Objective:To investigate 38 Y-chromosome short tandem repeat(Y-STR)genetic polymorphisms in Beijing Han and analyze the genetic distance with neighboring or linguistically similar populations.Materials and Methods:In ...Objective:To investigate 38 Y-chromosome short tandem repeat(Y-STR)genetic polymorphisms in Beijing Han and analyze the genetic distance with neighboring or linguistically similar populations.Materials and Methods:In the study,we selected 531 unrelated male individuals of Beijing Han,and the results were statistically analyzed by testing with GSTAR™41Y reagents.Results:The allele peak heights were balanced among the Y loci,the amplified fragment ranged from 100 to 500 bps.A total of 531 haplotypes were detected in 531 samples.Eight null genotypes were observed on locus DYS448.One and three double alleles were observed on single-copy locus DYS576 and DYS19,respectively.DYS385 a/b,DYF387S1 a/b,and DYS527 a/b were more common in double copies,but 3,13,and 11 triple alleles were detected,respectively.The gene diversity values of Y-STRs except DYS391,DYS438,and DYS645 were>0.5.Twenty-seven Y-STRs of Beijing Han population were selected for genetic distance comparison with 17 populations including Changchun Han,with Rst values ranging from 0.0002 to 0.1703.Conclusion:The 38 Y-STRs in this study have strong male lineage identification ability and have great potential for individual identification,kinship identification,Y-STR database construction,and genetic relationship research.展开更多
The short tandem repeat (STR) markers are widely used in human identification and paternity testing in the field of forensic genetics[1].Recent researches on polymorphic STRs have led to their applications to populati...The short tandem repeat (STR) markers are widely used in human identification and paternity testing in the field of forensic genetics[1].Recent researches on polymorphic STRs have led to their applications to population genetics,forensic DNA database,human individual identification,paternity testing,genetic mapping,disease linkage analysis,archaeology and potential inference of the ethnic origin of an individual[2].展开更多
Objective To analyze the genetic polymorphism of 6 STR loci (D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613) on chromosome 12 in Chinese Han population. Methods EDTA-blood specimens were collected from 1...Objective To analyze the genetic polymorphism of 6 STR loci (D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613) on chromosome 12 in Chinese Han population. Methods EDTA-blood specimens were collected from 153 unrelated individuals of Chinese Han population in Shaanxi province. Allele and genotype frequencies for the 6 STR loci were estimated and statistical parameters of polymorphism were calculated. Results 8 alleles and 18 genotypes, 10 alleles and 17 genotypes, 9 alleles and 15 genotypes, 12alleles and 29 genotypes, 12 alleles and 31 genotypes, 8 alleles and 11 genotypes were observed at D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613, respectively. No deviations of the observed allele frequency from Hardy-weinberg equilibrium expectations were found for any of these loci. The Heterozygotes of these 6 loci were 78.89%, 66.10%, 54.95%, 79.10%, 71.98% and 59.48%, respectively. It indicated the high genetic polymorphism of the loci in Chinese Han population. Conclusion The 6 STR loci belonged to the genetic marker system of high discriminutesation and high information in Chinese Han population and can be used in the study of gene-related diseases.展开更多
Context:As the increasing number of pet canines,the identification of canine has attracted much attentions in the forensic field,however,the genetic diversities of pet canines still remained unknown.Aims:To explore ge...Context:As the increasing number of pet canines,the identification of canine has attracted much attentions in the forensic field,however,the genetic diversities of pet canines still remained unknown.Aims:To explore genetic polymorphisms of 19 short tandem repeat(STR)loci and genetic relationships between the two studied canine groups and reference group.Subjects and Methods:In the present study,genetic polymorphisms of 19 STR loci and a sex-linked zinc finger locus were analyzed in a total of 594 canines in Standard Poodle and Bichon Frise groups from China.Results:A total of 166,159 alleles were observed in the Standard Poodle,Bichon Frise groups with the corresponding allelic frequencies ranging from 0.0030-0.6108 to 0.0012-0.6148,respectively.The combined discrimination power and probability of exclusion of 19 STR loci in Standard Poodle and Bichon Frise groups were 0.9999999999999497,0.999962884;and 0.99999999999999995,0.999965955,respectively.Furthermore,the genetic distances between the two canine groups and Labrador retriever group were calculated,and the results indicated that Standard Poodle and Bichon Frise groups showed a closer genetic relationship,while the two canine groups had distant genetic relationships with Labrador retriever group.The result of population genetic structure revealed that genetic component distributions in the three canine groups were different.The predicted accuracies of the constructed random forest prediction model for three validation sets(25%individuals randomly selected from three populations with 808 individuals)were higher than 0.9,especially for the individuals in validation set from the Bichon Frise group is 1.Conclusions:The 19 STR loci could be used for individual identification,canine breed identification and paternity testing in the two canine groups.展开更多
A six-color fluorescent multiplex amplification system for 31 Y-chromosomal short tandem repeats(Y-STRs)(DYS19,DYS390,DYS391,DYF399S1,DYF404S1,DYS439,DYS444,DYS449,DYS452,DYS456,DYS458,DYS460,DYS481,DYS508,DYS513,DYS5...A six-color fluorescent multiplex amplification system for 31 Y-chromosomal short tandem repeats(Y-STRs)(DYS19,DYS390,DYS391,DYF399S1,DYF404S1,DYS439,DYS444,DYS449,DYS452,DYS456,DYS458,DYS460,DYS481,DYS508,DYS513,DYS516,DYS518,DYS543,DYS547,DYS549,DYS552,DYS557,DYS570,DYS576,DYS612,DYS622,DYS626,DYS627,DYS630,DYS635,and Y-GATA-A10)was developed for investigating the mutation rates of 31 highly mutated Y-STR genes in the Han population of northern China.The mutation rates of the 31 highly mutated Y-STRs were calculated using the father-son pair study method after typing 526 Northern Han father-son pairs with this system.Statistically,148 Y-STR mutations were found,with mutation rates ranging from 0(95%confidence interval[CI]0 to 9.0×10^(−3),DYS622)to 7.0×10^(−2)(95%CI 5.1×10^(−2)to 9.7×10^(−2),DYF399S1).Out of these,126 father-son pairs were successfully identified,with a distinction rate of 24.0%(95%CI 20.4%-27.9%).The ability of the 31 highly mutated Y-STRs to distinguish closely related males from the same paternal lineage in the Northern Han population is extremely valuable for criminal investigations and other purposes.展开更多
China is a multinational country composed of 56 ethnic groups of which the Han Chinese accounts for 91.60%.Qinghai Province is located in the northeastern part of the Qinghai-Tibet Plateau,has an area of 72.12 km2,and...China is a multinational country composed of 56 ethnic groups of which the Han Chinese accounts for 91.60%.Qinghai Province is located in the northeastern part of the Qinghai-Tibet Plateau,has an area of 72.12 km2,and is the fourth largest province in China.In the present study,we investigated the genetic polymorphisms of 20 short tandem repeat (STR) loci in a Qinghai Han population,as well as its genetic relationships with other populations.A total of 273 alleles were identified in 2 000 individuals at 20 loci,and the allelic frequency ranged from 0.0002 to 0.5327.The 20 STR loci showed a relatively high polymorphic rate in the studied group.Observed and expected heterozygosities ranged 0.613 0-0.907 5 and 0.614 8-0.920 0,respectively.The combined power of discrimination,and the probability of exclusion in duo and trio cases were 0.999 999 999 999 999 999 999 999 34,0.9999960 and 0.9999999965,respectively.Analyses of interpopulation differentiation revealed that the most significant differences were found between the Qinghai Han and Malaysian,while no significant differences were found between the Qinghai Han and Han people from Shaanxi and Jiangsu.The results of principal component analysis,multidimensional scaling analysis and phylogenetic reconstructions also suggested the close relationships between the Qinghai Han and other two Han populations.The present results,therefore,indicated that these 20 STR loci could be used for paternity testing and individual identification in forensic applications,and may also provide information for the studies of genetic relationships between Qinghai Han and other groups.展开更多
Goldeneye™DNA ID 22NC Kit is a novel short tandem repeat(STR)genotyping system that investigate 20 non-CODIS loci(D4S2366,D6S477,D22GATA198B05,D15S659,D8S1132,D3S3045,D14S608,D17S1290,D3S1744,D2S441,D18S535,D13S325,D7...Goldeneye™DNA ID 22NC Kit is a novel short tandem repeat(STR)genotyping system that investigate 20 non-CODIS loci(D4S2366,D6S477,D22GATA198B05,D15S659,D8S1132,D3S3045,D14S608,D17S1290,D3S1744,D2S441,D18S535,D13S325,D7S1517,D1OS1435,D11S236&D19S253,D1S1656,D7S3O4&D10S14&and D5S2500),a CODIS locus(D3S1358),and a sex-determining locus amelogenin in one assay.In the present study,this STR genotyping system was validated according to the guidelines of"Wlidation Guidelines for DNA Analysis Methods(2016)"updated by the Scientific Working Group on DNA Analysis Methods.A series of tests,such as polymerase chain reaction-based studies,sensitivity,inhibitors,DNA mixture,species specificity,precision and accuracy evaluation,stutter percentage,and peak height ratio,was conducted.The genetic polymorphism of 21 STR loci that included in the 22NC system was also investigated in the Chinese Hunan Han population.The validation results demonstrated that Goldeneye™DNA ID 22NC Kit is a robust and reliable identification assay as required for genotyping in kinship analysis and forensic investigation.The 21 STR loci in this kit also showed a high level of genetic polymorphism for the Hunan Han population.Therefore,it can be used for forensic applications and population studies.展开更多
In recent years,paternity testing in ethnic minority areas in China increases rapidly.However,the number of existing genetic markers does not meet the needs.The objective is to study the information of 22 genetic mark...In recent years,paternity testing in ethnic minority areas in China increases rapidly.However,the number of existing genetic markers does not meet the needs.The objective is to study the information of 22 genetic markers in Mongolian,Tibetan,and Uygur Nationality.The genetic polymorphism of 22 short tandem repeat(STR)loci(D10S1435,D11S2368,D12S391,D13S325,D14S608,D15S659,D16S539,D17S1290,D18S535,D19S253,D1S1656,D20S470,D21S1270,D22GATA198B05,D2S1338,D3S3045,D4S2366,D5S2500,D6S477,D7S3048,D8S1132,and D9S925)was estimated in 259 Uyghur,251 Tibetan,and 250 Inner Mongolian individuals from China who were all unrelated.Allele frequencies and forensic parameters were evaluated.The Hardy-Weinberg equilibrium(HWE)of each locus and the linkage disequilibrium(LD)for all pairwise STR loci were tested.Additionally,the Nei's genetic distance was used to estimate the genetic heterogeneity between Tibetan,Uyghur,Mongolian,Chinese Northern Han and Chinese Li population.The 22 loci showed high genetic polymorphism in the three ethnic groups.An exact test for the genotype distribution of the markers showed no significant deviation from HWE.These 22 STR loci could be treated as independent loci at the population level in these three ethnic groups.Relatively short genetic distances were found between the Mongolian and Han and Uygur populations.The 22 loci had no LD in the three ethnic groups and showed high heterozygosity,providing genetic information and forensic statistics for the Uyghur,Tibetan,and Inner Mongolian groups.These 22 STR loci will be useful for identification and kinship analysis in these three populations in China.展开更多
We investigated the polymorphisms of 23 Y‑short tandem repeat(STR)loci in a Han population in the Beijing region.Blood samples were collected from 255 unrelated Han males.DNA templates were amplified using the PowerPl...We investigated the polymorphisms of 23 Y‑short tandem repeat(STR)loci in a Han population in the Beijing region.Blood samples were collected from 255 unrelated Han males.DNA templates were amplified using the PowerPlex®Y23 system,and the amplification products were detected with a 3130 genetic analyzer.A total of 254 haplotypes were detected from the 255 unrelated Han males in the Beijing region.The gene diversity of these 23 Y‑STR loci was 0.3952–0.9721.The haplotype diversity was 0.99996 and discrimination capacity(DC)was more than 99.6%.The 23 Y‑STR loci used in this study are highly polymorphic in Han individuals in the Beijing region and are therefore suitable for paternal kinship identification.Studying allelic deletions such as DYS448 and DYS549 are important for examining Y‑STR polymorphisms and forensic testing.展开更多
目的探讨短串联重复序列(short tandem repeat,STR)三带型基因座同一认定似然比(likelihood ratio,LR)的不同计算策略。方法通过忽略三带型基因座、基于人群中不同类型的观测值、基于三带型基因座形成机制推导公式三个模型,对三带型基...目的探讨短串联重复序列(short tandem repeat,STR)三带型基因座同一认定似然比(likelihood ratio,LR)的不同计算策略。方法通过忽略三带型基因座、基于人群中不同类型的观测值、基于三带型基因座形成机制推导公式三个模型,对三带型基因座似然比进行计算。结果得到三个模型六种策略的LR计算方法,并分析其保守性与局限性。结论根据三体综合征发生机制推导的三带型基因座LR计算公式,可得到较为准确且可用于司法鉴定的LR值。展开更多
Background:Exploring and identifying novel alleles of noncombined DNAIndex System(CODIS)short tandem repeat(STR)loci in different ethnic groups is important for the establishment of forensic reference databases and st...Background:Exploring and identifying novel alleles of noncombined DNAIndex System(CODIS)short tandem repeat(STR)loci in different ethnic groups is important for the establishment of forensic reference databases and study of population genetics.Aim:This study is aimed to explore the genetic polymorphism of 22 non-CODIS autosomal STR loci(D6S477,D18S535,D19S253,D15S659,D11S2368,D20S470,D1S1656,D22-GATA198B05,D8S1132,D4S2366,D21S1270,D13S325,D9S925,D3S3045,D14S608,D10S1435,D12S391,D7S3048,D17S1290,D5S2500,D2S1338,and D16S539)in Sierra Leone population and analyze the population genetic relationships in comparison with otherpopulations.Materialsand ethods:The amples of a total of 495 unrelated individuals(274 females and 221 males)from Sierra Leonewere examined by the Microreader^(TM)23SPID System,and their genetic polymorphisms and associated forensic parameters were calculated.The genetic relationships between Sierra Leonepopulation and other populations were evaluated as well.Results:Atotal of 287 alleles were observed with allelic frequencies ranging from 0.001 to 0.399.The cumulative power of discrimination(CPD)of the 22 autosomal STR loci was 0.99999999999999999999999999999538.The cumulative probability of exclusion(CPE)of the 22 autosomal STR loci was 0.9999998514(CPEdous)and 0.9999999999826(CPEtrios).All of the STR loci reached the Hardy–Weinberg equilibrium after Bonferroni correction.The population genetics analysis results demonstrated that Sierra Leone population exhibited distinctive genetic characteristics compared to those of East Asian populations and it had relatively close genetic distances to the Uygur population.Conclusion:The results of this study could enrich the forensic databases with Sierra Leone population.The 22 STR loci are highly polymorphic and could be used for forensic practice and population genetics studies.展开更多
目的 建立基于常用STR分型试剂盒的肿瘤组织身源鉴定方法。方法 采用ForenSeq^(TM) DNA Signature Prep试剂盒检测55例配对肿瘤组织样本(肿瘤组织和同一个体正常组织成对)以及75例无关个体全血样本27个常染色体STR基因座的分型情况,并模...目的 建立基于常用STR分型试剂盒的肿瘤组织身源鉴定方法。方法 采用ForenSeq^(TM) DNA Signature Prep试剂盒检测55例配对肿瘤组织样本(肿瘤组织和同一个体正常组织成对)以及75例无关个体全血样本27个常染色体STR基因座的分型情况,并模拟55例肿瘤组织的全同胞、亲子对分型数据,统计成对肿瘤(paired carcinoma,PC)、肿瘤-无关个体(tumor-unrelated individual,UI)、肿瘤-全同胞(tumor-simulated full sibling,FS)与肿瘤-亲子(tumor-simulated parent-offspring,PO)的共有等位基因个数(number of total identical alleles,A_n)及状态一致性(identity by state,IBS)评分。以上述统计结果作为参照,建立8个常用STR分型试剂盒的肿瘤组织身源鉴定预测模型,并尝试构建一个专用于肿瘤组织身源鉴定的模型。使用另外23例配对肿瘤组织样本的检测结果对鉴定模型的准确性、灵敏度及特异度进行验证与评估。结果 (1)在任一试剂盒中,全不同基因座数量(A_0)在PC组与PO组之间差异无统计学意义。1个相同基因座数量(A_(1))、2个相同基因座数量(A_(2))和IBS评分在PC组与UI、FS、PO组之间差异均有统计学意义。(2)不同STR基因座的A_n与IBS评分在不同组别存在差异,其中,13个STR基因座(CSF1PO、D12S391、D19S433、D20S482、D2S1338、D3S1358、D4S2408、D7S820、D8S1179、FGA、TH01、TPOX、vWA)的A_(2)在PC组均高于其他STR基因座;2个STR基因座(D6S1043、PentaE)的A_(2)在UI组低于其他STR基因座。(3)成功构建了8个常用STR分型试剂盒的肿瘤组织身源鉴定预测模型以及15个STR基因座的肿瘤组织身源鉴定模型(15-STRs),灵敏度均达100%,特异度为97.56%~99.88%,准确度为97.59%~99.89%。其中,15-STRs模型的灵敏度为100%,特异度为99.88%,准确率为99.89%,高于常用商业化试剂盒。结论 本研究成功建立了8个常用STR分型试剂盒的肿瘤组织身源鉴定方法,拓展了肿瘤组织身源鉴定的应用范围。通过比较不同基因座在肿瘤组织身源鉴定中的差异,筛选出了15个特别适用于肿瘤组织身源鉴定的STR基因座,为未来肿瘤组织溯源的试剂盒构建提供了数据基础。展开更多
The MiSeq FGx^(TM) Forensic Genomics System types 231 genetic markers in one multiplex polymerase chain reaction (PCR) assay.The markers include core forensic short tandem repeats (STRs) as well as identity,ancestry a...The MiSeq FGx^(TM) Forensic Genomics System types 231 genetic markers in one multiplex polymerase chain reaction (PCR) assay.The markers include core forensic short tandem repeats (STRs) as well as identity,ancestry and phenotype informative short nucleotide polymorphisms (SNPs).In this work,the MiSeq FGx^(TM) Forensic Genomics System was evaluated by analysing reproducibility,sensitivity,mixture identification and forensic phenotyping capabilities of the assay.Furthermore,the genotype calling of the ForenSeq^(TM) Universal Analysis Software was verified by analysing fastq.gz files from the MiSeq FGx^(TM) platform using the softwares STRinNGS and GATK.Overall,the performance of the MiSeq FGx^(TM) Forensic Genomics System was high.However,locus and allele drop-outs were relatively frequent at six loci (two STRs and four human identification SNPs) due to low read depth or skewed heterozygote balances,and the stutter ratios were larger than those observed with conventional STR genotyping methods.The risk of locus and allele drop-outs increased dramatically when the amount of DNA in the first PCR was lower than 250 pg.Two-person 50∶1 mixtures were identified as mixtures,whereas 100∶1 and 1000∶1 mixtures were not.Y-chromosomal short tandem repeats (Y-STRs) alleles were detected in the 100∶1 and 1000∶1 female/male mixtures.The ForenSeq^(TM) Universal Analysis Software provided the data analyst with useful alerts that simplified the analysis of the large number of markers.Many of the alerts were due to user-defined,locus-specific criteria.The results shown here indicated that the default settings should be altered for some loci.Also,recommended changes to the assay and software are discussed.展开更多
The population genetic data and forensic parameters of 19 X-chromosome short tandem repeat (X-STR) loci in Chinese Uygur ethnic minority are presented. These loci were detected in a sample of 233 (94 males and 139 ...The population genetic data and forensic parameters of 19 X-chromosome short tandem repeat (X-STR) loci in Chinese Uygur ethnic minority are presented. These loci were detected in a sample of 233 (94 males and 139 females) unrelated healthy individuals. We observed 238 alleles at the 19 X-STR loci, with the corresponding gene frequencies spanning the range from 0.0021 to 0.5644. After Bonferroni correction (P〉0.0026), there were no signif- icant deviations from Hardy-Weinberg equilibrium. The cumulative power of discrimination in females and males, and the probability of exclusion of the 19 X-STR loci were 0.999 999 999 999 999 999 998 091,0.999 999 999 999 966, and 0.999 999 986 35, respectively. The cumulative mean exclusion chance was 0.999 999 992 849 in deficiency cases, 0.999 999 999 999 628 in normal trios, and 0.999 999 998 722 in duo cases. The high value of the forensic parameters mentioned above revealed that the novel panel of 19 loci had important values for forensic applications in the LJygur group.展开更多
基金supported by opening research grants from Shanghai Key Lab of Forensic Medicine,Key Lab of Forensic Science,Ministry of Justice,PR.China(Academy of Forensic Science)(No.KF202111)supported by the Fundamental Research Funds for the Central Universities.
文摘Objective:To investigate 38 Y-chromosome short tandem repeat(Y-STR)genetic polymorphisms in Beijing Han and analyze the genetic distance with neighboring or linguistically similar populations.Materials and Methods:In the study,we selected 531 unrelated male individuals of Beijing Han,and the results were statistically analyzed by testing with GSTAR™41Y reagents.Results:The allele peak heights were balanced among the Y loci,the amplified fragment ranged from 100 to 500 bps.A total of 531 haplotypes were detected in 531 samples.Eight null genotypes were observed on locus DYS448.One and three double alleles were observed on single-copy locus DYS576 and DYS19,respectively.DYS385 a/b,DYF387S1 a/b,and DYS527 a/b were more common in double copies,but 3,13,and 11 triple alleles were detected,respectively.The gene diversity values of Y-STRs except DYS391,DYS438,and DYS645 were>0.5.Twenty-seven Y-STRs of Beijing Han population were selected for genetic distance comparison with 17 populations including Changchun Han,with Rst values ranging from 0.0002 to 0.1703.Conclusion:The 38 Y-STRs in this study have strong male lineage identification ability and have great potential for individual identification,kinship identification,Y-STR database construction,and genetic relationship research.
基金Acknowledgments The current research was supported by the Na- tional Natural Science Foundation of China (81302622), the Science Technology Foundation of Lanzhou (2012-1-22), and Youth Science and Tech- nology Foundation of Gansu (1208RYYA073).
文摘The short tandem repeat (STR) markers are widely used in human identification and paternity testing in the field of forensic genetics[1].Recent researches on polymorphic STRs have led to their applications to population genetics,forensic DNA database,human individual identification,paternity testing,genetic mapping,disease linkage analysis,archaeology and potential inference of the ethnic origin of an individual[2].
文摘Objective To analyze the genetic polymorphism of 6 STR loci (D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613) on chromosome 12 in Chinese Han population. Methods EDTA-blood specimens were collected from 153 unrelated individuals of Chinese Han population in Shaanxi province. Allele and genotype frequencies for the 6 STR loci were estimated and statistical parameters of polymorphism were calculated. Results 8 alleles and 18 genotypes, 10 alleles and 17 genotypes, 9 alleles and 15 genotypes, 12alleles and 29 genotypes, 12 alleles and 31 genotypes, 8 alleles and 11 genotypes were observed at D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613, respectively. No deviations of the observed allele frequency from Hardy-weinberg equilibrium expectations were found for any of these loci. The Heterozygotes of these 6 loci were 78.89%, 66.10%, 54.95%, 79.10%, 71.98% and 59.48%, respectively. It indicated the high genetic polymorphism of the loci in Chinese Han population. Conclusion The 6 STR loci belonged to the genetic marker system of high discriminutesation and high information in Chinese Han population and can be used in the study of gene-related diseases.
基金supported by Shaanxi Science and Technology Co‑ordination and Innovation Project under Grant(number 2015KTCL03‑03)。
文摘Context:As the increasing number of pet canines,the identification of canine has attracted much attentions in the forensic field,however,the genetic diversities of pet canines still remained unknown.Aims:To explore genetic polymorphisms of 19 short tandem repeat(STR)loci and genetic relationships between the two studied canine groups and reference group.Subjects and Methods:In the present study,genetic polymorphisms of 19 STR loci and a sex-linked zinc finger locus were analyzed in a total of 594 canines in Standard Poodle and Bichon Frise groups from China.Results:A total of 166,159 alleles were observed in the Standard Poodle,Bichon Frise groups with the corresponding allelic frequencies ranging from 0.0030-0.6108 to 0.0012-0.6148,respectively.The combined discrimination power and probability of exclusion of 19 STR loci in Standard Poodle and Bichon Frise groups were 0.9999999999999497,0.999962884;and 0.99999999999999995,0.999965955,respectively.Furthermore,the genetic distances between the two canine groups and Labrador retriever group were calculated,and the results indicated that Standard Poodle and Bichon Frise groups showed a closer genetic relationship,while the two canine groups had distant genetic relationships with Labrador retriever group.The result of population genetic structure revealed that genetic component distributions in the three canine groups were different.The predicted accuracies of the constructed random forest prediction model for three validation sets(25%individuals randomly selected from three populations with 808 individuals)were higher than 0.9,especially for the individuals in validation set from the Bichon Frise group is 1.Conclusions:The 19 STR loci could be used for individual identification,canine breed identification and paternity testing in the two canine groups.
基金supported by the Fundamental Research Funds for the Central Universities.In addition,this study was also supported by opening research grants from Shanghai Key Lab of Forensic Medicine,Key Lab of Forensic Science,the Ministry of Justice,PR.China(Academy of Forensic Science)(No.KF202111).
文摘A six-color fluorescent multiplex amplification system for 31 Y-chromosomal short tandem repeats(Y-STRs)(DYS19,DYS390,DYS391,DYF399S1,DYF404S1,DYS439,DYS444,DYS449,DYS452,DYS456,DYS458,DYS460,DYS481,DYS508,DYS513,DYS516,DYS518,DYS543,DYS547,DYS549,DYS552,DYS557,DYS570,DYS576,DYS612,DYS622,DYS626,DYS627,DYS630,DYS635,and Y-GATA-A10)was developed for investigating the mutation rates of 31 highly mutated Y-STR genes in the Han population of northern China.The mutation rates of the 31 highly mutated Y-STRs were calculated using the father-son pair study method after typing 526 Northern Han father-son pairs with this system.Statistically,148 Y-STR mutations were found,with mutation rates ranging from 0(95%confidence interval[CI]0 to 9.0×10^(−3),DYS622)to 7.0×10^(−2)(95%CI 5.1×10^(−2)to 9.7×10^(−2),DYF399S1).Out of these,126 father-son pairs were successfully identified,with a distinction rate of 24.0%(95%CI 20.4%-27.9%).The ability of the 31 highly mutated Y-STRs to distinguish closely related males from the same paternal lineage in the Northern Han population is extremely valuable for criminal investigations and other purposes.
基金This project was supported by the Fundamental Research Funds for the Central Universities,China[grant number xjj2018165]and the Key Project for Science Research and Development of Shaanxi Province(2018SF-119).
文摘China is a multinational country composed of 56 ethnic groups of which the Han Chinese accounts for 91.60%.Qinghai Province is located in the northeastern part of the Qinghai-Tibet Plateau,has an area of 72.12 km2,and is the fourth largest province in China.In the present study,we investigated the genetic polymorphisms of 20 short tandem repeat (STR) loci in a Qinghai Han population,as well as its genetic relationships with other populations.A total of 273 alleles were identified in 2 000 individuals at 20 loci,and the allelic frequency ranged from 0.0002 to 0.5327.The 20 STR loci showed a relatively high polymorphic rate in the studied group.Observed and expected heterozygosities ranged 0.613 0-0.907 5 and 0.614 8-0.920 0,respectively.The combined power of discrimination,and the probability of exclusion in duo and trio cases were 0.999 999 999 999 999 999 999 999 34,0.9999960 and 0.9999999965,respectively.Analyses of interpopulation differentiation revealed that the most significant differences were found between the Qinghai Han and Malaysian,while no significant differences were found between the Qinghai Han and Han people from Shaanxi and Jiangsu.The results of principal component analysis,multidimensional scaling analysis and phylogenetic reconstructions also suggested the close relationships between the Qinghai Han and other two Han populations.The present results,therefore,indicated that these 20 STR loci could be used for paternity testing and individual identification in forensic applications,and may also provide information for the studies of genetic relationships between Qinghai Han and other groups.
基金the National Natural Science Foundation of China(No.81302615,81302621,and 81571855).
文摘Goldeneye™DNA ID 22NC Kit is a novel short tandem repeat(STR)genotyping system that investigate 20 non-CODIS loci(D4S2366,D6S477,D22GATA198B05,D15S659,D8S1132,D3S3045,D14S608,D17S1290,D3S1744,D2S441,D18S535,D13S325,D7S1517,D1OS1435,D11S236&D19S253,D1S1656,D7S3O4&D10S14&and D5S2500),a CODIS locus(D3S1358),and a sex-determining locus amelogenin in one assay.In the present study,this STR genotyping system was validated according to the guidelines of"Wlidation Guidelines for DNA Analysis Methods(2016)"updated by the Scientific Working Group on DNA Analysis Methods.A series of tests,such as polymerase chain reaction-based studies,sensitivity,inhibitors,DNA mixture,species specificity,precision and accuracy evaluation,stutter percentage,and peak height ratio,was conducted.The genetic polymorphism of 21 STR loci that included in the 22NC system was also investigated in the Chinese Hunan Han population.The validation results demonstrated that Goldeneye™DNA ID 22NC Kit is a robust and reliable identification assay as required for genotyping in kinship analysis and forensic investigation.The 21 STR loci in this kit also showed a high level of genetic polymorphism for the Hunan Han population.Therefore,it can be used for forensic applications and population studies.
基金This study was supported by the Ministry of Education,Humanities and Social Science research projects(grant number 13YJA8200031).
文摘In recent years,paternity testing in ethnic minority areas in China increases rapidly.However,the number of existing genetic markers does not meet the needs.The objective is to study the information of 22 genetic markers in Mongolian,Tibetan,and Uygur Nationality.The genetic polymorphism of 22 short tandem repeat(STR)loci(D10S1435,D11S2368,D12S391,D13S325,D14S608,D15S659,D16S539,D17S1290,D18S535,D19S253,D1S1656,D20S470,D21S1270,D22GATA198B05,D2S1338,D3S3045,D4S2366,D5S2500,D6S477,D7S3048,D8S1132,and D9S925)was estimated in 259 Uyghur,251 Tibetan,and 250 Inner Mongolian individuals from China who were all unrelated.Allele frequencies and forensic parameters were evaluated.The Hardy-Weinberg equilibrium(HWE)of each locus and the linkage disequilibrium(LD)for all pairwise STR loci were tested.Additionally,the Nei's genetic distance was used to estimate the genetic heterogeneity between Tibetan,Uyghur,Mongolian,Chinese Northern Han and Chinese Li population.The 22 loci showed high genetic polymorphism in the three ethnic groups.An exact test for the genotype distribution of the markers showed no significant deviation from HWE.These 22 STR loci could be treated as independent loci at the population level in these three ethnic groups.Relatively short genetic distances were found between the Mongolian and Han and Uygur populations.The 22 loci had no LD in the three ethnic groups and showed high heterozygosity,providing genetic information and forensic statistics for the Uyghur,Tibetan,and Inner Mongolian groups.These 22 STR loci will be useful for identification and kinship analysis in these three populations in China.
文摘We investigated the polymorphisms of 23 Y‑short tandem repeat(STR)loci in a Han population in the Beijing region.Blood samples were collected from 255 unrelated Han males.DNA templates were amplified using the PowerPlex®Y23 system,and the amplification products were detected with a 3130 genetic analyzer.A total of 254 haplotypes were detected from the 255 unrelated Han males in the Beijing region.The gene diversity of these 23 Y‑STR loci was 0.3952–0.9721.The haplotype diversity was 0.99996 and discrimination capacity(DC)was more than 99.6%.The 23 Y‑STR loci used in this study are highly polymorphic in Han individuals in the Beijing region and are therefore suitable for paternal kinship identification.Studying allelic deletions such as DYS448 and DYS549 are important for examining Y‑STR polymorphisms and forensic testing.
文摘目的探讨短串联重复序列(short tandem repeat,STR)三带型基因座同一认定似然比(likelihood ratio,LR)的不同计算策略。方法通过忽略三带型基因座、基于人群中不同类型的观测值、基于三带型基因座形成机制推导公式三个模型,对三带型基因座似然比进行计算。结果得到三个模型六种策略的LR计算方法,并分析其保守性与局限性。结论根据三体综合征发生机制推导的三带型基因座LR计算公式,可得到较为准确且可用于司法鉴定的LR值。
基金This work was supported by the Key Program of National Natural Science Foundation of China(NSFC)(grant number 82230064)the General Program of National Natural Science Foundation of China(NSFC)(grant number 82271928).
文摘Background:Exploring and identifying novel alleles of noncombined DNAIndex System(CODIS)short tandem repeat(STR)loci in different ethnic groups is important for the establishment of forensic reference databases and study of population genetics.Aim:This study is aimed to explore the genetic polymorphism of 22 non-CODIS autosomal STR loci(D6S477,D18S535,D19S253,D15S659,D11S2368,D20S470,D1S1656,D22-GATA198B05,D8S1132,D4S2366,D21S1270,D13S325,D9S925,D3S3045,D14S608,D10S1435,D12S391,D7S3048,D17S1290,D5S2500,D2S1338,and D16S539)in Sierra Leone population and analyze the population genetic relationships in comparison with otherpopulations.Materialsand ethods:The amples of a total of 495 unrelated individuals(274 females and 221 males)from Sierra Leonewere examined by the Microreader^(TM)23SPID System,and their genetic polymorphisms and associated forensic parameters were calculated.The genetic relationships between Sierra Leonepopulation and other populations were evaluated as well.Results:Atotal of 287 alleles were observed with allelic frequencies ranging from 0.001 to 0.399.The cumulative power of discrimination(CPD)of the 22 autosomal STR loci was 0.99999999999999999999999999999538.The cumulative probability of exclusion(CPE)of the 22 autosomal STR loci was 0.9999998514(CPEdous)and 0.9999999999826(CPEtrios).All of the STR loci reached the Hardy–Weinberg equilibrium after Bonferroni correction.The population genetics analysis results demonstrated that Sierra Leone population exhibited distinctive genetic characteristics compared to those of East Asian populations and it had relatively close genetic distances to the Uygur population.Conclusion:The results of this study could enrich the forensic databases with Sierra Leone population.The 22 STR loci are highly polymorphic and could be used for forensic practice and population genetics studies.
文摘目的 建立基于常用STR分型试剂盒的肿瘤组织身源鉴定方法。方法 采用ForenSeq^(TM) DNA Signature Prep试剂盒检测55例配对肿瘤组织样本(肿瘤组织和同一个体正常组织成对)以及75例无关个体全血样本27个常染色体STR基因座的分型情况,并模拟55例肿瘤组织的全同胞、亲子对分型数据,统计成对肿瘤(paired carcinoma,PC)、肿瘤-无关个体(tumor-unrelated individual,UI)、肿瘤-全同胞(tumor-simulated full sibling,FS)与肿瘤-亲子(tumor-simulated parent-offspring,PO)的共有等位基因个数(number of total identical alleles,A_n)及状态一致性(identity by state,IBS)评分。以上述统计结果作为参照,建立8个常用STR分型试剂盒的肿瘤组织身源鉴定预测模型,并尝试构建一个专用于肿瘤组织身源鉴定的模型。使用另外23例配对肿瘤组织样本的检测结果对鉴定模型的准确性、灵敏度及特异度进行验证与评估。结果 (1)在任一试剂盒中,全不同基因座数量(A_0)在PC组与PO组之间差异无统计学意义。1个相同基因座数量(A_(1))、2个相同基因座数量(A_(2))和IBS评分在PC组与UI、FS、PO组之间差异均有统计学意义。(2)不同STR基因座的A_n与IBS评分在不同组别存在差异,其中,13个STR基因座(CSF1PO、D12S391、D19S433、D20S482、D2S1338、D3S1358、D4S2408、D7S820、D8S1179、FGA、TH01、TPOX、vWA)的A_(2)在PC组均高于其他STR基因座;2个STR基因座(D6S1043、PentaE)的A_(2)在UI组低于其他STR基因座。(3)成功构建了8个常用STR分型试剂盒的肿瘤组织身源鉴定预测模型以及15个STR基因座的肿瘤组织身源鉴定模型(15-STRs),灵敏度均达100%,特异度为97.56%~99.88%,准确度为97.59%~99.89%。其中,15-STRs模型的灵敏度为100%,特异度为99.88%,准确率为99.89%,高于常用商业化试剂盒。结论 本研究成功建立了8个常用STR分型试剂盒的肿瘤组织身源鉴定方法,拓展了肿瘤组织身源鉴定的应用范围。通过比较不同基因座在肿瘤组织身源鉴定中的差异,筛选出了15个特别适用于肿瘤组织身源鉴定的STR基因座,为未来肿瘤组织溯源的试剂盒构建提供了数据基础。
基金All procedures performed in studies involving human participants were in accordance with the ethical stand-ards of the Danish Ethical Committee(H-3-2012-023)and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.Samples were taken from the biobank of the Department of Forensic Medicine,University of Copenhagen(RIBVFapproved by the Danish Data Protection Agency,j.no.2002-54-1080).The Danish ethical committee waived the requirement for informed consent(H-3-2012-023).
文摘The MiSeq FGx^(TM) Forensic Genomics System types 231 genetic markers in one multiplex polymerase chain reaction (PCR) assay.The markers include core forensic short tandem repeats (STRs) as well as identity,ancestry and phenotype informative short nucleotide polymorphisms (SNPs).In this work,the MiSeq FGx^(TM) Forensic Genomics System was evaluated by analysing reproducibility,sensitivity,mixture identification and forensic phenotyping capabilities of the assay.Furthermore,the genotype calling of the ForenSeq^(TM) Universal Analysis Software was verified by analysing fastq.gz files from the MiSeq FGx^(TM) platform using the softwares STRinNGS and GATK.Overall,the performance of the MiSeq FGx^(TM) Forensic Genomics System was high.However,locus and allele drop-outs were relatively frequent at six loci (two STRs and four human identification SNPs) due to low read depth or skewed heterozygote balances,and the stutter ratios were larger than those observed with conventional STR genotyping methods.The risk of locus and allele drop-outs increased dramatically when the amount of DNA in the first PCR was lower than 250 pg.Two-person 50∶1 mixtures were identified as mixtures,whereas 100∶1 and 1000∶1 mixtures were not.Y-chromosomal short tandem repeats (Y-STRs) alleles were detected in the 100∶1 and 1000∶1 female/male mixtures.The ForenSeq^(TM) Universal Analysis Software provided the data analyst with useful alerts that simplified the analysis of the large number of markers.Many of the alerts were due to user-defined,locus-specific criteria.The results shown here indicated that the default settings should be altered for some loci.Also,recommended changes to the assay and software are discussed.
基金Project supported by the Scientific Research Program of the Higher Education Institution of the Xinjiang Uygur Autonomous Region(No.XJEDU2011i33),Chinathe National Natural Science Foundation of China(No.81373248)the National Science Foundation for Distinguished Young Scholars of China(No.81525015)
文摘The population genetic data and forensic parameters of 19 X-chromosome short tandem repeat (X-STR) loci in Chinese Uygur ethnic minority are presented. These loci were detected in a sample of 233 (94 males and 139 females) unrelated healthy individuals. We observed 238 alleles at the 19 X-STR loci, with the corresponding gene frequencies spanning the range from 0.0021 to 0.5644. After Bonferroni correction (P〉0.0026), there were no signif- icant deviations from Hardy-Weinberg equilibrium. The cumulative power of discrimination in females and males, and the probability of exclusion of the 19 X-STR loci were 0.999 999 999 999 999 999 998 091,0.999 999 999 999 966, and 0.999 999 986 35, respectively. The cumulative mean exclusion chance was 0.999 999 992 849 in deficiency cases, 0.999 999 999 999 628 in normal trios, and 0.999 999 998 722 in duo cases. The high value of the forensic parameters mentioned above revealed that the novel panel of 19 loci had important values for forensic applications in the LJygur group.