Objective To establish the northwest database of short tandem repeat(STR) loci in forensic medicine. Methods Bloodstains or whole blood samples were collected from the unrelated prisoners in Xi'an city. Genetic ...Objective To establish the northwest database of short tandem repeat(STR) loci in forensic medicine. Methods Bloodstains or whole blood samples were collected from the unrelated prisoners in Xi'an city. Genetic distribution for 13 STR loci and amelogenin locus were determined in prisons based on GeneScan. One primer for each locus was labeled with the fluorescent by 5 FAM, JOE, or NED. The forensic database were generated by using multiple amplification, GeneScan, genotype, and genetic distribution analysis. Results 113 alleles and 302 genotypes were observed, with the corresponding frequency between 0.0050-0.5250 and 0.0100-0.4100. The mean H was 0.7667. The accumulative DP was 0.9999999,. The accumulative EPP was 0.9999999. The scope of PIC was 0.6036- 0.8562 . PM was less than 10 -11 . The observed and expected genotype frequencies were evaluated using χ 2 test and all were in accordance with Hardy Weinberg equilibrium ( P > 0.05 ). Conclusion STR loci is an ideal genetic marker with powerful polymorphism and stable heredity. It can be used for individual identification and paternity in forensic medicine. The forensic DNA database model can be established successfully.展开更多
The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature （IUCN）（2017）. Short tandem repeats （STRs） refer to r...The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature （IUCN）（2017）. Short tandem repeats （STRs） refer to repetitive elements of genome sequence that range in length from 1-6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples. A total of 1 077 790 perfect STRs were mined from our assembly, with an N50 of 4 966 bp. Mono-nucleotide repeats were the most abundant, followed by tetra- and di-nucleotide repeats. Analysis of GC content and repeats showed consistent results with other macaques. Furthermore, using STR analysis software （IobSTR）, we found that the proportion of base pair deletions in the STRs was greater than that of insertions in the five Tibetan macaque individuals （P〈0.05, t-test）. We also found a greater number of homozygous STRs than heterozygous STRs （P〈0.05, t-test）, with the Emei and Jianyang Tibetan macaques showing more heterozygous loci than Huangshan Tibetan macaques. The proportion of insertions and mean variation of alleles in the Emei and Jianyang individuals were slightly higher than those in the Huangshan individuals, thus revealing differences in STR allele size between the two populations The polymorphic STR loci identified based on the reference genome showed good amplification efficiency and could be used to study population genetics in Tibetan macaques. The neighbor-joining tree classified the five macaques into two different branches according to their geographical origin, indicating high genetic differentiation between the Huangshan and Sichuan populations. We elucidated the distribution characteristics of STRs in the Tibetan macaque genome and provided an effective method for screening polymorphic STRs. Our results also lay a foundation for future genetic variation studies of macaques.展开更多
Summary: Wilson disease (WD) is an autosomal recessive disorder of copper metabolism. To establish an efficient, accurate and fast diagnostic method for carrier detection and presymptomatic identification of WD in Chi...Summary: Wilson disease (WD) is an autosomal recessive disorder of copper metabolism. To establish an efficient, accurate and fast diagnostic method for carrier detection and presymptomatic identification of WD in Chinese population, we studied haplotypes of short tandem repeat (STR) polymorphisms flanking the WD gene in 40 Chinese WD families. The results suggested that this genetic diagnosis system based on the four STR polymorphisms is of high value for the detection of potential carriers and WD homozygotes in families with at least one previously affected child. It is an efficient, accurate and fast diagnostic method that can be well suited for routine use in clinical laboratories.展开更多
Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study...Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.Results:We identified 5203 and 5868 significantly expression STRs(eSTRs,FDR<1%)in the F6 and F7 populations,respectively,most of which could be reciprocally validated(π1=0.92).The eSTRs explained 27.5%of the cisheritability of gene expression traits on average.We further identified 235 and 298 fine-mapped STRs through the Bayesian fine-mapping approach in the F6 and F7 pigs,respectively,which were significantly enriched in intron,ATAC peak,compartment A and H3K4me3 regions.We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs,which colocalized with epigenetic markers such as H3K27ac and ATAC peaks.These included eSTR of the CLPB,PGLS,PSMD6 and DHDH genes,which are linked with genome-wide association study(GWAS)SNPs for blood-related traits,leg conformation,growth-related traits,and meat quality traits,respectively.Conclusions:This study provides insights into the effects of STRs on gene expression traits.The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.展开更多
Interest in DNA analysis using short tandem repeats (STR) as finger printing tools in forensic medicine has gained tremendous application, as expression of these nuclear factors have enhanced forensic examination. Her...Interest in DNA analysis using short tandem repeats (STR) as finger printing tools in forensic medicine has gained tremendous application, as expression of these nuclear factors have enhanced forensic examination. Here we used this Biochemical characterization after conventional extraction process, polymerase chain reaction (PCR), gel electrophoresiss and a sequencer to distinguish and resolve parental dispute. The differential migration of labeled DNA fragments which attains excitation energy with a laser elicits fluorescent light of different wavelength depending on the dye used. A data collection software (Genemapper) collects raw data (spectrograph) and converts it to an electropherogram that is interpreted. By comparing the DNA profiles, inclusion and exclusion criteria were elucidated to resolve disputes. The inherent discriminating power of STRs used in analysis enhances resolution of cell mixtures, genetic aberration, substantiation of tissue origin and provides genetic distinction which is a robust and reliable approach in resolving parental disputes.展开更多
Objective : To find a simple and rapid way far the prenatal diagnosis of phenyUce-tonuria (PKU) during the first trimester in order to prevent inborn PKU patients as early as possible. Methods :DNA was extracted respe...Objective : To find a simple and rapid way far the prenatal diagnosis of phenyUce-tonuria (PKU) during the first trimester in order to prevent inborn PKU patients as early as possible. Methods :DNA was extracted respectively from the Mood sampleps of 9 families' members and chori-onic tissues of 9 embryoes by cliorionic vittus sampling (CVS). The independent short tandem repeat (STR) alleles of members in 9 families with classic form of PKU were analyzed and prenatal diagnosis were conducted using polymerase chain reaction (PCR) together with denaturing gradient gel elec-trophoresis(DGGE)and silver dyeing. Results-.We identified 1 embryo with PKU, 2 normal individuals and 5 carriers among 9 subjects. Conclusion: Prenatal diagnosis for PKU by STR is available in the first trimester. This procedure was promising and would be widely used in Chinese population.展开更多
Objective To study the allele genetic polymorphism of five short tandem repeat(STR) loci on X-chromosome in Ewenke population of north China and to provide basic data for forensic identification. Methods Genomic DNA w...Objective To study the allele genetic polymorphism of five short tandem repeat(STR) loci on X-chromosome in Ewenke population of north China and to provide basic data for forensic identification. Methods Genomic DNA was extracted from EDTA-whole blood of Ewenke population by Chelex-100. The DNA samples were amplified by PCR and were analyzed by polyacrylamide gel electrophoresis and silver staining. The sequence length variations of DXS6799,DXS8378,DXS101,HPRTB,and DXS6789 loci on X-chromosome in 98 unrelated Ewenke individuals were investigated. Results All five loci analyzed showed high polymorphism and genetic stability. The data of the five X-chromosome STR loci in Ewenke ethnic group of China was in accordance with Hardy-Weinberg equilibrium by Chi-square test. Conclusion Allele polymorphism of five X-chromosome STR loci can be used as a genetic marker for forensic identification and population genetic research.展开更多
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
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
基金ThisworkwassupportedbytheScientificResearchItemofXi’ancity (No .2 0 0 2 3 9)
文摘Objective To establish the northwest database of short tandem repeat(STR) loci in forensic medicine. Methods Bloodstains or whole blood samples were collected from the unrelated prisoners in Xi'an city. Genetic distribution for 13 STR loci and amelogenin locus were determined in prisons based on GeneScan. One primer for each locus was labeled with the fluorescent by 5 FAM, JOE, or NED. The forensic database were generated by using multiple amplification, GeneScan, genotype, and genetic distribution analysis. Results 113 alleles and 302 genotypes were observed, with the corresponding frequency between 0.0050-0.5250 and 0.0100-0.4100. The mean H was 0.7667. The accumulative DP was 0.9999999,. The accumulative EPP was 0.9999999. The scope of PIC was 0.6036- 0.8562 . PM was less than 10 -11 . The observed and expected genotype frequencies were evaluated using χ 2 test and all were in accordance with Hardy Weinberg equilibrium ( P > 0.05 ). Conclusion STR loci is an ideal genetic marker with powerful polymorphism and stable heredity. It can be used for individual identification and paternity in forensic medicine. The forensic DNA database model can be established successfully.
基金supported by the State Key Program of National Natural Science Foundation of China(31530068)National Natural Science Foundation of China(31770415)Sichuan Application Foundation Project(2015JY0268)
文摘The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature （IUCN）（2017）. Short tandem repeats （STRs） refer to repetitive elements of genome sequence that range in length from 1-6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples. A total of 1 077 790 perfect STRs were mined from our assembly, with an N50 of 4 966 bp. Mono-nucleotide repeats were the most abundant, followed by tetra- and di-nucleotide repeats. Analysis of GC content and repeats showed consistent results with other macaques. Furthermore, using STR analysis software （IobSTR）, we found that the proportion of base pair deletions in the STRs was greater than that of insertions in the five Tibetan macaque individuals （P〈0.05, t-test）. We also found a greater number of homozygous STRs than heterozygous STRs （P〈0.05, t-test）, with the Emei and Jianyang Tibetan macaques showing more heterozygous loci than Huangshan Tibetan macaques. The proportion of insertions and mean variation of alleles in the Emei and Jianyang individuals were slightly higher than those in the Huangshan individuals, thus revealing differences in STR allele size between the two populations The polymorphic STR loci identified based on the reference genome showed good amplification efficiency and could be used to study population genetics in Tibetan macaques. The neighbor-joining tree classified the five macaques into two different branches according to their geographical origin, indicating high genetic differentiation between the Huangshan and Sichuan populations. We elucidated the distribution characteristics of STRs in the Tibetan macaque genome and provided an effective method for screening polymorphic STRs. Our results also lay a foundation for future genetic variation studies of macaques.
文摘Summary: Wilson disease (WD) is an autosomal recessive disorder of copper metabolism. To establish an efficient, accurate and fast diagnostic method for carrier detection and presymptomatic identification of WD in Chinese population, we studied haplotypes of short tandem repeat (STR) polymorphisms flanking the WD gene in 40 Chinese WD families. The results suggested that this genetic diagnosis system based on the four STR polymorphisms is of high value for the detection of potential carriers and WD homozygotes in families with at least one previously affected child. It is an efficient, accurate and fast diagnostic method that can be well suited for routine use in clinical laboratories.
基金supported by National Natural Science Foundation of China(31790413)supported by National Natural Science Foundation of China(31760657)。
文摘Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.Results:We identified 5203 and 5868 significantly expression STRs(eSTRs,FDR<1%)in the F6 and F7 populations,respectively,most of which could be reciprocally validated(π1=0.92).The eSTRs explained 27.5%of the cisheritability of gene expression traits on average.We further identified 235 and 298 fine-mapped STRs through the Bayesian fine-mapping approach in the F6 and F7 pigs,respectively,which were significantly enriched in intron,ATAC peak,compartment A and H3K4me3 regions.We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs,which colocalized with epigenetic markers such as H3K27ac and ATAC peaks.These included eSTR of the CLPB,PGLS,PSMD6 and DHDH genes,which are linked with genome-wide association study(GWAS)SNPs for blood-related traits,leg conformation,growth-related traits,and meat quality traits,respectively.Conclusions:This study provides insights into the effects of STRs on gene expression traits.The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.
文摘Interest in DNA analysis using short tandem repeats (STR) as finger printing tools in forensic medicine has gained tremendous application, as expression of these nuclear factors have enhanced forensic examination. Here we used this Biochemical characterization after conventional extraction process, polymerase chain reaction (PCR), gel electrophoresiss and a sequencer to distinguish and resolve parental dispute. The differential migration of labeled DNA fragments which attains excitation energy with a laser elicits fluorescent light of different wavelength depending on the dye used. A data collection software (Genemapper) collects raw data (spectrograph) and converts it to an electropherogram that is interpreted. By comparing the DNA profiles, inclusion and exclusion criteria were elucidated to resolve disputes. The inherent discriminating power of STRs used in analysis enhances resolution of cell mixtures, genetic aberration, substantiation of tissue origin and provides genetic distinction which is a robust and reliable approach in resolving parental disputes.
文摘Objective : To find a simple and rapid way far the prenatal diagnosis of phenyUce-tonuria (PKU) during the first trimester in order to prevent inborn PKU patients as early as possible. Methods :DNA was extracted respectively from the Mood sampleps of 9 families' members and chori-onic tissues of 9 embryoes by cliorionic vittus sampling (CVS). The independent short tandem repeat (STR) alleles of members in 9 families with classic form of PKU were analyzed and prenatal diagnosis were conducted using polymerase chain reaction (PCR) together with denaturing gradient gel elec-trophoresis(DGGE)and silver dyeing. Results-.We identified 1 embryo with PKU, 2 normal individuals and 5 carriers among 9 subjects. Conclusion: Prenatal diagnosis for PKU by STR is available in the first trimester. This procedure was promising and would be widely used in Chinese population.
基金Supported by the National Natural Science Foundation of China(39970401).
文摘Objective To study the allele genetic polymorphism of five short tandem repeat(STR) loci on X-chromosome in Ewenke population of north China and to provide basic data for forensic identification. Methods Genomic DNA was extracted from EDTA-whole blood of Ewenke population by Chelex-100. The DNA samples were amplified by PCR and were analyzed by polyacrylamide gel electrophoresis and silver staining. The sequence length variations of DXS6799,DXS8378,DXS101,HPRTB,and DXS6789 loci on X-chromosome in 98 unrelated Ewenke individuals were investigated. Results All five loci analyzed showed high polymorphism and genetic stability. The data of the five X-chromosome STR loci in Ewenke ethnic group of China was in accordance with Hardy-Weinberg equilibrium by Chi-square test. Conclusion Allele polymorphism of five X-chromosome STR loci can be used as a genetic marker for forensic identification and population genetic research.
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.
