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PubMed2002

High-speed analysis of multiplexed short tandem repeats with an electrophoretic microdevice.

We report the development of a robust and effective method for multiplexed short tandem repeat (STR) analysis within a chip-based microdevice. The method uses a laser-induced fluorescence detection system and simultaneously detects three- and four-color multiplexed polymerase chain reaction (PCR) samples. Analyses of the eight combined DNA index system (CODIS) STR loci were performed in 20 min with single-base-pair resolution ranging from 0.75 to 1. A simultaneous analysis of fifteen loci-ladders and a gender marker Amelogenin based on the PowerPlexTM 16 System was achieved in less than 35 min. The system is capable of repetitive operation and may be extended to high-throughput multilane devices that could be readily interfaced to an automated sample loading system.

Electrophoresis↗
PubMed2004

Short tandem repeats are associated with diverse mRNAs encoding membrane-targeted proteins.

Within the genomes of multicellular organisms, short tandem repeating sequences (STRs) are ubiquitous, yet usage patterns remain obscure. The repeats (AC)n and (GU)n appear frequently in the untranslated regions (UTRs) of messenger RNAs (mRNAs). To investigate STR usage patterns, we used three approaches: (1) comparisons of individual mRNA database sequences including annotations and linked references, (2) statistical analysis of complete, UTR databases and (3) study of a large gene family, the aquaporins. Among 500 (AC)n- or (GU)n-containing mRNAs, 58 (12%) had known functions. Of these, 50 (86%) encoded proteins whose activities involved membranes or lipids, including integral membrane proteins, peripheral membrane proteins, ion channels, lipid enzymes, receptors and secreted proteins. A control sequence (AU)n also occurred in mRNAs, but only 5% encoded membrane-related functions. Investigation of all reported 3' UTR sequences, demonstrated that the STR (AC)n was 9 times more common in mRNAs encoding membrane functions than in the total UTR database (P < 0.001). Similarly, (GU)n was 8 times more common in membrane-function mRNAs than in the total database (P < 0.001). These observations suggest that (AC)n and (GU)n may be UTR signals for some mRNAs encoding membrane-targeted proteins.

3' Untranslated Regions↗
PubMed1997

Optimization of a hexaplex DNA amplification from short tandem repeat and amelogenin loci.

An automated DNA profiling system based on the multiplex amplification of highly polymorphic short tandem repeat (STR) markers and the amelogenin locus was developed. Five STR loci with nonoverlapping allele size ranges have been utilized in the multiplex amplifications, including HUMD1S103, HUMTH01, HUMD21S11, HUMD18S51, and HUMFIBRA. One primer for each locus was labeled with a fluorescent dye (fluorescein) which allows detection on the single wavelength ALF DNA Sequencer (Pharmacia Biotech). As part of the detailed evaluation of the suitability of the hexaplex system for routine forensic use, the effect of variation in amplification parameters on the efficiency of the system was examined. Polymerase chain reaction amplification conditions were optimized to provide specific, robust amplification of forensic samples.

Autoanalysis↗
PubMed1994

The validation of short tandem repeat (STR) loci for use in forensic casework.

A quadruplex reaction has been developed which amplifies the short tandem repeat (STR) loci HUM-VWA31/A, HUMTHO1, HUMF13A1 and HUMFES/FPS. Detection of the PCR products employs denaturing polyacrylamide gels coupled with fluorescent-based technology. This system has been evaluated for use in routine forensic casework and has been shown to be both robust and reproducible. The quadruplex reaction is as sensitive as the commercially available HLA DQ alpha Amplitype typing system and can be used on both degraded and aged material. The problems of environmental contamination have been shown to be limited provided strict procedural practices are followed-i.e. physical separation of sample extraction and amplified products; the use of dedicated equipment such as pipettes; the separation of amplification preparation area. The ability of the system to detect mixtures and the successful analysis of case stains has shown that this system is well suited as a tool for forensic investigation.

Alleles↗
PubMed1995

Structural variation of novel alleles at the Hum vWA and Hum FES/FPS short tandem repeat loci.

This paper reports the sequences of novel alleles identified during population databasing studies on the short tandem repeat loci HumvWA and HumFES/FPS. Two HumFES/FPS alleles follow the simple repeat pattern (ATTT)7 and (ATTT)15. Sequence variation corresponding to an A to C transversion occurred in the 5' flanking region in two individuals possessing the designated allele 7. Two HumvWA alleles exhibited compound repeat regions comprising TCTA and TCTG repeat units. Sequence analysis confirmed the putative designation of 11 for a 127 base pair allele. However, a 131 base pair allele, putatively designated as 12, exhibited a more complex sequence. Two different types of repeat unit structures were identified which also exhibited sequence variation in the 3' flanking region.

Alleles↗
PubMed1997

Short tandem repeat HumACTBP2 (SE33) and HumVWA: population genetic study on a north Italian population.

Allele frequencies at the short tandem repeat (STR) loci HumACTBP2 and HumVWA were determined in 118 unrelated individuals from Northern Italy (Milan area). For locus HumACTBP2 (SE33) a total of 39 alleles was observed. Furthermore, two interalleles (N18m+N19m) and one allele (> N35) were found which were not observed in a wider German population survey (n = 560). For the STR system HumVWA, 7 alleles could be detected. Both systems showed no significant deviation from Hardy-Weinberg equilibrium. A comparison of Italian and German population data revealed no significant differences for locus HumVWA, while significant differences were observed for locus HumACTBP2.

Actins↗
PubMed2002

Gabon black population data on the ten short tandem repeat loci D3S1358, VWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01 and FGA.

Allele frequencies for ten short tandem repeat (STR) loci D3S1358, VWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01 and FGA were determined in a Black African sample population from Gabon. All loci were highly polymorphic and except for TH01, D21S11 and D16S539, all met Hardy-Weinberg expectations. There was little evidence of association of alleles between the loci in this database. The combined power of exclusion for the ten STR loci was 0.999981. While significant differences between the Gabon population and the Austrian Caucasian population were found at all loci, significant differences were found between the Gabon population and Zimbabweans only for D3S1358 and between the Gabon population and African Americans only for TH01 and D8S1179.

Black People↗
PubMed2004

Evaluation of the species specificity for six human short tandem repeat loci CSF1PO, TPOX, TH01, F13A01, FESFPS and vWA, in the Japanese macaque.

We examined six human short tandem repeat (STR) loci (c-fms proto-oncogene for CSF-1 receptor, CSF1PO; thyroid peroxidase, TPOX; tyrosine hydroxylase, TH01; coagulation factor XIII a subunit, F13A01; c-fes/fps proto-oncogene, FESFPS and von Willebrand factor, vWA) in the Japanese macaque, Macaca fuscata, using commercially available human STR kits. No products were amplified by polymerase chain reaction (PCR) using the human CSF1PO, TH01, FESFPS and vWA primers. Macaque DNAs were amplified with human TPOX and F13A01 primers. Macaque PCR products amplified with the TPOX and F13A01 primers migrated more slowly than human ones during electrophoresis. Sequencing results showed that the nucleotide sequences of the counterpart of the TPOX and F13A01 STR loci in the Japanese macaque were closely similar to those of the human genes except for tandem repeat regions. The macaque products amplified with human TPOX and F13A01 primers were highly polymorphic, with four variants of the former and 15 variants of the latter in the nine samples. These results indicate that the commercially available kits can be used to discriminate the Japanese macaque samples from human samples.

Animals↗
PubMed1993

Automated DNA profiling employing multiplex amplification of short tandem repeat loci.

We have employed automated fluorescence-based technology to detect amplified tri-, tetra-, and pentanucleotide short tandem repeat (STR) loci electrophoresed on denaturing polyacrylamide sequencing gels. The system described incorporates an internal size standard in each sample, allowing the STR-PCR products to be sized automatically with a high degree of precision. By utilizing different fluorescent dye markers for loci that have overlapping allele size ranges, we have developed three multiplex STR systems containing a total of 14 different loci. These multiplex systems were then used to evaluate the usefulness of the 14 loci for the identification of individuals. Allele frequency data were collected from a minimum of 50 individuals from each of three different racial groups: Caucasians, Afro-Caribbeans, and Asians. Of the resulting 42 locus population sets, deviation from Hardy-Weinberg equilibria was detected in only the STR HUMCYARO3-Caucasian data. The probabilities of two unrelated individuals matching by chance (pM) at all 14 loci in the three multiplex reactions was < 1 x 10(14). The combination of multiplex STR-PCR and automatic fluorescence-based detection is thus a rapid and powerful technique for individual identification.

Autoanalysis↗
PubMed2006

[Detection of short tandem repeat (STR) polymorphisms by microchip electrophoresis for individual identification of cattle].

A simple and rapid detection of short tandem repeat (STR) markers was studied as a screening test for individual identification of cattle. DNAs were extracted from eight commercial beef samples by a proteinase K-boil method followed by purification with 2-propanol precipitation. Five STR markers, known to be highly polymorphic, were amplified by PCR and analyzed both by a conventional sequencing analysis (SEQ) and by a proposed microchip electrophoresis (MEP). Every marker revealed high polymorphism, such as 5-9 alleles in SEQ analysis, and 4-6 alleles in MEP analysis. This simple and rapid MEP analysis is expected to be an effective screening tool with use of confirmatory SEQ analysis.

Animal Identification Systems↗
PubMed1999

Population data on the thirteen CODIS core short tandem repeat loci in African Americans, U.S. Caucasians, Hispanics, Bahamians, Jamaicans, and Trinidadians.

Allele distributions for 13 tetrameric short tandem repeat (STR) loci, CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11, were determined in African American, United States Caucasian, Hispanic, Bahamian, Jamaican, and Trinidadian sample populations. There was little evidence for departures from Hardy-Weinberg expectations (HWE) in any of the populations. Based on the exact test, the loci that departed significantly from HWE are: D21S11 (p = 0.010, Bahamians); CSF1PO (p = 0.014, Trinidadians); TPOX (p = 0.011, Jamaicans and p = 0.035, U.S. Caucasians); and D16S539 (p = 0.043, Bahamians). After employing the Bonferroni correction for the number of loci analyzed (i.e., 13 loci per database), these observations are not likely to be significant. There is little evidence for association of alleles between the loci in these databases. The allelic frequency data are similar to other comparable data within the same major population group.

Adult↗
PubMed2005

[Gene frequencies and haplotypes of nine Y-short tandem repeat loci in four minority populations of China].

OBJECTIVE: To investigate the polymorphism of nine Y-short tandem repeat loci in 117 male individuals from four minority populations of China, and to obtain the polymorphism information in these populations. METHODS: Nine loci in all samples were amplified by PCR. Products were electrophoresed on ABI PRISM 377 DNA sequencer. The electrophoresis result was analyzed by Genotyper 2.0 software. Allele frequencies, diversities and genetic distance were calculated. RESULTS: Forty-three alleles and 32 haplotypes were found in Manchu population, 43 alleles and 33 haplotypes in Uygur population, 31 alleles and 15 haplotypes in Kirgiz population and 34 alleles and 23 haplotypes in Zhuang population. The closest genetic distance is 0.02530 between Manchu and Uygur, the highest genetic distance is 0.34590 between Kirgiz and Zhuang. CONCLUSION: High haplotype diversities were found in four populations. The study of genetic diversity among different populations is useful in research of their origins, migrations and their relationships.

China↗
PubMed2005

Allele distribution of five X-chromosome short tandem repeat loci in Ewenke population of north China.

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.

Asian People↗
PubMed1993

Identification of repeat sequence heterogeneity at the polymorphic short tandem repeat locus HUMTH01[AATG]n and reassignment of alleles in population analysis by using a locus-specific allelic ladder.

An allelic ladder containing amplified sequences of seven alleles of the polymorphic human tyrosine hydroxylase locus, HUMTH01, was constructed and employed as a standard marker. Sequence analysis of each ladder component indicates that fragments differ by integral multiples of the AATG core repeat sequence characteristic of this locus. Individual alleles are designated "5" through "11," according to the number of complete reiterations of the core repeat contained within them. Comparison of the HUMTH01 allelic ladder with DNA samples amplified at this locus revealed core repeat length heterogeneity (i.e., deletions or insertions shorter than one core repeat) within the human population. In particular, a common allele was identified which migrates more quickly than allele 10, but more slowly than allele 9, on electrophoresis through a denaturing polyacrylamide gel. Sequence analysis of this allele, designated "10-1," reveals lack of a single adenine normally present in the seventh copy of the AATG. The allelic ladder was used to reevaluate previously published population data. Results of testing for Hardy-Weinberg equilibrium and population substructure were not altered significantly by these modifications.

Alleles↗
PubMed2005

Combined laser-assisted microdissection and short tandem repeat analysis for detection of in situ microchimerism after solid organ transplantation.

Following the transplantation of a solid organ leukocytes of donor origin migrate out of the organ, contributing to a chimeric blood cell population ("peripheral microchimerism"). At the same time, leukocytes and pluripotent precursor cells of the recipient migrate into the organ, creating an "in situ microchimerism." A method is described for the identification of cells with the recipient's genotype in the transplanted organ by combining laser-assisted microdissection and short tandem repeat analysis. The microdissection allows the contamination-free isolation of morphologically and immunohistochemically characterized cells or groups of cells from histological tissue sections. The subsequent analysis of highly polymorphic short tandem repeats enables unequivocal genotyping in nearly all donor-recipient instances. Employing this new methodological approach, we could identify in individual transplanted organs differentiated parenchymal cells of recipient's origin, which most probably are derived from circulating precursor cells from the bone marrow.

Humans↗
PubMed1994

Allelic ladder characterization of the short tandem repeat polymorphism located in the 5' flanking region to the human coagulation factor XIII A subunit gene.

The short tandem repeat (STR) polymorphism present within the 5' untranslated region of the human coagulation factor XIII A subunit gene, HUMF13A01[AAAG]n, was evaluated using an allelic ladder, i.e., a standard size marker consisting of amplified alleles from the locus. The allelic ladder was constructed by pooling 12 polymerase chain reaction (PCR)-amplified alleles identified by their differential migration in denaturing polyacrylamide gel electrophoresis. This standard marker was used to distinguish 14 different alleles observed at this locus. Sequence analyses indicate that 13 of the alleles contain 4 through 16 iterations of the tandemly repeated AAAG sequence, respectively. The remaining allele carries four repeats and displays a deletion of two consecutive nucleotides (GT), one base distal to the repeat region. The allelic ladder was employed to type 326 F13A01 chromosomes rapidly and reliably in representatives of a German Caucasian population. Population data were analyzed with respect to Hardy-Weinberg Equilibrium (HWE) and compared with those of a previously studied Houston, Texas, Caucasian population.

Alleles↗
PubMed2006

Polymorphisms at fifteen tetrameric short tandem repeat loci in three ethnic populations of Bengal, India.

The study presents allele frequency data at 15 tetrameric short tandem repeat (STR) loci (D3S1358, THO1, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, D2S1338, D19S433 and FGA) in three ethnic populations--Mahishya, Bauri and Namasudra of Bengal to evaluate their utility in Forensic testing and understanding population structure and dynamics. A total of 169 individuals were studied from the selected populations. On an average the combined power of discrimination and power of exclusion in these groups was found 0.97 and 0.99, respectively. The allele distribution pattern shows possible genetic admixture between these ethnic groups which could be attributed to their close geographical proximity and occupying almost similar position in the social hierarchy. This study suggests that the 13 Combined DNA Index System (CODIS) markers and two added markers named D2S1338, D19S433 are highly informative and therefore suitable in matching biological specimen in human identification and population genetic study.

DNA Fingerprinting↗