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At least 73 records · Page 4Linked to original sources
PubMed2001

Examination of Y-STR mutations in sex chromosomal abnormality in forensic cases.

The Y-STR typing was carried out on eight DNA samples (three from criminal cases) demonstrating Klinefelter's syndrome. STR types in the X chromosome were randomly distributed. However, some Y-STR markers were distributed within the normal range but restricted to only one or two specific alleles, that is, some specific haplotypes were found in Klinefelter's syndrome. In addition, a single nucleotide polymorphism in DYS390 (transversion of G to A at the 28th position downstream of tandem repeats) was detected in Klinefelter samples. This Y-STR polymorphism and restricted Y-STR alleles in Klinefelter's syndrome is not known, but it might be related to the genesis of Klinefelter's syndrome. We also found that extended standard haplotypes of these samples are extremely rare in the normal population, according to the Y-STR haplotype reference database (YHRD). The extended standard haplotype database in a Japanese population is also reported. In 100 unrelated Japanese, 89 haplotypes were observed, and the haplotype diversity was calculated to be 0.9866.

Crime↗
PubMed2001

Allele sequences of six new Y-STR loci and haplotypes in the Chinese Han population.

Human chromosome Y-specific short tandem repeat (Y-specific STR) markers have useful properties for forensic applications. However, there is a need to develop more Y-specific STR markers, because the discriminating power of each STR locus is limited. In the present study, we describe our results on six new Y-specific STR markers that were initially located using sequence database information by Ayub et al. and were named DYS434, DYS435, DYS436, DYS437, DYS438 and DYS439. Our studies focused on the analysis of the DNA sequence for each allele at all six Y-specific STR loci in order to understand their structures in the human genome and to construct human allelic ladders, which are necessary for forensic DNA typing. In addition, the haplotype distribution for all six analyzed loci was studied in a Chinese Han population sample. The results indicate that DYS434, DYS435, DYS436, DYS437, DYS438 and DYS439 are useful Y-specific STR markers for forensic sciences.

Alleles↗
PubMed2002

Utility of Y-STR haplotype and mtDNA sequence in personal identification of human remains.

The utility of Y-STR haplotype and mtDNA sequence in personal identification from human remains is demonstrated. In five cases, severely damaged human remains were identified by Y-chromosomal short tandem repeat (STR) (Y-STR) haplotyping and mitochondrial DNA (mtDNA) sequencing. DNA was extracted from highly adipoceratous tissues using the phenol-chloroform method and polymerase chain reaction amplified for Y-STR haplotyping and sequencing of two hypervariable regions, HV1 and HV2, of the mtDNA. The authors also profiled the Y-STR haplotype and mtDNA sequence of a blood sample that was obtained from the presumptive brother of the decedent. Y-STR haplotyping and mtDNA sequencing results were compared with one another and with the Anderson sequence. It was concluded from these data that the lower part of the body (Case 1), the human head (Case 2), the upper part of the body (Case 3), and the right arm (Case 4) were from the same individual, whereas another lower part of a body (Case 5) was from a relative of the presumptive brother. A novel descriptive way of a statistical characteristic, gene or haplotype diversity, is shown.

Adult↗
PubMed2006

[Polymorphism analysis of seven Y-STR loci in Shui population in Guizhou, China].

The objective of this study was to investigate the polymorphism of seven Y-specific STR loci in Shui ethnic population of Guizhou, China, and to obtain the polymorphism information in this minority. One trinucleotide STR locus and six tetranucleotide STR loci were simultaneously amplified with fluorescently labeled primers, and genotypes were determined with ABI PRISM 377 DNA Sequencer. Allele frequencies, genetic diversity and haplotype diversity were calculated. Among 94 unrelated males, 6, 4, 6, 2, 3, 5, 4 alleles were observed in loci DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392 and DYS393, respectively. Altogether, 27 haplotypes were identified for the seven Y-STR loci. The genetic diversity values for each locus ranged from 0.124 (DYS389 I) to 0.630 (DYS19). The haplotype diversity value was 0.868. High haplotype diversities were found in Shui population of Guizhou. The study suggests that these seven Y-STR loci are valuable Y-specific markers for establishing a Y-STR database, understanding ethical origin and migrations and for personal identification.

China↗
PubMed2000

[Genetic polymorphisms of eight STR loci in a Chinese Han population].

OBJECTIVE: To understand the allele structure and genetic polymorphism at eight STR loci in Chinese Han population and construct a preliminary database. METHODS: EDTA-blood specimens were collected from the unrelated individuals in Chengdu, China. The DNA samples were extracted with Chelex method and were amplified by PCR technique. The PCR products were analyzed by the PAG horizontal electrophoresis with discontinuous buffer system and by the approach of the automated fluorescence detection. RESULTS: Five STR loci consist of simple repeat motifs, while three STR loci contain complex repeat structures. The STR polymorphisms at all of the eight loci have been observed in Chinese Han population. According to the obtained data, the combined exclusion probability and the combined discrimination power for these STR markers in Chinese population are 0.9978 and 0.999 999 992, respectively. CONCLUSION: The obtained data are beneficial to understanding the population genetics of the eight STR loci in Chinese Han population. For forensic genetics, the obtained data can be used to calculate the probabilities dealing with the paternity test and the individual identification.

China↗
PubMed2000

[STR polymorphisms in five Chinese ethnic groups(2)].

Population genetic studies were performed in Chinese Han, Hui, Mongolian, Tibetan and Uygur. Allele frequency distributions were analyzed for ten loci, i.e., D3S1358, VWA, CSF1PO, FGA, THO1, TPOX, D5S818, D13S317 and D7S820 by GeneScan. The results showed that there were 60 STR alleles and 149 genotypes in Han; 63 STR alleles and 144 genotypes in Hui; 69 STR alleles and 173 genotypes in Mongolian; 77 STR alleles and 168 genotypes in Tibetan; 70 STR alleles and 148 genotypes in Uygur. Significant differences were identified among ethnic groups (African-American, US-Caucasian and Chinese-Oriental), but similarity was found among the five Chinese populations, and immunogenomics and pharmacogenomics studied in this report. These findings indicated that the nine STR loci and amelogenin locus were very useful for individual identification in forensic science.

Alleles↗
PubMed2002

[Genetic structure of STR in Naci ethnic group in China].

STR is a universal genetic marker that has changeable polymorphism and stable heredity in human genome. It is a specific DNA segment composed of 2-7 base pairs as its core sequence, and is formed through the repeated connection of the same one. Since it has the characteristics such as numerous allelic genes, highly heterozygosity and easy recognition and short PCR segment, it is employed as an ideal DNA marker in such practical fields as human genetics and forensic medicine. In this study, we investigated the polymorphism of STR of Naci minority with STR genescan marked by fluorescence. Seventy-two alleles of 9 STR in Naci were detected with their frequency 0.0052-0.5208 and 165 genotypes were found out with frequency 0.0104-0.3021. Hi-Square test indicated the distribution of genotypes agreed with Hardy-Weinberg equilibrium (P > 0.05). Statistical analysis showed the followings: the heterozygosity (H) > 0.6 in each locus, the average polymorphism information content (PIC) > 0.7, Mean discrimination power (DP) > 0.8, probability of paternity exclusion (EPP) > 0.5, indicating that the STR markers used in the study were of great value in the researches of minority genetics. This not only founds the base for genetic structures of STR of Chinese but also provides valuable information for anthropology, forensic medicine and ethnology.

China↗
PubMed2003

Characterization of a novel dimorphism in the 5' flanking region of the short tandem repeat (STR) locus, c-fes/fps (FES).

The FES short tandem repeat (STR) locus contains seven to 14 repeats of the tetranucleotide sequence ATTT. A novel 10 base pair dimorphism in the 5' flanking region of the FES locus was characterized in four broad populations: African-American, Hispanic, Caucasian, and Asian. The absence of the 10 base pair sequence, or (-) allele, was closely linked to FES STR alleles with 10 or fewer repeats. The presence of the 10 base pair sequence, or (+) allele, was closely linked to FES STR alleles with 12 or more repeats. The (-) and (+) alleles occurred equally often in FES STR allele 11. The nucleotide sequence (5'-GGCTGTTTTG-3') of the (+) allele, located 179 base pairs upstream of the FES STR, was determined to be consistent within and among the four populations. Statistical and sequence analysis confirmed the linkage between the two polymorphic sites. The results indicate that the exclusion rate of the FES locus is increased, above that for the STR alone, when both polymorphic characteristics are considered.

5' Flanking Region↗
PubMed2002

[Evaluation on the number and value of STR loci applied in paternity identification].

OBJECTIVE: The study was carried out on the evaluation of number and value of STR loci applied in paternity identification. METHODS: A total of 13 STR loci, divided into four groups, was observed in 102 cases of paternity exclusion and 100 cases of paternity inclusion. PCR amplified products of 13 STR loci were injected into a capillary on the ABI PRISM 310 Genetic Analyzer. GeneScan software analyzed the collected data, which can then be imported into Genotyper software for genotyping of alleles. RESULTS: At least 3 STR loci incompatibilities between alleged father and child were found in all paternity exclusion cases of two observed groups which Cumulative Probability of Exclusion (CPE) was more than 99.99%, and in all paternity inclusion cases of those same observed groups, their Relative Chance of Paternity(RCP) could be over 99.99%. CONCLUSION: The exclusion of paternity should be based on at least three STR loci incompatibilities in the identification practice. As a criterion for evaluation of the number and value of STR loci applied in paternity test, CPE should reach 99.99%.

Adult↗
PubMed2004

A highly discriminating 21 locus Y-STR "megaplex" system designed to augment the minimal haplotype loci for forensic casework.

In order to increase significantly the discriminatory potential of Y-STR systems available to the forensic community, we have developed and validated a 21-locus Y-STR multiplex system. Since the system was designed specifically to augment the European Y chromosome typing community's "minimal haplotype" Y-STR set (MHL) for forensic casework, it contains a novel constellation of markers not contained therein. The system, which we refer to as Multiplex IV (MPIV), permits the co-amplification of DYS 443, DYS 444, DYS 445, DYS 447, DYS 448, DYS 449, DYS 452, DYS 453, DYS 454, DYS 455, DYS 456, DYS 458, DYS 463, DYS 464, DYS 468, DYS 484, DYS 522, DYS 527, DYS 531, DYS 557, and DYS 588. Although the multiplex contains 21 Y-STR loci, of which one is bi-local and one is tetra-local, there are actually 25 sites exhibiting allelic variation, and this has prompted us to use the descriptor "megaplex" to describe the system. This report describes a number of performance checks that were employed to characterize the system including sensitivity, specificity, discriminatory capacity, and nonprobative casework studies. Although 1 ng of male DNA was found to be the optimal amount of input template, a complete 21-locus profile was obtained with as little as 50 pg of male DNA (i.e., approximately 8 to 9 diploid cells). The specificity of the system was demonstrated by the lack of significant female DNA derived artifacts when tested using either 300 ng of female DNA alone or an admixture of male/female DNA in which the female component was present in a 100-fold excess. The ability of the system to determine the number of male donors was demonstrated by testing different admixtures of DNA at different ratios from two male donors. Cervicovaginal samples taken up to 48 h post coitus yielded a complete 21-locus Y-STR profile of the semen donor, thus confirming the potential utility of the system for forensic casework. Preliminary estimates of the gene diversity (h) of the individual loci for the Caucasian and African-American population indicated that 15 of the 21 loci possessed an h of > or = 0.5 in at least one population. Multi-locus haplotype analysis revealed that the 21-plex system could augment the use of the minimal haplotype loci and increase significantly the discriminatory capacity of Y-STR analysis.

Chromosomes, Human, Y↗
PubMed2004

The application of an automated allele concordance analysis system (CompareCalls) to ensure the accuracy of single-source STR DNA profiles.

A powerful method for validating a scientific result is to confirm specific results utilizing independent methodologies and processing pathways. Thus, we have designed, developed and validated an automated allele concordance analysis system (CompareCalls, patent pending) that performs comparisons between two independent DNA analysis platforms to ensure the highest accuracy for allele calls. Application of this system in a quality assurance role has shown the potential to eliminate greater than 90% of the STR analysis required of a DNA data analyst. While this system is broadly applicable for use with any two independent STR analysis programs, either prior to or following human data review, we are presenting its application to data generated with the ABI Prism Genotyper software system versus data generated with the SurelockID system. With the automated allele concordance analysis system, the GeneScan DNA fragment data generated from an ABI 377 gel image are analyzed in two independent pathways. In one analysis pathway, the GeneScan data are imported into Genotyper software where STR labels are assigned to the fragment data based upon the criteria of the Kazam 20% macro. The "Kazam" macro provided with the Genotyper program works by labeling all peaks in a category (or locus) and then filtering (or removing) the labels from peaks, such as those in stutter positions, that meet predefined criteria. In the second pathway, the GeneScan data are imported into the SurelockID analysis platform where STR labels and error messages are assigned to the fragment data based upon hard-coded allele calling criteria and quality parameters. The resulting STR allele calls for each analysis platform are then compared, utilizing the automated allele concordance analysis system. Any differences in the STR allele calls between the two systems are flagged in a discordance report for further review by a qualified DNA data analyst. The automated allele concordance analysis system guides the DNA data analyst to the discordant data generated by either analysis platform. Additionally, the analyst is also directed to data that are of less than pristine quality which may have an increased potential for errors in interpretation by either analysis platform or by a human DNA data analyst. Implementation of an automated allele concordance analysis system will yield high-quality data for CODIS and free the human DNA data analyst to perform other critical duties within the laboratory.

Alleles↗
PubMed2004

SWGDAM developmental validation of a 19-locus Y-STR system for forensic casework.

A Scientific Working Group on DNA Analysis Methods (SWGDAM) developmental validation study was carried out on two Y-STR multiplex systems (MPI and MPII) that collectively permit the co-amplification of 19 Y-STR markers, including DYS393, DYS392, DYS391, DYS389I, DYS389II, Y-GATA-A7.2 (DYS461), DYS438, DYS385a and DYS385b (MPI); DYS425, DYS388, DYS390, DYS439, DYS434, DYS437, Y-GATA-C.4, Y-GATA-A7.1 (DYS460), Y-GATA-H.4, and DYS 19 (MPII). Performance checks subsequent to PCR parameter optimization indicated that MPI and MPII were suitably reproducible, precise and accurate for forensic use. The sensitivity of the systems was such that a full 19-locus Y-STR profile was obtainable with 150-200 pg of male DNA, and some loci were detectable even with as little as 20-30 pg of input DNA. Primate specificity was demonstrated by the lack of cross-reactivity with a variety of commonly encountered bacterial and animal species, with the single exception of a monomorphic canine product that was outside of the size range of human alleles from any of the 19 loci. Not surprisingly, cross-reactivity was observed with a number of male and female nonhuman primates. Environmentally compromised samples produced full or partial Y-STR profiles. For example, a semen stain exposed to the outdoor elements for six months still gave a 13-locus Y-STR profile. Although a limited number of female DNA artifacts were observed in mixed stains in which the male DNA comprised 1/300 of the total, the full 19-locus male profile was easily discernible. Even at a 1500-to-2000-fold dilution of male DNA with female DNA partial Y-STR profiles were obtained. Furthermore, the potential utility of MPI and MPII for forensic casework is exemplified by their ability to dissect out the male haplotype in a variety of case-type samples, including, inter alia, post-coital vaginal swabs, admixed male and female bloodstains, the nonsperm fraction from a differentially extracted semen stain, and determination of the number of male donors in mixed semen stains.

Animals↗
PubMed2006

[An investigation for genetic polymorphisms of 10 STR loci on chromosome X of Chinese Hui nationality population in Ningxia region of China].

OBJECTIVE: To investigate the alleles and genotypes frequency of 10 short tandem repeat (STR) loci (DXS101, DXS6789, DXS6799, DXS6804, DXS7130, DXS7132, DXS7133, DXS7423, HPRTB, DXS8378) on X chromosome of Chinese Hui nationality population. METHODS: The study of 10 STR loci was performed by using the techniques of PCR, polyacylamide gel electrophoresis and silver staining. RESULTS: Among unrelated Hui individuals, the allele numbers of 10 STR loci DXS101, DXS6789, DXS6799, DXS6804, DXS7130, DXS7132, DXS7133, DXS7423, HPRTB, DXS8378 were 9, 8, 4, 6, 6, 6, 4, 4, 5 or 5 respectively; the numbers of genotypes were 17, 22, 7, 14, 14, 15, 6, 7, 12 or 8 respectively. The distribution of genotypes from these 10 STR systems fitted the Hardy-Weinberg equilibrium (P> 0.05). Polymorphisms information content of 10 STR loci, except for DXS7133 (0.48) and DXS7423 (0.48), ranged from 0.54 (DXS6799) to 0.80 (DXS6789); the power of discrimination were from 0.89 (DXS7133, DXS7423) to 0.99 (DXS6789, DXS7132, DXS101). CONCLUSION: The loci of 10 STR on chromosome X are appropriate for individual identification, paternity testing involving a female child and for study on related disease.

Alleles↗
PubMed2006

[The evaluation of 12 STR loci genetic polymorphism in Han population].

OBJECTIVE: To investigate the genetic polymorphism of 12 STR loci in 240 Han population and evaluate application of the 12 STR loci systems in forensic cases. METHODS: 12 STR loci were amplified with Muti-loci STR PCR system, which were genotyped with electrophoresis separation on dPAGE. RESULTS: 12 STR loci system had high power of discrimination (DP) and it was suited for analysis of dated bloodstain especially. CONCLUSION: The 12 STR loci systems is simple economy and practicality, which is useful in forensic identification and disputed paternity.

Alleles↗
PubMed2006

[Genetic polymorphisms and application of 9 STR loci of 5 ethnic groups in Gansu and Qinghai].

OBJECTIVE: To examine the genetic polymorphism of 9 STR loci in 5 ethnic groups (including Tu, Sala, Dongxiang, Baoan and Yugu) in Gansu and Qinghai, and to evaluate its application. METHODS: Nine STR loci (D3S1358, FGA, TH01, D7S820, VWA, CSF1PO, D5S818, D13S317 and TPOX) were selected as genetic markers. With STR compound amplification and genescan methods, in which STR loci were marked by fluorescence, the genotype of 5 ethnic groups were examined in 606 unrelated individuals by ABI 377 sequencer. These parameters, such as polymorphism information content (PIC), heterozygosity (H), discrimination power (DP) and probability of paternity exclusion (PPE) were calculated. RESULTS: The genotype frequencies of the 9 STR loci were in accordance with Hardy-Weinberg equilibrium. PIC was within 0.6054 - 0.8735, H was within 0.6158 - 0.8736, DP was within 0.7964 - 0.9691, and PPE was within 0.4610 - 0.8838. Cluster analysis based on allele frequencies in genesis showed Tu, Sala, Dongxiang and Baoan ethnic groups were very close, but Yugu was a little bit far. There were obvious gene exchanges among the populations in north and south of China. CONCLUSION: All the 9 STR loci are highly polymorphic in the 5 ethnic groups, which can be useful genetic markers in forensic medicine and population genetics.

China↗
PubMed1997

Validation studies of the CTT STR multiplex system.

Studies were performed to define the typing conditions and evaluate the forensic applicability of multiplex amplification of three STR loci, CSF1PO, TPOX, and THO1. Results were obtained using the GenePrint STR System (Promega Corporation, Madison, WI) Kit. To determine the utility of the GenePrint STR System for forensic casework analyses, the following experiments were conducted: 1) analysis of mixed body fluid; 2) determination of the sensitivity of detection; and 3) evaluation of results from biological samples from casework. In addition, the following simulated forensic conditions were assayed to detect whether or not there may be adverse effects on the ability to type these loci: 1) chemical contaminant effects on the DNA in body fluid samples; 2) the effects on DNA from samples deposited on various substrates; 3) the consequences of micro-organism contamination; and 4) the effect of sunlight and storage conditions on the integrity of the STR profiles/DNA. The data demonstrate that STR typing of biological samples exposed to a variety of environmental insults yields reliable results and that the analysis of the STR loci CSF1PO, TPOX, and THO1 can be applied in a forensic setting.

Alleles↗
PubMed2003

ATM mutations on distinct SNP and STR haplotypes in ataxia-telangiectasia patients of differing ethnicities reveal ancestral founder effects.

Due to the large size (150 kb) of the ataxia-telangiectasia mutated (ATM) gene and the existence of over 400 mutations, identifying mutations in patients with ataxia-telangiectasia (A-T) is labor intensive. We compared the SNP and STR haplotypes of A-T patients from varying ethnicities who were carrying common ATM mutations. We used SSCP to determine SNP haplotypes. To our surprise, all of the most common ATM mutations in our large multiethnic cohort were associated with specific SNP haplotypes, whereas the STR haplotypes varied, suggesting that ATM mutations predated STR haplotypes but not SNP haplotypes. We conclude that these frequently observed ATM mutations are not hot spots, but have occurred only once and spread with time to different ethnic populations. More generally, a combination of SNP and STR haplotyping could be used as a screening strategy for identifying mutations in other large genes by first determining the ancestral SNP and STR haplotypes in order to identify specific founder mutations. We estimate this approach will identify approximately 30% of mutations in A-T patients across all ethnic groups.

Ataxia Telangiectasia↗
PubMed1999

Phylogenetic placement and circumscription of tribes Inuleae s. str. and Plucheeae (Asteraceae): evidence from sequences of chloroplast gene ndhF.

DNA sequences from chloroplast gene ndhF were investigated in 15 species in tribes Inuleae Cass. s. str., Plucheeae (Benth.) A. Anderb., and Gnaphalieae Benth. (Asteraceae) and combined with 90 ndhF sequences from GenBank to evaluate the circumscription of the putative sister tribes Inuleae and Plucheeae. The data were subjected to phylogenetic analysis using parsimony jackknifing. The results are presented in a cladogram and discussed in comparison to previous analyses of both molecular and morphological data. The interpretations of specific diagnostic characters are also discussed. The majority of genera from Inuleae s. str. and Plucheeae comprise a monophyletic group, sister to the Heliantheae s. l. -Blepharispermum-Athroisma group. The genera of the Gnaphalieae belong to a different monophyletic group within the family that also includes tribes Anthemideae, Astereae, and Calenduleae. Within the Inuleae-Plucheeae complex, two well-supported subclades were identified, one corresponding to the Inuleae s. str. and the second to the Plucheeae. Three genera, Antiphiona, Pegolettia, and Geigeria, were outside of both tribes and were part of an unresolved polytomy at the base of the Inuleae-Plucheeae clade. Anisopappus, hitherto considered a member of Inuleae s. str., was found to be part of the Heliantheae-Athroisma-Blepharispermum clade. As discussed, the results of previous phylogenetic analyses, presenting Anisopappus as the basalmost taxon of Inuleae s. str., may be due to inadequate sampling.

Asteraceae↗