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PubMed2000

The presumptive reagent fluorescein for detection of dilute bloodstains and subsequent STR typing of recovered DNA.

A presumptive reagent for dilute blood detection other than luminol is fluorescein. The sensitivity of fluorescein approaches the sensitivity of detection levels of luminol. The fluorescein detection method offers the advantages of working in a lighted environment, and the reaction persists longer than luminol. A series of diluted bloodstains, ranging from neat to 1:1,000,000, was placed on a variety of substrates. Three sets were made per substrate. One set was exposed to fluorescein, one set was exposed to luminol, and one set served as an uncontaminated control. The fluorescein signal persisted longer than luminol. However, background staining for fluorescein was observed on some substrates within 30 s to 1 min, and no background staining was observed for luminol. Stains on non-absorbent surfaces were detectable at 1:100,000 dilutions, and stains on absorbent surfaces were detectable usually at no more than 1:100. The sensitivity of detection of fluorescein was comparable to that of luminol in this study. In all cases, where sufficient DNA was recovered, typeable results at all 13 core CODIS STR loci were obtained from treated bloodstains and controls. The results from STR typing indicate that there was no evidence of DNA degradation.

Blood Chemical Analysis↗

PubMedDate not supplied

[Typing of STR locus in biological objects with pronounced degeneration: analysis of DNA in exhumed remains of victims of war actions].

The authors describe some specific features of enzymatic amplification typing of DNA preparations obtained from degraded tissues of remains of humans, which were brought from regions of war actions in the Chechen Republic. Special attention is paid to the specific artefact of polymerase chain reaction, for the first time detected by the authors in examinations of the above-mentioned objects. This so-called "ladder" effect manifesting by simultaneous nonspecific amplification of many variants of allele fragments of the STR locus on the individual DNA matrix, which can be erroneously interpreted as an evidence of mixed DNA preparation, is apparently characteristic of individual objects with pronounced degradation of biological material. Such phenomena were observed in typing of STR locuses in biological tissues subjected to biological, thermal, and physicohemical degradation. The phenomenon was studied in detail.

Bone and Bones↗

PubMed2001

[A new pentanucleotide STR-marker, located in the intron of the ING1 tumor suppressor gene and its allelic polymorphism].

DNA samples of unrelated subjects from the Volga-Ural region of Russia were examined to study allele polymorphism of the pentanucleotide repeat (TTGTG)8 localized to an intron of the tumor suppressor gene ING1. STR marker was registered in the EMBL database with the accession number AJ277387. In a sample of 119 individuals, three pentanucleotide alleles consisting of seven, eight, and nine repeated monomers were revealed. The allele frequencies were 0.24, 0.74, and 0.02, respectively. Heterozygosity was 0.45. On the basis of these data, the repeat can be regarded as a polymorphic STR marker for the ING1 gene and used in population and clinical studies.

Alleles↗

PubMed2001

CODIS STR loci data from 41 sample populations.

Allele distributions for 12 or 13 CODIS core tetrameric short tandem repeat (STR) loci CSFIPO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, and vWA were determined in 41 population data sets. The major population groups comprise African Americans, U.S. Caucasians, Hispanics, Far East Asians, and Native Americans. There was little evidence for departures from Hardy-Weinberg expectations (HWE) in any of the populations. The FST estimates over all thirteen STR loci are 0.0006 for African Americans, -0.0005 for Caucasians, 0.0021 for Hispanics, 0.0039 for Asians, and 0.0282 for Native Americans.

Ethnicity↗

PubMed2001

TWGDAM validation of the AmpFlSTR Profiler Plus and AmpFlSTR COfiler STR multiplex systems using capillary electrophoresis.

Prior to forensic implementation, a profiling system requires validation following the recommendations presented by the Technical Working Group on DNA Analysis Methods (TWGDAM). In this work two such systems, AmpFlSTR Profiler Plus and AmpFfSTR COfiler have been validated according to the guidelines provided by TWGDAM. Profiler Plus and COfiler simultaneously amplify nine and six STR loci respectively; both also amplify a portion of the amelogenin gene. Performance of the two STR multiplex systems under conditions set forth by TWGDAM was robust and reproducible, indicating that these systems are suitable for use in forensic analysis. Additionally, specific sections of the TWGDAM validation guidelines are especially valuable in terms of familiarizing users with particular limitations of the systems prior to taking on casework.

Amelogenin↗

PubMed2001

[Estimating probabilities and dealing with mutations in paternity testing--verification of DNA testing with commercially available STR kits].

Since Jeffreys devised a DNA fingerprint in 1985, DNA analysis has been applied to paternity testing. The progress of the techniques, especially the development of polymerase chain reaction (PCR), makes it possible to type 10-15 short tandem repeat (STR) loci in paternity testing by a single test tube. When using a well qualified database, we can now obtain a paternity index (PI) as high as 10(6) in usual trio cases. Furthermore, the DNA testings are now applied to unusual cases, such as personal identification of Japanese war orphans left in China. Here, we reviewed how to calculate the PI likelihood ratio and exclusion probability in a trio case, a motherless case, parent identification without reliable evidence of mother and child relationship, and a sibling case. We also reviewed how to handle single exclusion cases usually derived from a single mutation that is no longer rare when many STR loci are used. Finally, we emphasized the importance of ethical, legal and social counseling for clients in paternity testing. From that point of view, paternity tests by mail should not be allowed because of lack of such counseling.

Female↗

PubMed2002

Typing Y chromosome STR haplotypes using redesigned primers.

A panel of Y-specific STR loci, including DYS19, DYS389, DYS390, DYS391, DYS392, and DYS393 was analyzed using horizontal nondenaturing polyacrylamide gel electrophoresis with a discontinuous buffer system (horizontal disk-PAGE). In order to obtain correct results for the larger DYS389 and DYS392 alleles, it was necessary to design new primers that bind closer to the repeat region and lead to a significant reduction of the amplified fragment size. Using the modified primer sets the horizontal disk-PAGE results were consistent with a nondenaturing approach using fluorescent primers and a 377 automated sequencer. The modified procedure also amplifies the second repeat stretch at the duplicated DYS389 locus as a single fragment, which results in an immediate allele identification. The results indicate that horizontal disk-PAGE with silverstaining is a simple approach to type the recommended Y-specific STR markers.

DNA Primers↗

PubMed2002

Characterization and validation studies of powerPlex 2.1, a nine-locus short tandem repeat (STR) multiplex system and penta D monoplex.

In order to increase the power of discrimination for human identification purposes, a nine-locus short tandem repeat (STR) multiplex, the GenePrint PowerPlex 2.1 system (PowerPlex 2.1) developed by Promega Corporation and a separate pentanucleotide-repeat locus, Penta D, were tested. This megaplex system includes the highly polymorphic loci FGA, TPOX, D8S1179, vWA, Penta E, D18S51, D21S11, TH01, and D3S1358 and may be used in combination with the eight-locus STR multiplex, the GenePrint PowerPlex 1.1 system (PowerPlex 1.1) that has been previously developed. Three of the loci, TPOX, TH01 and vWA, have been included in both systems for quality control purposes. As with PowerPlex 1.1, PowerPlex 2.1 is also based on a two-color detection of fluorescent-labeled DNA products amplified by polymerase chain reaction (PCR) and provides a valuable tool for accurate and rapid allele determination. The primer sequences used in the PowerPlex 2.1/Penta D system are also presented in this report. To meet the "Quality Assurance Standards for Forensic DNA Testing Laboratories" (FBI), we tested the efficiency and reproducibility of the PowerPlex 2.1/PentaD system by several validation studies that were conducted as a joint project among seven laboratories. Validation tests included concordance studies, sensitivity, and species specificity determination, as well as performance in forensic and environmentally impacted samples. The results produced from these tests demonstrated the consistency and reliability of the PowerPlex 2.1/Penta D system.

Animals↗

PubMed2001

[Chinese Hans population study of fluorescent labelled 8 STR multiplex system].

OBJECTIVE: Chinese Hans population study of 8 STR loci was carried out in 350 unrelated individuals. METHODS: The 8 STR loci(vWA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820, D16S539) and a sexual distinction locus Amelogenin, were amplified simultaneously in one PCR reaction tube, the products were separated by electrophoresis with PE-377 DNA sequencer, and analyzed by Genescan analysis software, then the accurate PCR fragment length and designation of genotypes were finished automatically by the sequencer. RESULTS: 63 alleles and 2 sex determination alleles were found in Hans population altogether; the minimum allele frequency in Chinese Hans population at these loci was 0.17%, the maximum was 50.17%; the fragments were 119-327 base pairs long; the TDP of this system reached 99.99999998%; this system inherited steadily, and was accord with Mandel inheritance rule, no gene mutation was found, all loci met Hardy-Weinberg equilibrium, but the frequencies of Hans population differed from those of African-Americans, Caucasion-Americans and Hispanic-Americans. CONCLUSION: This method is good for identification of little amount and degraded DNA samples from blood stain, semen stain mixed with vaginal excretion, hair root, cigarette root, muscle tissue and ancient bone. It can also make a foundation of establishing the National DNA Database.

Alleles↗

PubMed2000

[Evaluation of 9 STR loci in paternity identification].

9 STR loci obtained by four-dye fluorescent labeling technique in paternity identification provides much information at one test and the cumulative chance of exclusion gets up to 0.9999. Our result of 268 paternity test cases shows that there are at least two incompatible loci in all Mother-Child-Alleged Father (M-C-AF) exclusive cases. To those unexclusive cases, The RCP all reaches international standard. It is suggested that more STR loci be used for accurate test in Child-Alleged Father(C-AF) case.

China↗

PubMed2003

[Gene frequencies of 4 STR loci in Tibetan population of Yunnan province].

OBJECTIVE: To investigate the gene frequencies of 4 STR loci in Tibetan population of Yunnan. METHODS: Multiple polymerase chain reaction (PCR), denaturing polyacrylamide gel electrophoresis and silver staining were used to detect D21S11, D8S1179, D16S539 and LPL loci. DNA samples collected from 105 unrelated Tibetan individuals in Yunnan province were analyzed. RESULTS: At D21S11, D8S1179, D16S539 and LPL loci, 13, 8, 7, 6 alleles and 33, 21, 16 and 9 genotypes were observed, respectively. The genotype distribution of the 4 STR was in accordance with the Hardy-Weinberg equilibrium. CONCLUSION: The high combined discrimination power and exclusion power of the four loci in Tibetan population make multi-PCR detection a valuable tool for forensic identity, genetics and anthropology.

Alleles↗

PubMed2003

Analysis of polymorphism of three human Y-chromosome STR loci: DYS390, DYS392 and DYS393 in the population of northern Poland.

The study aimed at development of a multiplex PCR system for amplification of three Y-chromosome STR loci: DYS390, DYS392 and DYS393, and its application in haplotype polymorphism analysis in the population of northern Poland. Due to interactions between originally published primers, a new DYS392 primer pair was proposed. In a population of 158 unrelated males, 28 different haplotypes could be observed, 12 of which were seen only once. The haplotype diversity is 0.805. Distribution of haplotypes of the studied loci is specific to the population of northern Poland and distinguishes it from compared West-European populations. To our knowledge, this is the first report on a Y-STR multiplex system that can be analysed on native polyacrylamide gels.

Analysis of Variance↗

PubMed2002

[Genetic polymorphism of 9 STR loci in Han nation population in Shandong Province].

OBJECTIVE: To study genetic polymorphism of 9 STR loci in Han nation population in Shangdong Province. METHODS: We investigated 100 unrelated individuals of Han nation population in Shandong Province and studied their genetic distribution of 9 STR loci and Amelogenin locus. Primers of 10 loci were labeled with the NHS-ester fluorescent dye 5-FAM (blue), Joe (green) or NED (yellow). The data of Han nation population were generated by multiple amplification and subjected to GeneScan, genotype and genetic distribution analysis. RESULTS: 83 alleles and 220 genotypes were observed, with the corresponding frequency of 0.0050-0.4050 and 0.0100-0.2100. The average of heterozygosity was 0.7778, the accumulated discrimination power was 0.9999. The accumulated probability of exclusion paternity was 0.9999. The polymorphism information content was 0.5823-0.8396. CONCLUSIONS: Chi-Square test indicated that the distribution of genotypes agreed with Hardy-Weinberg equilibrium.

Alleles↗

PubMed2003

[Genetic polymorphism and the population difference of 7 Y-STR loci and haplotypes in Chinese Han and Japanese populations].

OBJECTIVE: To investigate the genetic polymorphism of 7 Y-STR loci and haplotypes and analyze their population difference. METHODS: The DNA samples from 45 Chinese Han and 59 Japanese men were analyzed by PCR and the denatured PAGE followed by silver staining. RESULTS: 33 alleles were identified for 6 loci including DYS393, DYS389 I, DYS19, DYS390, DYS389 II and DYS392, 39 alleles were identified for DYS 385, the frequency distributions were between 0.0169-0.6444, the DP value distributions of them were between 0.5406-0.9579, the DP value of DYS 385 was the highest. With the comparison of data of the 7 loci, significant difference in genetics was observed between the two populations(P < 0.05). There were 95 haplotypes that consisted of the 7 loci, Chinese Han had 41 haplotypes, DP value 0.9960, Japanese population had 54 haplotypes, DP value 0.9965, no common haplotypes were found between them. CONCLUSION: The 7 STR loci above belong to loci of high discriminating ability, the haplotypes are highly polymorphic and their ethical character is apparent.

Asian People↗

PubMed2003

[The genetic polymorphism of 8 STR loci in northern Chinese Han and Uygur populations].

OBJECTIVE: The genetic polymorphism of 8 STR loci, was studied in northern Chinese Han and Uygur populations. METHODS: The 8STR loci(vWA,TH01, TP0X, CSF1P0, D5S818, D13S317, D7S820, D16S539) were analyzed and genotyped by fluorescent prime labeling kit and gene scan technology. RESULTS: 62 alleles were found in 100 individuals of Han population, CPE value was 0.9975; And 52 alleles were found in 50 individuals of Uygue population, CPE value was 0.9973. The TDP of both was beyond 0.9999. The difference of gene frequency between the two populations was significant. CONCLUSION: The genetic polymorphism of the 8 STR loci in the Han and Uygue populations is high, there are ethic differences in frequency distribution.

Alleles↗

PubMed2003

Development and validation of the Y-PLEX 5, a Y-chromosome STR genotyping system, for forensic casework.

A genotyping system, Y-PLEX 5, has been developed for use in human identification. The Y-PLEX 5 enables simultaneous amplification of five polymorphic short tandem repeat (STR) loci residing on the Y-chromosome, which are DYS389I, DYS389II, DYS439, DYS438, and DYS392. As little as 0.1 ng of template DNA can be used for analysis. The specificity of the amplification reaction enabled analysis of male DNA in a male: female DNA mixture at a ratio of 1:600. Mean stutter values ranged from 3.60-10.97%. Among the different primates investigated, the DNA from orangutan exhibited amplification at DYS438 locus and from gorilla at DYS439 and DYS438 loci. The DNA from cat, dog, and horse did not yield any amplified product. Studies on development of the genotyping system, generation and description of the allelic ladder, and validation of the multiplex PCR as per the FBI Director's Quality Assurance Standards were carried out. Y-STR allele and haplotype frequencies in two populations were generated. The data indicate that the Y-PLEX 5 genotyping system is sensitive and reliable, and can be used in human forensic and male lineage identification cases.

Alleles↗

PubMed2003

Validation and uses of a Y-chromosome STR 10-plex for forensic and paternity laboratories.

Y-chromosome short tandem repeats (Y-STRs) provide valuable information in cases of rape and questioned paternity, and they allow for the genetic identification of male lineages. The present study validated a Y-STR 10-plex on the ABI PRISM 3100 Genetic Analyzer for use in forensic and paternity laboratories at Orchid Cellmark. Following optimization of the polymerase chain reaction, father-son pairs were analyzed to ensure that each pair generated identical haplotypes. This study demonstrated that the 10-plex is sensitive to 0.125 ng of input DNA and that female samples mixed with male samples did not interfere with Y-STR haplotyping. In a sample of 525 males, there were three instances of locus multiplication, two at DYS19 and one at DYS435. Overall, haplotype diversity was 0.996, suggesting that the 10-plex can effectively distinguish among male lineages.

Chromosomes, Human, Y↗

PubMed2004

Mutation in the STR locus D21S1 1 of father causing allele mismatch in the child.

We analyzed a case of paternity dispute with 15 autosomal STR loci and found a mismatch in one of the alleles of the locus D21S11 in the child. The composition of the alleles of this locus in the mother, suspicious father, and child were 29/32, 29/29, and 29/30, respectively. The combined paternity index (2.4 x 10(10)) and paternity probability (0.9999) suggest that the suspicious father is the biological father of the child. Further analysis of 6 Y chromosome STR loci revealed matching of all the Y chromosomal alleles of the child with that of the suspicious father. Since there was a perfect match of all the paternal alleles inherited (15 autosomal and 6 Y chromosomal) in the child with that of the suspicious father except the allele D21S11, it is suggested that this might be a case of mutation. Cloning and sequencing of all the alleles of the locus D21S11 of the suspicious father, mother, and the child helped in determining that the suspicious father contributed the mutated allele.

Alleles↗