12, GATA172D05, GATA31E08, and HPRTB. Samples from 591 unrelated individuals (293 males and 298 females) and 400 two‐generation families were successfully analyzed using this multiplex system. Allele frequencies and mutation rates of the 16 loci were investigated, with the comparison of allele frequency distributions among different populations performed. Polymorphism information contents of these loci were all >0.6440 except the locus DXS6800 (0.4706). Nine cases of mutations were detected in the 16 loci from the investigation of 9232 meioses. Pairwise comparisons of allele frequency distributions showed significant differences for most loci among populations from different countries and ethnic groups but not among the Han population living in other areas of China. These results suggest that the 16 X‐STR loci system provides highly informative polymorphic data for paternity testing and forensic identification in the Han population in Shanghai, China, as a complementary tool.  相似文献   

2.
This paper describes the development and validation of a novel 31-locus, six-dye STR multiplex system, which is designed to meet the needs of the rapidly growing Chinese forensic database. This new assay combines 20 extended-CODIS core loci (D3S1358, D5S818, TPOX, CSF1PO, TH01, vWA, D7S820, D21S11, D8S1179, D18S51, D16S539, D13S317, FGA, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, and D22S1045), nine highly polymorphic loci in Chinese Han population (D3S3045, D6S1043, D6S477, D8S1132, D10S1435, D15S659, D19S253, Penta D, and Penta E), and two gender determining markers, amelogenin and Y-Indel, which could amplify DNA from extracts, as well as direct amplification from substrates. To demonstrate the suitability for forensic applications, this system was validated by precision and accuracy evaluation, concordance tests, case sample tests, sensitivity, species specificity, stability, stutter calculation, and DNA mixtures, according to the guidelines described by the Scientific Working Group on DNA Analysis Methods (SWGDAM) and regulations published by the China Ministry of Public Security. The validation results indicate the robustness and reliability of this new system, and it could be a potentially helpful tool for human identification and paternity testing in the Chinese population, as well as facilitating global forensic DNA data sharing.  相似文献   

3.
Currently, two of the most widely used X‐chromosome STR (X‐STR) multiplexes are composed by ten (GHEP‐ISFG decaplex) and 12 markers (Investigator Argus X‐12 Kit). The number of markers included is a drawback for complex relative testing cases, likewise the large size of some amplicons difficult their application to degraded samples. Here, we present a new multiplex of 17 X‐STRs with the aim of increasing both the resolution power and forensic applicability. This newly proposed set includes the X‐STRs of the GHEP‐ISFG decaplex, four X‐STRs from the Investigator Argus X‐12 Kit, three of them also included in the decaplex, and six additional more. In order to ensure the allele designation, an allelic ladder was developed. The validation of the present multiplex was carried out according to the revised guidelines by the SWGDAM (Scientific Working Group on DNA Analysis Methods). A total of 488 unrelated individuals from four different continents were analyzed. The forensic efficiency evaluation showed high values of combined power of discrimination in males (≥0.999999996) and females (≥0.999999999999995) as well as combined paternity exclusion probabilities in trios (≥0.99999998) and duos (≥0.999996). The results presented herein have demonstrated that the new 17 X‐STR set constitutes a high‐resolution alternative to the current X‐STR multiplexes.  相似文献   

4.
In this study, we describe the developmental validation assay performed on a novel designed STR multiplex system, AGCU 21+1 STR kit. This kit contains a sex‐determining locus amelogenin and 21 noncombined DNA index system STR loci, that are, D6S474, D12ATA63, D22S1045, D10S1248, D1S1677, D11S4463, D1S1627, D3S4529, D2S441, D6S1017, D4S2408, D19S433, D17S1301, D1GATA113, D18S853, D20S482, D14S1434, D9S1122, D2S1776, D10S1435, and D5S2500. The 21+1 kit was validated by a series of tests including optimized PCR conditions, sensitivity, precision and accuracy, stutter ratio, DNA mixture, inhibitors, and species specificity according to the revised validation guidelines issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM). Our results in this study show that the kit is a useful tool for forensic application.  相似文献   

5.
《Electrophoresis》2017,38(8):1154-1162
Nonbinary single‐nucleotide polymorphisms (SNPs) are potential forensic genetic markers because their discrimination power is greater than that of normal binary SNPs, and that they can detect highly degraded samples. We previously developed a nonbinary SNP multiplex typing assay. In this study, we selected additional 20 nonbinary SNPs from the NCBI SNP database and verified them through pyrosequencing. These 20 nonbinary SNPs were analyzed using the fluorescent‐labeled SNaPshot multiplex SNP typing method. The allele frequencies and genetic parameters of these 20 nonbinary SNPs were determined among 314 unrelated individuals from Han populations from China. The total power of discrimination was 0.9999999999994, and the cumulative probability of exclusion was 0.9986. Moreover, the result of the combination of this 20 nonbinary SNP assay with the 20 nonbinary SNP assay we previously developed demonstrated that the cumulative probability of exclusion of the 40 nonbinary SNPs was 0.999991 and that no significant linkage disequilibrium was observed in all 40 nonbinary SNPs. Thus, we concluded that this new system consisting of new 20 nonbinary SNPs could provide highly informative polymorphic data which would be further used in forensic application and would serve as a potentially valuable supplement to forensic DNA analysis.  相似文献   

6.
Liu QL  Lu DJ  Quan L  Chen YF  Shen M  Zhao H 《Electrophoresis》2012,33(8):1299-1305
The aim of this study is to develop a new multiplex PCR system that simultaneously amplifies the 15 X-chromosome short tandem repeats (X-STRs) loci in the same PCR reaction, and to obtain the 15 X-STR loci database in three nationality populations from China. This multiplex system includes DXS7133, DXS6801, DXS981, DXS6809, DXS7424, DXS6789, DXS9898, DXS7132, GATA165B12, DXS101, DXS10075, DXS6800, GATA31E08, DXS10074, and DXS10079, which were successfully analyzed on 1251 DNA samples (670 males and 581 females) from Guangdong Han population, Xinjiang Uigur and Kazakh. The allele frequencies and mutation rates of the 15 loci were investigated, and the allele frequency distribution among different populations was compared. A total of 6-17 alleles for each locus were observed and altogether 170 alleles for all the selected loci were found. Thirteen cases with mutation of the above loci were detected in 11,850 meioses. Pairwise comparisons of the allele frequencies distribution showed significant differences in most loci among different populations. The results indicate that this multiplex system may provide high polymorphism information for kinship testing and relationship investigations, and it is necessary to gain allele frequency and mutation rate of different population for forensic application.  相似文献   

7.
The Uygur ethnic minority is the largest ethnic group in the Xinjiang Uygur Autonomous Region of China, and is a precious resource for the study of ethnogeny and forensic biology. Previous studies have focused on the genetic background of the Uygur group, however, the patrilineal descent of the group is still unclear. In this study, we investigated the genetic diversity of 24 Y‐STR loci in the Uygur group and analyzed the population differentiations as well as the genetic relationships between the Uygur group and other previously reported populations using 17 Y‐filer loci. According to haplotypic analysis of the 24 Y‐STR loci in 109 Uygur individuals, 104 different haplotypes were obtained, 99 of which were unique. The haplotypic diversity and discrimination capacity of these 24 Y‐STR loci in Uygur group were 0.9992 and 0.9541, respectively. An additional 7 loci (DYS388, DYS444, DYS447, DYS449, DYS522, and DYS527a,b) showed high genetic diversity and improved the overall discrimination capacity of the 24 Y‐STR system. Pairwise Fst and neighbor‐joining analysis showed that the Uygur group was genetically close to the Han populations from different regions.  相似文献   

8.
Insertion/deletion (InDel) polymorphisms have been widely used in the fields of population genetics, genetic map constructions, and forensic investigations owing to the advantages of their low mutation rates, widespread distributions in the human genome, and small amplicon sizes. In order to provide more InDels with high discrimination power in Chinese populations, we selected and constructed one novel multiplex PCR‐InDel panel for forensic individual identification. Genetic distributions of these 35 InDels in five reference populations from East Asia showed low genetic differentiations among these populations. Forensic efficiency evaluations of these InDels revealed that these loci could perform well for forensic individual identifications in these reference populations. In the meantime, genetic diversities and forensic parameters of these InDels were further investigated in the studied Kazak group. Mean value of polymorphism information content for 35 InDels was 0.3611. Cumulative power of discrimination of 35 InDels was 0.99999999999999603 in Kazak group. Given these results, the panel is suitable for individual identifications in the studied Kazak and these reference populations.  相似文献   

9.
DNA samples of 523 unrelated anonymized individuals (307 males and 216 females) born and living in the Czech Republic were genotyped using Investigator® Argus X‐12 system in the following loci localized in four linkage groups: DXS10148, DXS10135, DXS8378, DXS7132, DXS10079, DXS10074, DXS10103, HPRTB, DXS10101, DXS10146, DXS10134, DXS742. Haplotype frequencies were calculated for each LG (Linkage Group). The frequency of most common haplotype was 0.016, 0.036, 0.042, and 0.023 for LG1, LG2, LG3, and LG4, respectively. The combined power of discrimination was more than 0.999999999 both for female and male samples. The mean exclusion chance was 0.99999999 (trios) and 0.999999 (duos). Informativity and suitability of Investigator® Argus X‐12 for kinship determination was assessed by computing in several female–female duos using LR (Likelihood Ratio) determination for autosomal STR (PowerPlex ESI‐17), linked (Investigator® Argus X‐12 system), and unlinked (X‐STR Decaplex) X‐STR kits. Investigator® Argus X‐12 proved to be very useful for sibship determination, since its LR values were relatively similar to LR for autosomal STR kit. This work presents the first population data for Investigator® Argus X‐12 system in the Czech Republic.  相似文献   

10.
With a unique inheritance pattern compared to autosomal short tandem repeats (A-STRs), X chromosomal STRs (X-STRs) have special usage in forensic relationship testing. In this study, we designed a multiplex amplification system (named TYPER-X19 multiplex assay) consisting of 18 STR loci spreading from 7.837 to 149.460 Mb on the X chromosomes (DXS9895, DXS8378, DXS9902, DXS6810, DXS7132, DXS10079, DXS6789, DXS7424, DXS101, DXS6797, DXS7133, DXS6804, GATA165B12, DXS10103, HPRTB, GATA31E08, DXS8377, and DXS7423), and the amelogenin. PCR primers were marked with four kinds of fluorophores including FAM, HEX, TAMRA, and ROX. The multiplex system was optimized and tested for precision, concordance, reproducibility, sensitivity, stability, DNA mixture, and species specificity according to the conventional validation guidelines. The results indicated that the system was accurate, reliable, and sensitive enough, and was suitable for common forensic case-type samples. In the population genetic study, a total of 148 alleles were detected at the 18 X-STR loci in 398 Southern Han Chinese. Relatively high combined power of discrimination in male (PDm), power of discrimination in female (PDf), mean paternity exclusion chance in trios (MECtrio), and mean paternity exclusion chance in duos (MECDuo) by Desmarais were detected, and HPRTB-DXS10103 was in linkage disequilibrium. The results suggested that the TYPER-X19 multiplex assay was suitable for forensic applications.  相似文献   

11.
Insertion/deletion polymorphisms (Indels) have been considered as potential markers for forensic DNA analysis. However, the discrimination power of Indels is relatively lower due to the poor polymorphisms of diallelic markers. Here, two to three Indel loci that were very tightly linked in physical position were combined into a specific multi‐Indel marker to improve the discrimination, as well as a multiplex that consisted of a set of multi‐Indel markers was developed for forensic purpose. Finally, a multiplex system with 20 multi‐Indel markers including 43 Indel loci from dbSNP database was constructed and DNA sample can be analyzed by this multiplex in one PCR reaction and one CE run. A total of 150 unrelated individuals from Hunan province in South‐central China were genotyped by the multiplex system. The result showed that a total of 63 specific amplicons were detected, three alleles were observed in multi‐Indel markers including two Indel loci and four alleles were observed in the markers including three Indel loci. The cumulative probability of exclusion and the accumulated discrimination power were 0.9989 and 0.9999999999994, respectively. Our result demonstrated that the strategy could be efficient to develop higher polymorphic multi‐Indel markers, and the new multiplex could provide Supporting Information for forensic application.  相似文献   

12.
A previously developed multiplex assay with 44 individual identification SNPs was expanded to a 55plex assay. Fifty‐four highly informative SNPs and an amelogenin sex marker were amplified in one PCR reaction and then detected with two SNaPshot reactions using CE. PCR primers for four loci, 28 single‐base extension primers, and the reaction conditions were altered to improve the robustness of the method. A detailed approach for allele calling was developed to guide analysis of the electropherogram. One hundred and eighty unrelated individuals and 100 father‐child‐mother trios of the Han population in Hebei, China were analyzed. No mutation was found in the SNP loci. The combined mean match probability and cumulative probability of exclusion were 1.327 × 10?22 and 0.999932, respectively. Analysis of the 54 SNPs and 26 STRs (included in the AmpFLSTR Identifiler and Investigator HDplex kits) showed no significant linkage disequilibriums. Our research shows that the expanded SNP multiplex assay is an easily performed and valuable method to supplement STR analysis.  相似文献   

13.
Many studies have been proposed to identify insertion/deletion (InDel) polymorphisms in humans for forensic genetic studies. However, the discriminatory power of InDels is limited by the poor polymorphisms of diallelic markers. To improve their discriminatory power, we developed multi‐InDel, a novel autosomal marker comprising more than two InDel loci that are tightly linked by their physical position and combined into a specific marker by a pair of PCR primers. This strategy gives at least three haplotypes for each multi‐InDel marker. Such markers can be potentially very useful in forensic applications. In this study, we focused on multi‐InDel markers located on X chromosome (ChrX). A multiplex system with 13 multi‐InDel markers, including 28 InDel loci in ChrX, was developed. To validate the multi‐InDel panel, the haplotype distribution in a population sample and in a set of pedigrees was investigated. This study demonstrates usefulness of these markers for individual identification and relationship studies. We highlight the fact that the multi‐InDel markers located on ChrX can provide new supporting information for complex kinship testing.  相似文献   

14.
Marker sets based on insertion/deletion polymorphisms (InDels) combine the characteristics of both short tandem repeats (STRs) and single nucleotide polymorphisms and have served as effective complementary or stand-alone systems for human identification in forensics. We developed a novel multiplex amplification detection system, designated the AGCU InDel 60 kit, containing 57 autosomal InDels, 2 Y-chromosomal InDels, and the amelogenin locus and validated the kit in a series of studies, which included tests of the PCR conditions; tests for sensitivity, species specificity, reproducibility, stability, and mock case samples; degradation studies; and a population study. The results indicated that the AGCU InDel 60 kit was accurate, specific, reproducible, stable, and robust. Complete DNA profiles were obtained even with 125 pg of human DNA. In tests of artificially degraded samples, we found that the number of alleles detected by the validated kit was considerably greater than that detected by the STR-based AGCU 21+1 kit, even as the degree of degradation increased. Additionally, 564 unrelated individuals from three Han groups were investigated using this novel system, and the values of combined power of discrimination and combined power of exclusion were not less than 1–4.9026 × 10−24 and 1–3.1123 × 10−5, respectively. Thus, the results indicated that the novel kit was more powerful than the previous version of the InDel kit (the AGCU InDel 50 kit). Our results suggest that the AGCU InDel 60 kit can serve as an efficient tool for human forensics and a supplementary kit for population genetics research.  相似文献   

15.
We have developed a novel STR 25‐plex florescence multiplex‐STR kit (DNATyper25) to genotype 23 autosomal and two sex‐linked loci for forensic applications and paternity analysis. Of the 23 autosomal loci, 20 are non‐CODIS. The sex‐linked markers include a Y‐STR locus (DYS391) and the Amelogenin gene. We present developmental validation studies to show that the DNATyper25 kit is reproducible, accurate, sensitive, and robust. Sensitivity testing showed that full profiles were achieved with as low as 125 pg of human DNA. Specificity testing demonstrated a lack of cross reactivity with a variety of commonly encountered non‐human DNA contaminants. Stability testing showed that full profiles were obtained with humic acid concentration ≤60 ng/μL and hematin concentration <400 μM. For forensic evaluation, the 23 autosomal STRs followed the Hardy–Weinberg equilibrium. In an analysis of 509 Chinese (CN) Hans, we detected a combined total of 181 alleles at the 23 autosomal STR loci. Since these autosomal STRs are independent from one another, PM was 8.4528 × 10?22, TDP was 0.999 999 999 999 999 999 999, CEP was 0.999 999 8395. The forensic efficiency parameters demonstrated that these autosomal STRs are highly polymorphic and informative in the Han population of China. We performed population comparisons and showed that the Northern CN Han has a close genetic relationship with the Luzhou Han, Tujia, and Bai populations. We propose that the DNATyper25 kit will be useful for cases where paternity analysis is difficult and for situations where DNA samples are limited in quantity and low in quality.  相似文献   

16.
Recently, next generation sequencing has shown the promising application value in forensic research. In this study, we constructed a multiplex amplification system of different molecular genetic markers based on the previous selected ancestry informative single nucleotide polymorphisms (SNPs), multi-allelic insertion/deletion (InDel) polymorphisms, microhaplotypes, and Y-chromosomal SNP/InDel loci, and evaluated forensic efficiencies of the system in Chinese Shaanxi Han, Chinese Hui, and Chinese Mongolian groups via the next generation sequencing platform. Ancestry information analyses of Shaanxi Han, Hui, and Mongolian groups revealed that most Mongolian individuals could be differentiated from Shaanxi Hans and Huis based on the selected ancestry informative SNPs. Multi-allelic InDels and microhaplotypes showed the multiple allele variations and possessed relatively high genetic polymorphisms in these three groups, indicating these loci could provide higher forensic efficiencies for individual identification and paternity testing. Based on Y-chromosomal SNPs, different haplogroup distributions were observed among Shaanxi Han, Hui, and Mongolian groups. In conclusion, the self-developed system could be used to simultaneously carry out the individual identification, paternity analysis, mixture deconvolution, forensic ancestry information analysis, and Y-chromosomal haplogroup inference, which could provide more valuable investigative clues in forensic practices.  相似文献   

17.
The Y-chromosome short tandem repeats (Y-STRs) loci with different mutation rates existing in the Y chromosome non-recombination region (NRY) allow to be applied in human forensics, genealogical researches, historical investigations and evolutionary studies. Currently, there is a high demand for pedigree search to narrow the scope of crime investigations. However, the commonly used Y-STRs kits generally contain Y-STRs with high mutation rates that could cause individuals from the same pedigree to display different haplotypes. Herein, we put forward a new strategy of Slowly Mutating (SM) Y-STRs plus Y-SNPs typing, which could not only improve the resolution and accuracy of pedigree search, but also be applicable to evolutionary research. First, we developed a nine SM Y-STRs assay by evaluating their mutation rates in 210 pedigrees. Then the gene diversity and efficiency of the SM Y-STRs and 172 Y-SNPs sets were investigated by 2304 unrelated males from 24 populations. Furthermore, network and time estimation analyses were performed to evaluate the new strategy's capability to reconstruct phylogenetic tree and reliability to infer the time to the most recent common ancestor (TMRCA). The nine SM Y-STRs assay even had a higher resolution and a comparable capacity of revealing population genetic differentiation compared to 172 Y-SNPs system. This new strategy could optimize the phylogenetic tree generated by commonly used Y-STR panels and obtain a quite consistent time estimations with the published dating.  相似文献   

18.
《Electrophoresis》2018,39(12):1466-1473
Massively parallel sequencing (MPS) technologies, also termed as next‐generation sequencing (NGS), are becoming increasingly popular in study of short tandem repeats (STR). However, current library preparation methods are usually based on ligation or two‐round PCR that requires more steps, making it time‐consuming (about 2 days), laborious and expensive. In this study, a 16‐plex STR typing system was designed with fusion primer strategy based on the Ion Torrent S5 XL platform which could effectively resolve the above challenges for forensic DNA database‐type samples (bloodstains, saliva stains, etc.). The efficiency of this system was tested in 253 Han Chinese participants. The libraries were prepared without DNA isolation and adapter ligation, and the whole process only required approximately 5 h. The proportion of thoroughly genotyped samples in which all the 16 loci were successfully genotyped was 86% (220/256). Of the samples, 99.7% showed 100% concordance between NGS‐based STR typing and capillary electrophoresis (CE)‐based STR typing. The inconsistency might have been caused by off‐ladder alleles and mutations in primer binding sites. Overall, this panel enabled the large‐scale genotyping of the DNA samples with controlled quality and quantity because it is a simple, operation‐friendly process flow that saves labor, time and costs.  相似文献   

19.
Massively parallel sequencing (MPS) technology allows to simultaneously type multitudinous molecular genetic markers for many samples in one run with the feature of high detection resolution, and thereby arouses the increasing attention from forensic science. Herein, multiple allelic single nucleotide polymorphisms (multi-allelic SNPs) were screened for personal identification and parentage testing, and then were genotyped using MPS platform. Unrelated individuals of Chinese Mongolian and Kazakh groups were investigated to further estimate forensic effectiveness and applicability of these multi-allelic SNPs. The results of sequencing efficiency estimations and forensic genetic statistical parameters demonstrated that this MPS panel of multi-allelic SNPs was expected to be work for forensic applications. Subsequently, the exploration of population genetic variation patterns among the two investigated groups and other 26 reference populations revealed that these Chinese Mongolian and Kazakh groups had the similar population genetic patterns with the populations from East Asian, but European ancestral composition in the Kazakh group was higher than that in the Mongolian group. Currently, the present results were the preliminary research to scrutinize genetic information of these two ethnic minority groups employing multi-allelic SNPs.  相似文献   

20.
Forensic laboratories routinely conduct analysis of glass fragments to determine whether or not there is an association between a fragment(s) recovered from a crime scene or from a suspect to a particular source of origin. The physical and optical (refractive index) properties of the fragments are compared and, if a “match” between two or more fragments is found, further elemental analysis can be performed to enhance the strength of the association. A range of spectroscopic techniques has been used for elemental analysis of this kind of evidence, including inductively coupled plasma mass spectrometry (ICP-MS). Because of its excellent sensitivity, precision, and accuracy, several studies have found that ICP-MS methods (dissolution and laser-ablation) provide the best discrimination between glass fragments originating from different sources. Nevertheless, standard unit-resolution ICP-MS instruments suffer from polyatomic interferences including 40Ar16O+, 40Ar16O1H+, and refractory oxide 40Ca16O+ that compromise measurements of trace levels of Fe56+ and Fe57+, for example. This is a drawback in the analysis of glass fragments because iron has been previously identified as a good discriminating element. Currently, several techniques are available that enable reduction of such interferences. However, there are no data comparing detection limits of iron in glass using those techniques. The aim of this study was to compare, the analytical performance of high-resolution sector field inductively coupled plasma mass spectrometry (HR-SF-ICP-MS) and quadrupole ICP-MS equipped with a dynamic reaction cell (DRC-ICP-MS), for the detection of iron in glass, in terms of accuracy, precision, and method detection limits (MDLs). Analyses were conducted using conventional acid-digestion and laser-ablation methods. For laser-ablation analyses, carrier gases were compared to assess the effect on detection limits in the detection of iron isotopes. Iron polyatomic interferences were reduced or resolved by using a dynamic reaction cell and high-resolution ICP-MS. MDLs as low as 0.03 μg g−1 and 0.14 μg g−1 were achieved in laser-ablation and solution-based analyses, respectively. Use of helium as carrier gas improved detection limits for both iron isotopes in medium-resolution HR-SF-ICP-MS and in DRC-ICP-MS.  相似文献   

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