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PubMed2005

Sobo, a recently amplified satellite repeat of potato, and its implications for the origin of tandemly repeated sequences.

Highly repetitive satellite DNA sequences are main components of heterochromatin in higher eukaryotic genomes. It is well known that satellite repeats can expand and contract dramatically, which may result in significant genome size variation among genetically related species. The origin of satellite repeats, however, is elusive. Here we report a satellite repeat, Sobo, from a diploid potato species, Solanum bulbocastanum. The Sobo repeat is mapped to a single location in the pericentromeric region of chromosome 7. This single Sobo locus spans approximately 360 kb of a 4.7-kb monomer. Sequence analysis revealed that the major part of the Sobo monomer shares significant sequence similarity with the long terminal repeats (LTRs) of a retrotransposon. The Sobo repeat was not detected in other Solanum species and is absent in some S. bulbocastanum accessions. Sobo monomers are highly homogenized and share >99% sequence identity. These results suggest that the Sobo repeat is a recently emerged satellite and possibly originated by a sudden amplification of a genomic region including the LTR of a retrotransposon and its flanking genomic sequences.

Base Sequence↗
PubMed2004

[Genetic polymorphisms of six short tandem repeat loci in the Han population of Henan province in China].

OBJECTIVE: To investigate the allele frequencies of six short tandem repeats (STR) loci D12S391, D5S818, D18S51, PAHI3, D8S1179, D3S1358 in the Han population of Henan province and to obtain preliminary data. METHODS: DNA was extracted with phenol-chloroform from 140 EDTA-blood specimens of healthy unrelated individuals in Henan population; multiplex PCR technique and PAGE vertical electrophoresis were used to screen the genotype frequencies of six STR systems in Henan population. RESULTS: The test for Hardy-Weinberg equilibrium revealed that the genotype distribution was correspondent with the expected. The observed heterozygosities of six loci were 0.871, 0.769, 0.871, 0.773, 0.901, 0.722. The calculated discrimination power is 0.9999998, the calculated power of exclusion is 0.99845, the calculated matching probability is 2.39 x 10(-7). CONCLUSION: All of the six loci in this study have high power of discrimination and exclusion; they may be very useful genetic markers for individual identification, paternity test and genetics purposes.

Alleles↗
PubMed1995

Mass disasters: rapid molecular screening of human remains by means of short tandem repeats typing.

Human remains identification represents a challenging situation and constitutes a difficult task associated with mass disasters. The only highly efficient means for individual and family group reconstruction is that based on DNA typing. On July 18, 1994 an explosion destroyed the A.M.I.A. (Argentine Israeli Association). Over 100 people died; however, the exact number of victims is still being investigated. Our Service received over 70 remains to be characterized by DNA typing in order to determine the number of victims and to try to reconstruct the family groups to which they belonged. DNA was extracted by a cetyltrimethylammonium bromide (CTAB) based protocol, a rapid molecular screening of all samples was carried out by multiplex STR amplifications including HUMTH01, HUMFABP, HUMHPRTB, HUMRENA4, HUMVWA, HUMFES/FPS and Y27H39LR. Samples with identical genotypes were HaeIII-digested. Southern blotted and probed with YNH-24 (D2S44). PH-30 (D4S139). LH-1 (D5S110) and MS-1 (D1S7) for variable number of tandem repeats (VNTR) evaluation. The minisatellite variant repeat (MVR) approach was used in those cases in which band or profile shift were detected in Southern blot assays. Kinship between victims and putative relatives was initially evaluated by comparison of short tandem repeat (STR) profiles and then confirmed by VNTR with the above probes. The high identification efficiency attained in this case is, in part, supported by a previous experience, the DNA-based molecular characterization of human remains caused by the explosion of the Israeli Embassy in Buenos Aires, March 1992.

Blotting, Southern↗
PubMed2002

A powerful, novel, multiplex typing system for six short tandem repeat loci and the allele frequency distributions in two Japanese regional populations.

A new multiplex system for six tetranucleotide short tandem repeat (STR) loci was devised based on multicolor dye technology. Six loci (D20S480, D6S2439, D6S1056, D9S1118, D4S2639, and D17S1290), each with high discriminating power (each unbiased estimates of expected heterozygosity, Exp. Hz, > 0.80 in a preliminary test), were selected from more than 100 tetranucleotide STRs included in a commercially available primer set. These loci were also selected so as not to link with general STRs in commercially released kits including the combined DNA index system (CODIS) 13 core STRs. The primers were newly designed in the present study, in which each amplicon size had a range of less than 200 base pairs (bp), in order to genotype from highly degraded template DNA. Using this system, we genotyped 270 Honshu (mainland)-Japanese and 187 Okinawa-Japanese. From these allele frequencies, we performed three tests, a homozygosity test, a likelihood ratio test and an exact test for Hardy-Weinberg equilibrium (HWE), and no significant deviations (p < 0.05) from HWE were observed. We also compared the allele distributions at six STRs between both populations, and they were significantly different (p < 0.05) at three loci (D6S2439, D9S1118 and D4S2639). Furthermore, the Exp. Hz and the power of discrimination (PD) at all loci in the Honshu-Japanese population were higher than 0.80 and 0.93, respectively. These statistical values for discriminating power in the Honshu-Japanese were almost the same as in the Okinawa-Japanese. This novel, multiplex polymerase chain reaction (PCR) amplification and typing system for six STR loci thus promises to be a convenient and informative new DNA profiling system in the forensic field.

Alleles↗
PubMed2006

[Allele frequencies and species specificity of five short tandem repeat loci of Chinese Han population in Chengdu].

OBJECTIVE: To obtain the data in polymorphism distribution of the five short tandem repeat (STR) loci: D18S979, D11S2014, D18S548, D1S1667 and GATA164F07 of Chinese Han population in Chengdu, and to evaluate their usefulness in the field of species specificity in forensic science. METHODS: PCR, polyacrylamide gel electrophoresis (PAGE) and silver staining techniques were used to analyze the DNA samples from 100 unrelated individuals of Chinese Han ethnic group in Chengdu. Twelve different animals: monkey, pig, dog, bull, goat, chicken, duck, eel, mudfish, rabbit, guinea pig and mouse were selected as controls in this study for evaluating the species specificity of the five STR loci. RESULTS: Six alleles and twelve genotypes were observed in D18S979. Five alleles and eleven genotypes were observed in D11S2014. Five alleles and thirteen genotypes were observed in D18S548. Seven alleles and nineteen genotypes were observed in D1S1667. Six alleles and fourteen genotypes were observed in GATA164F07. The genotype distributions of the five loci were analyzed by some related software and no deviation from the Hardy-Weinberg equilibrium was observed. Evaluated by way of using different animals as controls, monkey had amplification products at the extra-typing field of D18S979, D11S2014 and D1S1667. Bull, dog and eel had amplification product at typing field of D18S979, and pig, duck, mouse and rabbit had weak product. Bull had weak product at the typing field of D18S548. Dog, goat and eel had product at the typing field of D1S1667. Dog had weak product at the typing field of GATA164F07. Mudfish, chicken and guinea pig had no amplification product at the five loci. CONCLUSION: These data indicate that D18S979, D18S548, D1S1667 and GATA164F07 are highly polymorphic and D11S2014, D18S548 and GATA164F07 can play a key role in species identification.

Animals↗
PubMed2002

Determination of the donor:host blood cell ratio after haematological stem cell transplant by means of semiquantitative detection of short tandem repeat polymorphisms.

An improved method of quantifying the donor:host blood cell ratio after haematological stem cell transplantation (PBSCT) using a variable number of tandem repeat (VNTR) markers is presented. The post-transplant DNA is extracted from the patient's blood and amplified by semiquantitative polymerase chain reaction (PCR) without prior mock transplant and plotting of a standard curve. The amplification products are then analysed by ABI PRISM 310 capillary electrophoresis apparatus. The resultant peak areas are correlated with the corresponding microsatellite allele by GeneScan software and the donor:host cell ratio is calculated. Improvements to PCR amplification conditions are essential for the outcome of the quantification since preferential amplification of alleles in the PCR process can account for the marked deviation found between the results gained by measurement of different microsatellite loci. To assess the accuracy of the method, the post-transplant blood samples of 6 patients who had undergone either myeloablative or non-myeloablative transplantation regimens were analysed retrospectively (median observation time 298 days). By analysing 3 or 4 microsatellite loci we were able to detect full engraftment or mixed chimaerism after transplant with a measurement precision of < or = 4.5 (standard deviation). Sensitivity for different primers ranges from 2% to 5%. The results of the microsatellite analysis correlated well with the corresponding clinical findings. We conclude that post-transplant analysis of microsatellite loci using semiquantitative PCR without standard is suitable for clinical purposes.

Humans↗
PubMed1997

Molecular characterization of the alpha-amylase genes of Lactobacillus plantarum A6 and Lactobacillus amylovorus reveals an unusual 3' end structure with direct tandem repeats and suggests a common evolutionary origin.

The alpha-amylase gene (amyA) of Lactobacillus plantarum A6 was isolated from the genome by polymerase chain reaction with degenerated oligonucleotides, synthesized according to the tryptic peptide amino acid sequences of the purified enzyme. Nucleic acid sequence analysis revealed one open reading frame of 2739 bp encoding a 913 amino acid protein. The amylase appears to be divided into two equal parts. The N-terminal part has the typical characteristics of the well-known alpha-amylase family (65% identity with the alpha-amylase of Bacillus subtilis and 97% identity with the partial sequence available for the alpha-amylase of Lactobacillus amylovorus). The C-terminal part displays a fairly unusual structure. It consists of four direct tandem repeated sequences of 104 amino acids sharing 100% similarity. The complete nucleotide sequence of the alpha-amylase gene of L. amylovorus was also determined. An open reading frame of 2862 bp encoding a 954 amino acid protein was identified. Perfect homology between the two amyA genes was observed in the N-terminal region. The C-terminal part of L. amylovorus alpha-amylase also included tandem repeat units but striking differences were observed: (i) the addition of one repeat unit; (ii) a shorter, 91 amino acid repetition unit. These structural homologies suggest that both genes have a common ancestor and may have evolved independently by duplication with subsequent recombination and mutation.

Amino Acid Sequence↗
PubMed2002

Analysis of variation in tandem repeats in the intron of the major surface glycoprotein expression site of the human form of Pneumocystis carinii.

Variation in the tandem repeats in the expression site of the human-derived Pneumocystis carinii major surface glycoprotein gene was characterized by denaturing gel electrophoresis. The number of repeats in 147 isolates ranged from 2 to 6, with 2, 3, and 4 repeats being the most common. Sequence analysis identified 3 types of repeat units that differed by 1 nucleotide, which suggests a hierarchy of evolution of human-derived P. carinii. Examination of sequential samples obtained from 6 patients at an interval of 10-90 days showed an identical repeat pattern in each patient. However, in 2 of 4 patients with 2-3 different samples obtained within 4 days, different repeat patterns were observed among the samples. Quantifying the number of repeats by denaturing gel electrophoresis is a simple and rapid-typing method that can be used alone or in combination with other methods to study the epidemiology of P. carinii.

Base Sequence↗
PubMed2003

[Genotype reliability of short tandem repeats typing from minute DNA].

OBJECTIVE: To understand the forensic practice of DNA profiling from minimal amount of DNA. METHODS: Serial dilutions of DNA were amplified with the PowerPlex 16 System Kit, then the genotyping of short tandem repeat(STR) was performed by ABI 377 DNA automated Sequencer. RESULTS: When the mount of DNA template was less than 250 pg, allelic drop-out apparently occurred at several loci. Other disturbed peaks, such as artefact bands and imbalanced heterozygote, also presented. CONCLUSION: The anomalous results may result in incorrect genotyping. Careful and comprehensive considerations are needed to interpret the STR profile of minute DNA.

Alleles↗
PubMed2000

Sequence variation of new alleles at the short tandem repeat D19S253 locus.

This paper reports the sequences of two new alleles identified in a population database study on the short tandem repeat D19S253 locus. A Portuguese Caucasian population and a Portuguese African population were studied. Forty-four selected alleles were sequenced and 11 different alleles were found. All the sequenced alleles shown to possess a simple tetranucleotide GATA repeat region structure. The two new alleles, alleles 6 and 16, follow the simple repeat pattern. During paternity investigation casework, 1028 meiosis were analyzed and five isolated genetic incompatibilities detected. In one case, a non-detectable allele with the used set of primers could be the explanation. In the other four cases, single-step mutations could be considered. The mutation rate obtained for this locus was 3.89 x 10(-3).

Alleles↗
PubMed2000

Application of short tandem repeat of genomic DNA and mitochondrial DNA for identification of mixed-up tissue specimens.

Deoxyribonucleic acid (DNA) typing methods, short tandem repeat of genomic DNA and mitochondrial DNA with the use of polymerase chain reaction amplification, were applied to formalin-fixed, paraffin-embedded tissues submitted for diagnosis, to identify and sort out mixed-up tissue specimens. These techniques were found to be reliable, reproducible and specific for personal identification, and thus to eliminate the need for further examinations and to prevent unnecessary surgery.

Aged↗
PubMed2001

Differentiation of strains of Xylella fastidiosa by a variable number of tandem repeat analysis.

Short sequence repeats (SSRs) with a potential variable number of tandem repeat (VNTR) loci were identified in the genome of the citrus pathogen Xylella fastidiosa and used for typing studies. Although mono- and dinucleotide repeats were absent, we found several intermediate-length 7-, 8-, and 9-nucleotide repeats, which we examined for allelic polymorphisms using PCR. Five genuine VNTR loci were highly polymorphic within a set of 27 X. fastidiosa strains from different hosts. The highest average Nei's measure of genetic diversity (H) estimated for VNTR loci was 0.51, compared to 0.17 derived from randomly amplified polymorphic DNA (RAPD) analysis. For citrus X. fastidiosa strains, some specific VNTR loci had a H value of 0.83, while the maximum value given by specific RAPD loci was 0.12. Our approach using VNTR markers provides a high-resolution tool for epidemiological, genetic, and ecological analysis of citrus-specific X. fastidiosa strains.

Bacterial Typing Techniques↗
PubMed1998

Italian population data on thirteen short tandem repeat loci: HUMTH01, D21S11, D18S51, HUMVWFA31, HUMFIBRA, D8S1179, HUMTPOX, HUMCSF1PO, D16S539, D7S820, D13S317, D5S818, D3S1358.

A population study on thirteen short tandem repeat (STR) loci was performed on 223 unrelated Italian Caucasians. The DNA was amplified by PCR. Separation and detection of the amplified STR fragments was carried out by use of 377 automated system (Applied Biosystems Division/Perkin Elmer). All loci meet Hardy-Weinberg expectations, and the data show only five departures out of seventy-eight pairwise locus tests which is close to expectations of 5% (5/78 = 6.4%). When correcting for multiple tests, there is little evidence for departures from expectations between loci. The combined Power of Exclusion for the thirteen STR loci is 0.99999270. The results demonstrate that these loci will be very useful for human identification in forensic cases in Italy.

Alleles↗
PubMed2005

Radiation-induced mutation at tandem repeat DNA Loci in the mouse germline: spectra and doubling doses.

The spectra and dose response for mutations at expanded simple tandem repeat (ESTR) loci in the germline of male mice acutely exposed to low-LET X or gamma rays at pre-meiotic stages of spermatogenesis were compared in five strains of laboratory mice. Most mutation events involved the gain or loss of a relatively small number of repeat units, and the distributions of length changes were indistinguishable between the exposed and control males. Overall, a significant bias toward gains of repeats was detected, with approximately 60% of mutants showing gains. The values for ESTR mutation induction did not differ substantially between strains. The highest values of doubling dose were obtained for two genetically related strains, BALB/c and C.B17 (mean value 0.98 Gy). The estimates of doubling dose for three other strains (CBA/H, C57BL/6 x CBA/H F1 and 129SVJ x C57BL/6) were lower, with a mean value of 0.44 Gy. The dose response for ESTR mutation across all five strains was very close to that for the specific loci (Russell 7-locus test). The mechanisms of ESTR mutation induction and applications of this system for monitoring radiation-induced mutation in the mouse germline are discussed.

Animals↗
PubMed2006

[Polymorphic analysis of two Y chromosome short tandem repeat loci in Chinese Chengdu Han population].

OBJECTIVE: To reveal the distribution of genetic polymorphism of two novel Y chromosome short tandem repeat (Y-STR) loci (DYS508, DYS516) in Chinese Chengdu Han population. METHODS: Two Y-STR loci were amplified with PCR. The products of PCR were analyzed with polyacrylamide gel electrophoresis. Each allele of these 2 Y-STR loci was sequenced and the allele ladders were constructed. Alleles of these Y-STR loci were nominated according to recommendations of the International Society of Forensic Genetics (ISFG). RESULTS: Six and 6 alleles were observed in loci DYS508 and DYS516 respectively. The gene diversity of DYS508 and DYS516 was 0.7242 and 0.7931 respectively. The diversity of haplotype for these Y-STR loci was 0.9397. The value of discrimination power and the exclusion chance of paternity for these Y-STR loci were same as the value of haplotype diversity. CONCLUSION: Both Y-STR loci are high genetic polymorphic. They are beneficial to the test of male-female mixtures and paternity identification in forensic science.

Asian People↗
PubMed2004

Development of a pentaplex X-chromosomal short tandem repeat typing system and population genetic studies.

Quadruplex and pentaplex systems for polymerase chain reaction amplification of X-chromosomal short tandem repeats DXS101, HPRTB, DXS8377, DXS981 (STRX1) and DXS6789 were developed for automated profiling of liquid and membrane-bound DNA samples. Chinese, Japanese and Thai populations were typed using a quadruplex system, while German and Philippine populations were analyzed using a five-locus system. Out of 88 meioses studied in Philippine family samples at each locus, a possible one repeat deletion (allele 51 to 50) at DXS8377 was observed in a father-daughter pair. Exact tests performed on genotype data from females in the Philippine, German and Thai populations indicated that these groups conform to Hardy-Weinberg equilibrium. Exact tests for population differentiation indicate significant variations in allele distributions, particularly at loci DXS101, DXS981 and DXS6789. Considered individually, DXS8377 was the most polymorphic and HPRTB the least polymorphic locus in these five populations. When the forensic efficiency of the quadruplex system was calculated, the combined power of discrimination among males (PD(M)) was no lower than 0.998, while among females the combined PD(F) was at least 0.9999 in all populations. The combined power of paternity exclusion was a minimum of 0.998 in trio cases and 0.98 in motherless cases. The addition of locus DXS6789 to the German and Philippine population databases using a pentaplex increased the forensic efficiency of the analysis system.

Asia↗
PubMed2004

Y-chromosome 10 locus short tandem repeat haplotypes in a population sample from Sicily Italy.

This study reports the first data on Y-chromosome-specific short tandem repeat (STR) haplotype frequencies, in the population of the island of Sicily (Italy), based on the combination of alleles at the following 10 Y-chromosome loci DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, and DYS439. In a total of 117 males, 108 unique haplotypes were observed, with 99 of them being singletons. The 10 locus haplotypes generated a diversity value of 0.9987 and discriminatory power (DP) of 92.30%. The data on the seven of the 10 polymorphisms (DYS19; DYS389I; DYS389II; DYS390; DYS391; DYS392 and DYS393) that have been most studied in worldwide populations were compared with similar data from neighboring Mediterranean populations in order to address the question of shared ancestry, gene flow and population affinities. Overall, results indicate Sicily is closest genetically to the mainland Italian population but also with evidence of a significant African component in the male gene pool. These findings are consistent with those obtained from other genetic markers (autosomal and mitochondrial DNA as well as the classical blood groups) and also with the recorded settlement history (either peaceful or due to invasion) of the island.

Chromosomes, Human, Y↗
PubMed2004

Short tandem repeat technology has diverse applications: individual identification, phylogenetic reconstruction and chimerism based post haematopoietic stem cell transplantation graft monitoring.

BACKGROUND: Short Tandem Repeat (STR) loci are widely considered to be effective for variety of applications including forensic applications, phylogenetic reconstruction and chimerism based post Haematopoietic Stem Cell Transplantation (HSCT) graft monitoring. For each application, specific sets of STR loci are used. AIMS: In the present study, we have attempted to use same set of STR loci for varied purposes based on their efficacy and informativity. SETTINGS AND DESIGN: Population and patient based study. MATERIALS AND METHODS: We have analyzed 5 STR loci--vWA, Tho1, FES, F13 and TPOX in 1000 North Indians. All five markers were also analyzed for chimerism based graft monitoring after HSCT in 42 HLA matched pair of patient-donor to predict the outcome of transplantation. STATISTICAL ANALYSIS: The analysis was done for Hardy Weinberg equilibrium (HWE), Heterozygosity, Polymorphism information content (PIC) and Power of Exclusion and Phylogenetic assessment. RESULTS AND CONCLUSIONS: High allelic variability in term of Heterozygosity (0.68-0.76), PIC (0.66-0.74) and high Power of exclusion (0.28-0.38) indicating high forensic utility. The ensuing PC plots finely resolved three basal clusters corresponding to three geo-ethnic groups of African, Orientals, and Caucasians. In post HSCT chimerism analysis, it was found that together these markers were informative in 38 pairs (98%) and were able to predict the chimerism status successfully. There is a possibility that these STR loci along with forensic and phylogenetic importance, can predict the outcome of HSCT successfully.

Gene Frequency↗