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PubMed2001

Sequence variation in humans and other primates at six short tandem repeat loci used in forensic identity testing.

A large number of alleles from the six different short tandem repeat (STR) loci FGA, D3S1358, vWA, CSF1PO, TPOX and TH01, used in human identity testing were sequenced to provide support for the robustness of fluorescent STR DNA typing by allele size. Sequence information for some of these loci (FGA, vWA, TH01) is an extension of published work, whereas no extensive sequence information is available with respect to the D3S1358, CSF1PO, and TPOX loci. Sequencing of alleles at each locus has provided quantitative data with respect to the true nucleotide length of common alleles, and of alleles that vary in length from the common alleles. All alleles that were identified as "off-ladder" alleles through fluorescent typing at these STR loci have proven to be true length variant alleles. Sequencing at the D3S1358 and CSF1PO loci allowed for the establishment of a common nomenclature for these loci. A correlation between percent stutter and the length of the core tandem repeat is demonstrated at the FGA locus. Alleles in which the core tandem repeat is interrupted by a repeat unit of different sequence have a reduced percent stutter. DNA samples from three non-human primates (chimpanzee, orangutan, and gorilla) were compared to the human sequences, and shown to differ markedly across loci with respect to their homology. The effects of primer binding site mutations on the amplification efficiency at a particular locus, and methods used to interpret amplification imbalance of heterozygous alleles at a locus is also addressed.

Animals↗
PubMed2002

Genomic diversity at 15 fluorescent labeled short tandem repeat loci in few important populations of State of Uttar Pradesh, India.

Genomic diversity at 15 short tandem repeat loci is studied in four major endogamous populations of Uttar Pradesh (UP), India. The studied populations included Thakur, Khatri, Kurmi and Jat; all of whom belong to Hindi speaking linguistic group of UP State of India. All the STR loci of Powerplex 16 System have been found highly significant in showing genomic diversity among the addressed populations. Homozygosity test values for all the 15 loci in studied population range between 0.053 and 0.999, following Hardy-Weinberg equilibrium. Distribution of allele pattern at fluorescent labeled 13 tetranucleotide repeat loci and two pentanucleotide repeat loci of Powerplex 16 System portrays that these markers are highly polymorphic, and thus, suitable in human identity testing and human genetic studies.

Gene Frequency↗
PubMed1997

A genetic study of the short tandem repeat systems VWA and TH01 in an Austrian population.

Allele- and genotype frequencies of the two short tandem repeat (STR) systems VWA and TH01 were determined in an Austrian population sample by polymerase chain reaction (PCR) analysis. A total of 9 alleles for VWA and 6 alleles for TH01 could be observed in a population of 278 (VWA) and 276 (TH01) individuals. Both systems are in accordance with Hardy-Weinberg equilibrium. They are highly informative for individualization from stain analysis and, in addition, they are very useful for paternity testing. The data presented here allow the statistical interpretation of PCR results for an Austrian population.

Alleles↗
PubMed1995

Rapid sizing of short tandem repeat alleles using capillary array electrophoresis and energy-transfer fluorescent primers.

Genetic typing of the short tandem repeat (STR) polymorphism HUMTHO1 has been performed using capillary array electrophoresis and energy-transfer fluorescent dye-labeled polymerase chain reaction primers. Target alleles were amplified by use of primers labeled with one fluorescein at the 5' end and another fluorescein at the position of the 15th (modified) base to produce fragments that fluoresce in the green (lambda max = 525 nm). Unknown alleles were electrophoretically separated together with a standard ladder made up of alleles having 6, 7, 8, and 9 four-base pair repeats, each of which was amplified with an energy-transfer primer having a donor fluorescein at the 5' end and a rhodamine acceptor at the position of the 7th (modified) base to produce standard fragments fluorescing in the red (> 590 nm). Separations were performed on arrays of hollow fused-silica capillaries filled with a replaceable sieving matrix consisting of 0.8% hydroxyethyl cellulose plus 1 microM 9-aminoacridine to enhance the resolution. The labeled DNA fragments were excited at 488 nm, and the fluorescence was detected with a two-color confocal fluorescence scanner. Separations are complete in less than 20 min and allow sizing with an average absolute error or accuracy of less than 0.4 base pair and an average standard deviation of approximately 0.5 base pair with no correction for mobility shift and cross-talk between the fluorescence channels. This work establishes the feasibility of high-speed, high-throughput STR typing of double-stranded DNA fragments using capillary array electrophoresis.

Alleles↗
PubMed1993

Variation of short tandem repeats within and between populations.

Using the polymerase chain reaction (PCR) the frequency distributions of three short tandem repeats (STR) were investigated in five populations: North European, Cypriot, Pakistani, Gujarati and Vietnamese. Each STR is situated within an intron; the markers are in the genes for human coagulation factor XIII (4bp repeat), lipoprotein lipase (4bp repeat) and CD4 (5bp repeat). Population data were generated for each STR and allele frequencies calculated. A calculation of the level of population substructuring for the three systems was also made. The lipoprotein lipase STR data showed no evidence for population substructuring, but there was a significant level of substructuring in the other two systems. This initial pilot study demonstrates the need to validate each marker used for DNA profiling in different human populations, and that some markers (such as LPL) can be used with confidence in widely differing ethnic groups, while others (such as CD4 and F13A) may be of value in distinguishing sub-groups.

Alleles↗
PubMed2002

Role of short tandem repeat DNA in forensic casework in the UK--past, present, and future perspectives.

The analysis of short tandem repeat (STR) DNA sequences is of fundamental importance to forensic science because they have become the recognized standard in constructing national public databases. Consequently, considerable effort has been expended in developing multiplexed (one tube) reactions that analyze several loci in combination. The implementation of STRs in casework cannot take place without a full understanding of the systems used. The purpose of validation is to characterize multiplexes when one is challenged with forensic samples. For example, mixtures are often encountered that may be particularly difficult to interpret against a background of allelic artifacts. By increasing the number of PCR amplification cycles, it is possible to dramatically boost the sensitivity of the system so that just a handful of cells may be successfully analyzed. However, interpretation is much more complex because the origin of DNA profiles may be less certain and complicated by issues such as contamination, the potential for innocent transfer and a predominance of mixtures. This review provides a brief historical background of the development of STRs in forensic casework that culminated in the creation of national DNA databases. The development of guidelines to interpret complex DNA profiles, such as mixtures, is outlined. Finally, the recent innovation of low copy number DNA profiling is explained along with the special considerations needed to report in court.

DNA↗
PubMed1999

[A preliminary study of human Y chromosome specific short tandem repeat loci].

OBJECTIVE: To understand the allele structure and reveal genetic polymorphism of Y chromosome specific short tandem repeat (Y-specific STR) loci in Chinese Han population. METHODS: The authors used a set of five Y-specific STR loci which were tetrameric tandem repeat loci chosen from the Genome Database. EDTA-blood specimens were collected from the unrelated individuals. DNA was extracted by Chelex method and amplified by the polymerase chain reaction (PCR). The PCR products were analyzed using both the PAGE horizontal electrophoresis with discontinuous buffer system and the automated fluorescence detection approach. RESULTS: The authors observed that the alleles at the five Y-specific STR loci were composed of some complex repeat structures. They successfully prepared a set of human allele ladders for the typing of the five Y-specific STRs and demonstrated the polymorphisms at the five Y-specific STR loci in Chinese Han population. CONCLUSION: Y-specific STRs are good genetic markers for the purpose of analysis of genetic relationship between populations. This preliminary study not only reveals allele frequencies and haplotype distribution of Y-specific STR in Chinese Han population, but also indicates a reference population for detecting male migration events and for reconstructing paternal history.

Chromosome Mapping↗
PubMed1999

[A preliminary study of human Y chromosome specific short tandem repeat loci]

OBJECTIVE: To understand the allele structure and reveal genetic polymorphism of Y chromosome specific short tandem repeat (Y-specific STR) loci in Chinese Han population. METHODS: The authors used a set of five Y-specific STR loci which were tetrameric tandem repeat loci chosen from the Genome Database. EDTA-blood specimens were collected from the unrelated individuals. DNA was extracted by Chelex method and amplified by the polymerase chain reaction (PCR). The PCR products were analyzed using both the PAGE horizontal electrophoresis with discontinuous buffer system and the automated fluorescence detection approach. RESULTS: The authors observed that the alleles at the five Y-specific STR loci were composed of some complex repeat structures. They successfully prepared a set of human allele ladders for the typing of the five Y-specific STRs and demonstrated the polymorphisms at the five Y-specific STR loci in Chinese Han population. CONCLUSION: Y-specific STRs are good genetic markers for the purpose of analysis of genetic relationship between populations. This preliminary study not only reveals allele frequencies and haplotype distribution of Y-specific STR in Chinese Han population, but also indicates a reference population for detecting male migration events and for reconstructing paternal history.

Journal Article↗
PubMed2000

Improved haplotype analysis of human myelin basic protein short tandem repeat loci.

We report an improved haplotype analysis of the human myelin basic protein gene (MBP) short tandem repeat (STR) polymorphism. The polymorphic G-->A transition and 2 conventional STR polymorphisms, MBPA and MBPB, were simultaneously determined by an amplified product length polymorphism technique. After the MBPC fragments containing MBPA and MBPB were amplified, the linkage of these 2 STR loci was determined by a second amplification, using polymerase chain reaction (PCR) technique, of the isolated MBPC fragments. The present haplotype analysis dispensed with family studies for the haplotyping of MBPA and MBPB. Polymorphisms of the MBP loci studied in German and Japanese populations showed a high genomic variation. Haplotype analysis of the MBP loci showed distinct differences between the German and the Japanese populations. Consequently, haplotype analysis of the MBP loci promises to be useful in forensic identification and paternity testing.

Alleles↗
PubMed2002

Online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations.

We describe here an online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations, which represents 9-locus Y-STR haplotypes for 1705 African-Americans, European-Americans and Hispanics as of October 2001. This database is available online (http://www.ystr. org/usa/), free to access and was generated in order to supply the U.S. forensic DNA community with a valuable resource for frequencies of complete or incomplete 9-locus Y-STR haplotypes, as well as information about typing protocols and population genetic analyses. Pairwise R(ST)-statistics derived from the Y-STR haplotypes indicate no significant substructure among African-American populations from different regions of the U.S., nor (usually) among European-American and Hispanic populations. Thus, pooling of Y-STR haplotype data from regional populations within these three major groups is appropriate in order to obtain larger sample sizes. However, pooling of different major populations is generally not recommended due to statistically significant differences between African-American populations and all European-American/Hispanic populations, as well as between some European-American and Hispanic populations.

Black People↗
PubMed2003

Performance evaluation of two multiplexes used in fluorescent short tandem repeat DNA analysis.

The performance of two commercial multiplex kits that together amplify the 13 core short tandem repeat (STR) loci currently in use by forensic laboratories and the U.S. national Combined DNA Indexing System (CODIS) were evaluated. The typing systems examined were AmpFlSTR Profiler Plus and AmpFlSTR COfiler (PE Applied Biosystems, Foster City, CA). Electrophoretic separation and detection of the fluorescent PCR products was achieved by capillary electrophoresis (CE) using an ABI Prism 310 Genetic Analyzer. The studies addressed the on-site validation of the instrument, the software, and each typing system. These studies included instrument sensitivity, resolution, precision, binning, peak height ratios, mixtures, stutter, and the amplification of non-probative and simulated forensic samples. Other additional developmental-type work is also reported herein, such as species specificity testing and amplification of environmentally insulted samples. Amplification conditions were found to be robust and the primer sets shown to be specific to human DNA. Stutter and peak height ratios fell within limits published by the manufacturer and other laboratories. The data demonstrate that the CE instrument can consistently resolve fragments differing in length by one base and that the +/-0.5 base bin used by the Genotyper software is acceptable for making accurate allele calls. Correct typing results were obtained from non-probative and simulated case samples, as well as samples exposed to outdoor environmental conditions. The results support the conclusion that DNA extracted from biological samples routinely encountered in the forensic laboratory can be reliably analyzed with AmpFlSTR Profiler Plus and COfiler using CE.

Alleles↗
PubMed2003

Allele and haplotype frequencies of Y-short tandem repeat loci in Turkey.

AIM: To assess the frequency distribution of six Y-chromosomal specific short tandem repeat (STR) polymorphisms and frequencies of haplotypes in Turkish population. METHODS: Blood samples were taken from 200 unrelated Turkish men from different regions of Turkey, who were involved in legal proceedings concerning paternity. The DNA was amplified and typed by use of Y-Plex 6 kit containing 6 Y-STR markers (DYS393, DYS19, DYS389 II, DYS390, DYS391, and DYS385). Capillary electrophoresis was carried out on an ABI 310 Genetic Analyzer. RESULTS: Allele frequency profiles of the Turkish men showed no significant differences compared with previously published results for Swiss and German populations. The range of gene diversity was determined between 48.3% for DYS391 and 96.0% for DYS385. Of 184 determined haplotypes, 170 occurred once, and the rest more than once. The most common haplotypes had a frequency of 1.5%. CONCLUSION: High degree of haplotype diversity in Turkish population makes analysis of Y-STRs a useful tool in forensic cases.

Chromosomes, Human, Y↗
PubMed2005

[Genetic polymorphism of 5 short tandem repeat loci in Hui population in Ningxia area].

OBJECTIVE: To analyze the genetic polymorphism of 5 short tandem repeat(STR) loci in Hui population in Ningxia area. METHODS: The genetic polymorphisms of five selected STR loci(D11S1984, D14S306, D14S617, D17S1290 and D19S433) in chromosomes 11, 14, 17 and 19 in 144 unrelated individuals in Hui population in Ningxia area were analyzed by PCR amplification, denaturing polyacrylamide gel electrophoresis(PAGE) and silver staining. RESULTS: 10, 8, 11, 13 and 8 alleles, 30, 25, 33, 40 and 23 genotypes of the 5 STR loci in Hui population in Ningxia were detected. The measured values of the heterozygosity of the 5 STR loci were 0.8413, 0.8033, 0.8331, 0.8369 and 0.7703; of the polymorphism information content were 0.8217, 0.7746, 0.8121, 0.8174 and 0.7332; of the discrimination power (DP) were 0.9516, 0.9257, 0.9611, 0.9660 and 0.9135. The calculated discrimination power was 0.9999995. The measured values of paternity exclusion were 0.7046, 0.6367, 0.6911, 0.7012 and 0.5801; the calculated paternity exclusion was 0.9958. The genotype distributions were in accordance with Hardy-Weinberg equilibrium. CONCLUSION: The 5 STR loci have better polymorphism in Hui population in the Ningxia area, and thus could serve as useful markers for population genetics research and for individual identification and paternity test in forensic medicine.

Asian People↗
PubMed2005

[Analysis on allele frequencies of 7 short tandem repeat loci of Kashing-Beck disease patients on].

OBJECTIVE: To analyze the allele frequencies of 7 short tandem repeat (STR) loci (D12S1718, D12S1675, D12S358, D12S367, D12S1638, D12S1646 and D12S1682) on chromosome 12 among Kashing-Beck disease (KBD) patients and the control population living in the KBD areas and non-KBD area. METHODS: EDTA-blood specimens were collected from 102 unrelated individuals of Chinese Han population in Shaanxi province including 29 KBD patients,30 controls living in the KBD area and 43 living in the non-KBD area. DNA samples were extracted using the Wizard Genomic DNA purification kit (http://www. Promega. com) and were amplified by polymerase chain reaction (PCR) technique. The PCR products were analyzed by ABI 3100 Genetic Analyzer. RESULTS: (1) In KBD patients group, the allele number for 7 STR loci were 4,7,7,8,5,5 and 7, the genotype number were 5,12,13,11,10,9 and 13; (2) In the control population living in KBD area, the allele number for 7 STR loci were 4,9,7,6,6,6 and 8,t he genotype number were 5,10,12,14,12,9 and 13;(3) In the control population living in the non-KBD area, the allele number for 7 STR loci were 7,9,7,7,5,8 and 11, the genotype number were 9,16, 17,16,12,15 and 20;(4) Compared with the allele frequencies among three groups, there were significant differences between KBD patients and the controls living in the KBD area (D12S367: P = 0.034; D12S1638: P = 0.041) and the controls living in the non-KBD area (D12S367: P = 0. 029; D12S1638: P= 0 .028) in the D12S367 and D12S1638 loci; (5) There were significant differences among KBD patients (P = 0.036), controls living in the KBD area (P = 0.039) and controls living in the non-KBD area in the D12S1646. CONCLUSION: There was significant difference between KBD patients and the controls in the D12S367 and D12S1638 loci.

Adult↗
PubMed2004

Design of a multiplex PCR for genotyping 16 short tandem repeats in degraded DNA samples.

The molecular genotyping of individuals and reconstruction of kinship through short and high polymorphic DNA markers, so-called short tandem repeats (STR), has become an important and efficient method in anthropology and forensic science. The here introduced experimental design describes a multiplex PCR capable of simultaneously amplifying 16 STRs and the sex determinant locus amelogenin in a short fragment lengths range from 84 bp to 275 bp. Thus, the design depends predominantly on the routines for DNA typing of historical samples with highly degraded ancient DNA. It is shown, that the newly designed multiplex PCR is suitable for successful typing of both forensic and historical material.

Alleles↗
PubMed2001

Genotyping short tandem repeats using flow injection and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.

Characterizing polymerase chain reaction (PCR) amplicons has been accomplished for the first time using flow injection analysis coupled to electrospray ionization mass spectrometry (ESI-MS). The PCR amplicons were amplified at the human tyrosine hydroxylase short tandem repeat locus from an individual homozygotic for the 9.3 allele. One product was amplified using Pfu polymerase and yielded a blunt-ended amplicon of 82 base-pairs (bp) in length. The second PCR product was amplified using Taq polymerase that resulted in an amplicon with cohesive termini of 82 bp plus either mono- or diadenylation. The two PCR amplicons were alternatively injected using a 0.5-microL loop at 2 microM for the Pfu amplicon and 1 microM for the Taq amplicon with a flow rate of 200 nL/min during data acquisition. Both PCR amplicons were accurately identified using mass measurements illustrating the compatibility of ESI-MS for genotyping short tandem repeat sequences and the potential for high-throughput genotyping of large PCR amplicons.

Alleles↗
PubMed2004

Whole genome amplification of DNA from laser capture-microdissected tissue for high-throughput single nucleotide polymorphism and short tandem repeat genotyping.

Genome-wide screening of genetic alterations between normal and cancer cells, as well as among subgroups of tumors, is important for establishing molecular mechanism and classification of cancer. Gene silencing through loss of heterozygosity is widely observed in cancer cells and detectable by analyzing allelic loss of single nucleotide polymorphism and/or short tandem repeat markers. To use minute quantities of DNA that are available through laser capture microdissection (LCM) of cancer cells, a whole genome amplification method that maintains locus and allele balance is essential. We have successfully used a ø29 polymerase-based isothermal whole genome amplification method to amplify LCM DNA using a proteinase K lysis procedure coupled with a pooling strategy. Through single nucleotide polymorphism and short tandem repeat genotype analysis we demonstrate that using pooled DNA from two or three separate amplification reactions significantly reduces any allele bias introduced during amplification. This strategy is especially effective when using small quantities of source DNA. Although a convenient alkaline lysis DNA extraction procedure provided satisfactory results from using 1500 to 3000 LCM cells, proteinase K digestion was superior for lower cell numbers. Accurate genotyping is achieved with as few as 100 cells when both proteinase K extraction and pooling are applied.

Female↗