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
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
We investigated the forensic efficacy of the 30 insertion/deletion(Indel)markers included in the Qiagen Investigator■DIPplex kit in 529 Pakistani individuals from five major subpopulations in Pakistan(Punjabi,Pashtun...We investigated the forensic efficacy of the 30 insertion/deletion(Indel)markers included in the Qiagen Investigator■DIPplex kit in 529 Pakistani individuals from five major subpopulations in Pakistan(Punjabi,Pashtun,Sindhi,Saraiki,and Baloch).In the Sindhi population,the distribution of HLD81 and HLD97 alleles deviated from Hardy-Weinberg equilibrium after Bonferroni correction.The combined match probability ranged from 2.0E-12(Pashtun and Baloch)to 1.0E-12(Sindhi),and the mean paternity exclusion power varied from 0.995(Punjabi,Sindhi,and Saraiki)to 0.996(Pashtun and Baloch).The high combined power of discrimination(0.99999999999997)and low combined match probability(1.7E-12)for all subpopulations studied support the utility of the 30 Indel markers for forensic identification in the studied subpopulations.The allele frequencies of the Indel markers in the Pakistani subpopulations were compared with those from 18 other populations.The results show that the populations clustered according to geography.The subpopulations investigated in this work showed a close genetic relationship with others from Pakistan,as well as with South Central Asian and Middle Eastern populations.The results suggest that the Investigator■DIPplex kit can be useful as a supplementary tool for human identification in the five Pakistani subpopulations investigated in this study.展开更多
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.
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The study was supported by an overseas research grant to Muhammad Adnan Shan from the University of the Punjab,Pakistan[grant number D-1829-Est-I/2017].
文摘We investigated the forensic efficacy of the 30 insertion/deletion(Indel)markers included in the Qiagen Investigator■DIPplex kit in 529 Pakistani individuals from five major subpopulations in Pakistan(Punjabi,Pashtun,Sindhi,Saraiki,and Baloch).In the Sindhi population,the distribution of HLD81 and HLD97 alleles deviated from Hardy-Weinberg equilibrium after Bonferroni correction.The combined match probability ranged from 2.0E-12(Pashtun and Baloch)to 1.0E-12(Sindhi),and the mean paternity exclusion power varied from 0.995(Punjabi,Sindhi,and Saraiki)to 0.996(Pashtun and Baloch).The high combined power of discrimination(0.99999999999997)and low combined match probability(1.7E-12)for all subpopulations studied support the utility of the 30 Indel markers for forensic identification in the studied subpopulations.The allele frequencies of the Indel markers in the Pakistani subpopulations were compared with those from 18 other populations.The results show that the populations clustered according to geography.The subpopulations investigated in this work showed a close genetic relationship with others from Pakistan,as well as with South Central Asian and Middle Eastern populations.The results suggest that the Investigator■DIPplex kit can be useful as a supplementary tool for human identification in the five Pakistani subpopulations investigated in this study.
