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PubMed2002

[Genetic polymorphism of fifteen short tandem repeat loci in Chinese Drungs].

OBJECTIVE: To study the short tandem repeat (STR) polymorphism in Chinese Drungs (Tulungs). METHODS: The genetic distributions of fifteen STR loci were investigated with the use of coamplification, genescan and genotype from 67 Drungs. RESULTS: There were 144 STR alleles in Drung nationality, with their frequencies ranging from 0.0077 to 0.7846, heterozygosity(H) 0.3723-0.8639, discrimination power(DP) 0.5567-0.9548, probability of paternity exclusion(EPP) 0.2738-0.8358, polymorphism information content (PIC) 0.3461-0.8456 the accumulative DP 0.99999998 and EPP 0.99999894. CONCLUSION: The results of this study on the STR polymorphism in Chinese Drungs could be used as a basis for the genetic structure of Chinese ethnic groups and also be of significant application in anthropology and forensic science.

Alleles↗
PubMed1995

Three short tandem repeat loci in Japanese population.

Allele frequencies of three short tandem repeat loci, vWF, TH and GCG, were examined for 210 unrelated Japanese individuals. Eight alleles were identified with PCR and gel electrophoresis for vWF, 7 for TH and 13 for GCG, indicating that these loci are highly polymorphic. Combined discrimination power of the 3 STRs was 0.995. These results imply that the loci are useful as probes for the identification of Japanese individuals. Thus, we applied the probes to the identification of a forensic specimen that was decomposed severely. The vWF and TH probes successfully gave clear bands in gel electrophoresis, but GCG failed to be typed because of a lot of shadow bands. The results suggests the usefulness of at least the former two probes in forensic studies.

Alleles↗
PubMed1996

Analysis of the short tandem repeat systems HUMF13B and HUMvWF in Chinese (Liaoning).

The short tandem repeat (STR) systems HUMF13B and HUMvWF were investigated in 200 healthy Chinese individuals living in Liaoning (The northeast of China). The HUMF13B allele frequencies were 6 = 0.0025, 8 = 0.1825, 9 = 0.1750, 10 = 0.6325 and 11 = 0.0075; and the HUMvWF allele frequencies were 13 = 0.0300, 14 = 0.2475, 15 = 0.0450, 16 = 0.1750, 17 = 0.2600, 18 = 0.1525, 19 = 0.0725 and 20 = 0.0175. The distribution of genotypes corresponded to the Hardy-Weinberg equilibrium. The distinguishing probabilities (D.P) were calculated as 0.7318 and 0.9366; the polymorphism information content (PIC) were calculated as 0.4827 and 0.7822; and the heterozygosity (h) were calculated as 0.5378 and 0.8128, respectively. The HUMF13B and HUMvWF systems provide a useful genetic marker for human genetics, anthropological studies, and forensic science in the chinese population.

Alleles↗
PubMed1997

Analysis of allele distribution for six short tandem repeat loci in the French Canadian population of Québec.

Short tandem repeat (STR) loci represent a rich source of highly polymorphic markers in the human genome which are useful for the purposes of forensic identification and determination of biological relatedness of individuals. Here, as a part of an ongoing extensive study, we report the analysis of a multilocus genotype survey of 642 to 870 chromosomes in the French Canadian Caucasian population of Québec at six STR loci. The loci HUMCSF1PO, HUMTPOX, HUMTH01, HUMF13A01, HUMFESFPS, and HUMvWA were typed using two multiplex polymerase chain reactions (PCR). Amplified DNA samples were subsequently analyzed by polyacrylamide gel electrophoresis followed by silver staining. The heterozygote frequencies of the loci range from 0.614 to 0.820 (0.661 to 0.818 expected) and the number of alleles from 7 to 12 per locus. Although statistically significant deviation from Hardy-Weinberg expectations of genotype frequencies was noted at some loci by one or more tests, in general, the genotype frequencies are well estimated from the product of allele frequencies at all loci. The most frequent six-locus genotype is expected to occur in the French Canadian population with a frequency of 3.50 by 10(-5) and together, these six loci have an average probability of discrimination of 0.9999985. The study presented here indicates that these six STR loci are informative genetic markers for identity testing purposes in the French Canadian Caucasian population of Québec.

Adult↗
PubMed2001

Short tandem repeat profiling provides an international reference standard for human cell lines.

Cross-contamination between cell lines is a longstanding and frequent cause of scientific misrepresentation. Estimates from national testing services indicate that up to 36% of cell lines are of a different origin or species to that claimed. To test a standard method of cell line authentication, 253 human cell lines from banks and research institutes worldwide were analyzed by short tandem repeat profiling. The short tandem repeat profile is a simple numerical code that is reproducible between laboratories, is inexpensive, and can provide an international reference standard for every cell line. If DNA profiling of cell lines is accepted and demanded internationally, scientific misrepresentation because of cross-contamination can be largely eliminated.

Cell Line↗
PubMed1996

Sequence variation found in the flanking region of a trimeric short tandem repeat at the PLA2 locus: its considerable effect on estimating alleles.

Amplified alleles at the PLA2 short tandem repeat locus were sequenced and analyzed using different combinations of the PCR primer. When changing one side of the primers from the previous design to our original one, additional alleles, which had been previously hidden, could be newly detected in two out of 60 DNA samples of unrelated Japanese individuals. The sequence data revealed both 'hidden alleles' to be accompanied by a 3-bp deletion in the 5'-flanking region of the trimeric short tandem repeat. The position of the deletion corresponded to the exact 3' end of the primer, which had been formerly used. In the present case, both of the base numbers, which constituted the core repeat unit and which were deleted in the 'hidden alleles', were equal. Therefore, it was impossible to distinguish an allele from that with not only an additional trimeric repeat but a 3-bp deletion without the sequence analysis. This result indicates that the estimated allele size does not always reflect the difference in the repeat number even if the alleles regularly differ in size by one repeat unit. Moreover, this study suggests the presence of apparent homozygotes, of which the fellow of the heterozygous alleles is hidden by an unsuccessful amplification due to the sequence variation.

Alleles↗
PubMed1993

Short tandem repeat loci: application to forensic and human remains identification.

The short tandem repeat (STR) locus ACTBP2 (common name SE33) was analyzed for its potential use in forensic and human remains identification. PCR amplification conditions were determined, and an allele-specific ladder was generated so that discrete alleles could be scored. The allele frequency distributions were determined for both Caucasian and Black populations. The frequency data meets Hardy-Weinberg expectations, and the allele distributions were similar from one racial group to another and between ethnic groups. SE33 analysis was subsequently used to confirm the identification of human remains for the Office of the Armed Forces Medical Examiners.

Alleles↗
PubMed1996

French Caucasian population data obtained from fluorescently detected HUMvWFA31/A and HUMF13A01 short tandem repeat loci.

Allele and phenotype frequencies for two tetranucleotide STR (short tandem repeat or microsatellite) systems, HUMvWFA31/A and HUMF13A01, were obtained from a sample of approximately 240 unrelated individuals randomly selected from the French Caucasian population. PCR (polymerase chain reaction) products were analysed on 6% polyacrylamide denaturing gels and visualized using fluorescently labelled primers on the automated 373A ABI DNA sequencer (Applied Biosystems Inc.). French Caucasian allele frequencies were compared to other published Caucasian data. Conditions were optimised for the quadruplex PCR amplification of these two STR loci together with the HUMFESFPS and HUMTH01 loci and the quadruplex PCR was also performed on various forensic DNA samples.

Alleles↗
PubMed2005

Unusual variant alleles in commonly used short tandem repeat loci.

Unusually large variant alleles were observed in the short tandem repeat (STR) systems D3S1358 and D21S11, both of which are included in the international standard set of loci (ISSOL) and routinely typed in National DNA intelligence databases worldwide. The observed alleles fell within the size range of the adjacent STR marker, which could easily cause problems with respect to correct allele assignments for both loci concerned. We compared the amplification and potential interpretation with three different commercially available kits, which are frequently used in forensic work. PCR products were cloned and sequenced in order to determine the structure of these unusual allele variants and confirm their size and designation (D3S1358 allele 26, D21S11 allele 46). In the locus D21S11 we observed an as yet undescribed partial duplication of the constant region.

Alleles↗
PubMed1998

Validation studies and characterization of variant alleles at the short tandem repeat locus D12S391.

Validation studies were carried out on the short tandem repeat (STR) locus D12S391 including the determination of the allele frequencies, forensic application and sequence analysis of variant alleles. A total of 16 alleles were found in a population survey of 158 unrelated individuals from the Rhine area, none of which exceeded the 0.20 frequency level. In 316 alleles analysed so far 18 alleles were found with an incomplete repeat unit in the 5'-end of the repeat region. The statistical values were similar to those of other European populations and no deviation from Hardy-Weinberg equilibrium (HWE) was observed.

Alleles↗
PubMed2006

Parentally imprinted allele typing at a short tandem repeat locus in intron 1a of imprinted gene KCNQ1.

A short tandem repeat (STR) in the intron 1a of paternally imprinted gene, KCNQ1, is evaluated as a new probe for use in parentally imprinting allele (PIA) typing. This typing can determine the inheritance of one allele from father by the methylation difference. Allelic and genotypic frequencies of the STR were determined using samples from 175 unrelated Japanese and 170 unrelated Germans. The polymorphism information contents were 0.652 and 0.634 for the Japanese and the Germans, respectively, indicating usefulness in individual identification. This method was applied to five Japanese families consisting of 19 individuals. Genomic DNA was digested by methylation-sensitive restriction endonucleases, HhaI and HapII, followed by PCR amplification using two-step sandwich primer sets and the products were analyzed on polyacrylamide gel electrophoresis. For all of the families, each child's paternal allele given by PIA typing corresponded to one of the two alleles from father, not the two from mother, that were determined by the STR genotyping. The results demonstrate that this STR probe is feasible for use in PIA typing and that its typing method can contribute to paternity testing.

DNA Probes↗
PubMed1998

Comparison of slab gel electrophoresis and capillary electrophoresis for the detection of the fluorescently labeled polymerase chain reaction products of short tandem repeat fragments.

The sizing capability of slab gel electrophoresis for short tandem repeat (STR) fragments was compared to the sizing capability of capillary electrophoresis (CE). Both systems used automated laser fluorescence detection to detect four fluorescent dyes, enabling the use of an internal lane standard within each sample. The STR fragments were amplified using a multiplex polymerase chain reaction (PCR) in which the STR fragments Hum CD-4, Hum TH01, Hum D21S11 and Hum SE33 were amplified simultaneously. The reproducibility of the size calling was determined for both systems. The average standard deviation obtained for the slab gel system was 0.2, which was comparable to the standard deviation of 0.12 obtained for the CE system. The CE system produced results comparable to those obtained on the slab gel system, with a level of precision of +/- 1.0 bp (between instruments).

DNA↗
PubMed1997

The screening of 13 short tandem repeat loci in the Chinese population.

Population studies of 13 short tandem repeat (STR) loci were carried out on Chinese in Taiwan. The STR loci included HUMF13B, HUMF13A01, HUMFES/FPS, HUMFABP, HUMPLA2A1, HUMTPOX, HUMTH01, HUMVWFA31/A, HUMCSFIPO, HUMLPL, HUMGPP3A09, HUMCYAR04 and HUMCD4. DNA samples from 100 unrelated individuals were screened. The STR allele patterns were detected by the fluorescence detector of an automated DNA sequencer. Two PCR amplifications were performed for each STR locus in this study. The first PCR amplification strategy used 26 base pairs of the T7 sequence extension in the 5' end of the forward primer of each STR locus. The second PCR amplification used a dye-labeled T7 primer instead of the forward primer in the first PCR amplification, and the first PCR products as template to produce fluorescent dye-labeled PCR products. PCR products of different STR loci with overlapping allele sizes could be detected in the same lane of the polyacrylamide gel on an automated DNA sequencer using different colored dye-labeled T7 primers. There was no need to directly conjugate the fluorescent dye to individual STR primers. The PCR products were obtained using 2 ng of template DNA in 25 microliters of PCR reaction mixture. No deviations from the Hardy-Weinberg equilibrium were observed for the 13 STR loci. The distributions of these STR alleles were different from those of Caucasians or Blacks. The probability of matching from the combination of the 13 STR loci was 5.9 x 10(-10) for our Chinese population. However, HUMF13B, HUMLPL and HUMCD4 loci were not as highly polymorphic as observed in other populations.

Alleles↗
PubMed1997

The HumD21S11 system of short tandem repeat DNA polymorphisms in Japanese and Chinese.

HumD21S11 is a short tandem repeat DNA polymorphic system with a complex basic structure of (TCTA)4-6 (TCTG)5-6 (TCTA)3 TA (TCTA)3 TCA (TCTA)2 TCCA TA (TCTA)n. Using the allelic ladder prepared by us, the distribution of alleles among Japanese and Chinese was investigated, and four new alleles 28.2, 34, 35.2, and 36.2, were discovered. DNA sequencing was performed on the newly found alleles as well as on family samples and led to the discovery of different gene structures within alleles 28 and 32. Forensic materials, including hairs and seminal stains, were tested in parallel with blood samples from the same individual and were successfully typed for D21S11.

Alleles↗
PubMed2002

Analysis of the polymorphic structure of the D7S808-short tandem repeat (STR) locus.

We analyzed the polymorphic structure of the short tandem repeat (STR) (AARG) locus D7S808 by DNA sequencing and examined the D7S808 allele distribution in a Japanese population. The sequence analysis confirmed that this locus consists of repeats of the tetranucleotides cttt and cctt, but that the number of repeats of the cctt motif does not vary with the allele, and that this STR polymorphism is due to variation in the number of cttt repeats alone. Although the results in this study suggest that the numbers of repeats range from 7 (allele 7) to 22 (allele 22), alleles 9, 10, 19, and 21 were not observed in the Japanese samples examined. Analysis of DNA samples from 355 unrelated individuals revealed the occurrence of 286 heterozygotes (observed heterozygosity 80.6%). Alleles 15, 14, 16, and 17 had high frequencies of 0.261, 0.192, 0.166, and 0.120, respectively and, together with allele 7 with a slightly high frequency of 0.059, showed a bimodal distribution. In addition, we prepared primers yielding shorter amplification products (232-292 bp) than those (435-480 bp) obtained with the originally reported primers. The newly designed primers can be used for polymerase chain reaction, making this locus extremely useful in forensic science practice.

Journal Article↗
PubMed2003

Analysis of the polymorphic structure of short tandem repeats locus D18S555.

We analyzed the polymorphic structure of the short tandem repeats (STR) (RRGG) locus D18S555 by DNA sequencing, and examined the distribution of alleles in DNA samples from Japanese and Chinese individuals. DNA sequence analysis showed that the alleles at this locus consisted of deletions or insertions of (gaaagaaagaat), (ggaa), (ggaaggaaggag), (ggaaggagggaaggaaggag), (gggaggaa), and (ggga) 5, with each allele having its own DNA sequence. Analysis of 200 unrelated Japanese and 169 unrelated Chinese subjects identified 11 alleles, of which alleles 4, 6, and 13 occurred with a high frequency. There was no difference in allele frequency between the two ethnic groups. These results indicate that the genotyping of D18S555 alleles requires no sequence analysis, and making the locus applicable to forensic identity.

Asian People↗
PubMed1998

Reuse of denaturing polyacrylamide gels for short tandem repeat analysis.

Denaturing polyacrylamide gel electrophoretic analysis of amplified polymorphic short tandem repeat (STR) loci using fluorescent markers is a mainstay of forensic and paternity testing. To reduce the drawback of preparing gels or using expensive precast gels, we have developed a simple and rapid method to reuse gels between 2 and 8 times over a period of several days. Following the initial electrophoresis and scan, the original samples are removed from the gel by a 1-1.5-h reverse-electrophoresis step. This step heats the gel for the next set of samples and can be performed several days after the initial electrophoresis. Sample bands remain sharp on subsequent runs, but edge effects (frowning of the outside lanes) become progressively worse and ultimately limit gel reuse. Well distortions and separation of the gel from the plates become problems if the gel is used more than twice. However, degassing the gel solution and bonding the gel to both plates eliminate these problems. Precast gels also can be used multiple times. Using this technique, we have successfully analyzed samples amplified with a nine-locus multiplex system and characterized the separated products using a fluorescent scanner and software.

Acrylic Resins↗
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↗