Objective Population genetic analysis based on genetic markers harbors valuable forensic applications.In this regard,it is informative and imperative to explore Han groups as they are the largest population of China.I...Objective Population genetic analysis based on genetic markers harbors valuable forensic applications.In this regard,it is informative and imperative to explore Han groups as they are the largest population of China.In particular,there is a largely underrepresented amount of information from recent decades regarding the southeast costal Han Chinese.Therefore,the aim of this study is to investigate the available genetic characteristics of the Han population living in the Jinjiang,Fujian Province,Southeastern China.Methods We sampled 858 saliva samples and used the commercially available Microreader^(TM) Y Prime Plus ID System to identify population data of Y-short tandem repeat(STR)loci of this region.Results A total of 822 different haplotypes were observed.The overall haplotype diversity,discriminatory power and haplotype match probability were 0.9999,0.9999 and 0.0012,respectively.Conclusion Our results showed that the Jinjiang Han population was closely genetically related to Han groups of China.Overall,we identified a set of 37 Y-STRs that are highly polymorphic,and that can provide meaningful information in forensic practice and human genetic research.展开更多
目的比较DNATyperTM15和IdentifilerTM试剂盒的遗传学调查应用结果,以评价DNATyperTM15试剂盒的指标和性能。方法用DNATyperTM15和IdentifilerTM试剂盒同时对290份北方汉族群体的血样本进行扩增检测,比较遗传学统计数据。结果DNATyperT...目的比较DNATyperTM15和IdentifilerTM试剂盒的遗传学调查应用结果,以评价DNATyperTM15试剂盒的指标和性能。方法用DNATyperTM15和IdentifilerTM试剂盒同时对290份北方汉族群体的血样本进行扩增检测,比较遗传学统计数据。结果DNATyperTM15和IdentifilerTM荧光检测试剂盒中各基因座在汉族群体中的基因型分布均符合Hardy-W e inberg平衡,累积个人识别率和累计非父排除率:DNATyperTM15试剂盒分别为2.66×10-18和0.9999997;IdentifilerTM试剂盒分别为1.28×10-17和0.9999984。且两个试剂盒对相同基因座的频率调查数据一致。结论DNATyperTM15具有较高的个体识别和亲权鉴定能力,对法医学检案和DNA数据库建设具有应用价值。展开更多
目的应用HID Ion GeneStudio^(TM) S5测序系统对毛干样本线粒体全基因组分型结果的异质性进行探讨。方法采集8名无关个体的口腔拭子、血液及同一个体不同部位毛干样本,使用Precision ID mtDNA Whole Genome Panel对线粒体全基因组进行扩...目的应用HID Ion GeneStudio^(TM) S5测序系统对毛干样本线粒体全基因组分型结果的异质性进行探讨。方法采集8名无关个体的口腔拭子、血液及同一个体不同部位毛干样本,使用Precision ID mtDNA Whole Genome Panel对线粒体全基因组进行扩增,应用HID Ion GeneStudio^(TM) S5测序系统对线粒体全基因组进行分析检测。结果2名个体的颞部毛干样本线粒体DNA出现异质性,其余6名无关个体的口腔拭子、血液及不同部位毛干样本的线粒体全基因组分型结果均一致。8名无关个体共观察到119个碱基变异,个体的变异位点数目分别为29、40、38、35、13、36、40和35。结论应用HID Ion GeneStudio^(TM) S5测序系统可全面了解序列多态性。展开更多
Massively parallel sequencing(MPS)offers a useful alternative to capillary electrophoresis(CE)based analysis of human identification markers in forensic genetics.By sequencing short tandem repeats(STRs)instead of dete...Massively parallel sequencing(MPS)offers a useful alternative to capillary electrophoresis(CE)based analysis of human identification markers in forensic genetics.By sequencing short tandem repeats(STRs)instead of determining the fragment lengths by CE,the sequence variation within the repeat region and the flanking regions may be identified.In this study,we typed 264 Uyghur individuals using the MiSeq FGx^(^(TM)) Forensic Genomics System and Primer Mix A of the ForenSeq^(^(TM)) DNA Signature Prep Kit that amplifies 27 autosomal STRs,25 Y-STRs,seven X-STRs,and 94 HID-SNPs.STRinNGS v.1.0 and GATK 3.6 were used to analyse the STR regions and HID-SNPs,respectively.Increased allelic diversity was observed for 33 STRs with the PCR-MPS assay.The largest increases were found in DYS389II and D12S391,where the numbers of sequenced alleles were 3–4 times larger than those of alleles determined by repeat length alone.A relatively large number of flanking region variants(28 SNPs and three InDels)were observed in the Uyghur population.Seventeen of the flanking region SNPs were rare,and 12 of these SNPs had no accession number in dbSNP.The combined mean match probability and typical paternity index based on 26 sequenced autosomal STRs were 3.85E36 and 1.49Eþ16,respectively.This was 10000 times lower and 1000 times higher,respectively,than the same parameters calculated from STR repeat lengths.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
基金This study was supported by the Shaanxi Basic Research Program of Natural Science(No.2021JQ-392).
文摘Objective Population genetic analysis based on genetic markers harbors valuable forensic applications.In this regard,it is informative and imperative to explore Han groups as they are the largest population of China.In particular,there is a largely underrepresented amount of information from recent decades regarding the southeast costal Han Chinese.Therefore,the aim of this study is to investigate the available genetic characteristics of the Han population living in the Jinjiang,Fujian Province,Southeastern China.Methods We sampled 858 saliva samples and used the commercially available Microreader^(TM) Y Prime Plus ID System to identify population data of Y-short tandem repeat(STR)loci of this region.Results A total of 822 different haplotypes were observed.The overall haplotype diversity,discriminatory power and haplotype match probability were 0.9999,0.9999 and 0.0012,respectively.Conclusion Our results showed that the Jinjiang Han population was closely genetically related to Han groups of China.Overall,we identified a set of 37 Y-STRs that are highly polymorphic,and that can provide meaningful information in forensic practice and human genetic research.
文摘目的比较DNATyperTM15和IdentifilerTM试剂盒的遗传学调查应用结果,以评价DNATyperTM15试剂盒的指标和性能。方法用DNATyperTM15和IdentifilerTM试剂盒同时对290份北方汉族群体的血样本进行扩增检测,比较遗传学统计数据。结果DNATyperTM15和IdentifilerTM荧光检测试剂盒中各基因座在汉族群体中的基因型分布均符合Hardy-W e inberg平衡,累积个人识别率和累计非父排除率:DNATyperTM15试剂盒分别为2.66×10-18和0.9999997;IdentifilerTM试剂盒分别为1.28×10-17和0.9999984。且两个试剂盒对相同基因座的频率调查数据一致。结论DNATyperTM15具有较高的个体识别和亲权鉴定能力,对法医学检案和DNA数据库建设具有应用价值。
文摘目的应用HID Ion GeneStudio^(TM) S5测序系统对毛干样本线粒体全基因组分型结果的异质性进行探讨。方法采集8名无关个体的口腔拭子、血液及同一个体不同部位毛干样本,使用Precision ID mtDNA Whole Genome Panel对线粒体全基因组进行扩增,应用HID Ion GeneStudio^(TM) S5测序系统对线粒体全基因组进行分析检测。结果2名个体的颞部毛干样本线粒体DNA出现异质性,其余6名无关个体的口腔拭子、血液及不同部位毛干样本的线粒体全基因组分型结果均一致。8名无关个体共观察到119个碱基变异,个体的变异位点数目分别为29、40、38、35、13、36、40和35。结论应用HID Ion GeneStudio^(TM) S5测序系统可全面了解序列多态性。
文摘Massively parallel sequencing(MPS)offers a useful alternative to capillary electrophoresis(CE)based analysis of human identification markers in forensic genetics.By sequencing short tandem repeats(STRs)instead of determining the fragment lengths by CE,the sequence variation within the repeat region and the flanking regions may be identified.In this study,we typed 264 Uyghur individuals using the MiSeq FGx^(^(TM)) Forensic Genomics System and Primer Mix A of the ForenSeq^(^(TM)) DNA Signature Prep Kit that amplifies 27 autosomal STRs,25 Y-STRs,seven X-STRs,and 94 HID-SNPs.STRinNGS v.1.0 and GATK 3.6 were used to analyse the STR regions and HID-SNPs,respectively.Increased allelic diversity was observed for 33 STRs with the PCR-MPS assay.The largest increases were found in DYS389II and D12S391,where the numbers of sequenced alleles were 3–4 times larger than those of alleles determined by repeat length alone.A relatively large number of flanking region variants(28 SNPs and three InDels)were observed in the Uyghur population.Seventeen of the flanking region SNPs were rare,and 12 of these SNPs had no accession number in dbSNP.The combined mean match probability and typical paternity index based on 26 sequenced autosomal STRs were 3.85E36 and 1.49Eþ16,respectively.This was 10000 times lower and 1000 times higher,respectively,than the same parameters calculated from STR repeat lengths.
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.