SEARCH · Search PubMed

Results for “Short tandem repeat”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16Linked to original sources

PubMed2001

A new allele of the short tandem repeat (STR) locus, CSF1PO.

CSF1PO is one of the thirteen core loci used for the CODIS database, and alleles reported for this short tandem repeat (STR) locus contain from 6 to 15 repeats of the tetranucleotide AGAT. Screening of DNA from 76 individuals by gel electrophoresis and silver stain detection yielded one sample that contained a rare, off-ladder CSF1PO allele; an allele larger than CSF1PO15 was detected in a heterozygote that also contained a CSF1PO10 allele. Capillary electrophoresis analysis using GeneScan software demonstrated that the variant allele contained four bases more than CSF1PO15. Following agarose gel electrophoresis to separate the two alleles of the heterozygote and cycle sequencing using dye terminators, sequence analysis showed that the variant, which was otherwise identical to the CSF1PO GenBank sequence, contained exactly 16 AGAT repeats. These results demonstrate the existence of an additional CSF1PO allele, a previously unreported size variant, CSF1PO16.

Alleles↗

PubMed1998

[Application of capillary non-gel sieving electrophoresis to the analysis of short tandem repeat in phenylalanine hydroxylase gene and gene diagnosis of phenylketonuria].

OBJECTIVE: To establish a sensitive, accurate and reliable method for analysis of short tandem repeat (STR) markers for gene diagnosis, capillary electrophoresis (CE) was used for analysis of a polymorphic tetranucleotide (TCTA)n in intron 3 of the phenylalanine hydroxylase (PAH) gene. METHODS: Capillary non-gel sieving electrophoresis (CNGSE) system was used to analyze PCR products of PAH STR among 61 normal Chinese individuals and 6 phenylketonuria (PKU) families. RESULTS: The PCR fragments that differ 4 bp from each other were well separated by CNGSE. Ten alleles were identified, with a continuous distribution from 224 bp to 260 bp. The largest allele (260 bp) was first detected in Chinese population. The alleles frequencies were calculated and PIC is 0.738. The genotypes of PAH STR of total 80 Chinese people were also analyzed and the heterozygosity is 75%. We used this procedure to PAH gene linkage analysis in 6 PKU families, in which pathogenic gene could be affirmed in 3 families, including one case of prenatal diagnosis. CONCLUSIONS: In comparison with denaturing polyacrylamide gel electrophoresis, CE is an accurate, rapid, automatic and with high resolution analytical tool. CE in combination with PCR is a hopeful technique and might be widely used for gene diagnosis of genetic diseases in the future.

Alleles↗

PubMed2005

[Genetic polymorphism of D6S477, D9S1118, D18S865, D19S400, and D20S161 short tandem repeat loci in Qingdao Han population].

OBJECTIVE: To illuminate the preliminary genotype and allele frequency distribution of D6S477 and the other four short tandem repeat(STR) loci in Chinese Han population in Qingdao area and to probe the possibility of their genetic application. METHODS: Two hundred ACD-blood specimens were collected from the unrelated individuals in Qingdao. The DNA samples were extracted with Chelex method and were amplified by polymerase chain reaction technique. The PCR products were analyzed by polyacrylamide gel electrophoresis and displayed using silver staining. RESULTS: The authors obtained the allele frequency distribution and preliminary genotype of D6S477, D9S1118, D18S865, D19S400 and D20S161 STR loci. No deviation from Hardy-Weinberg equilibrium was observed in the five loci. CONCLUSION: All the five loci have higher chance of exclusion and discriminating power, and they will be useful markers for researches in genetics.

Asian People↗

PubMed2005

Genetic variation at nine short tandem repeat loci among islanders of the eastern Adriatic coast of Croatia.

We have analyzed the extent of genetic variation at nine autosomal short tandem repeat loci (D3S1358, VWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820) among six populations from Croatia: five distributed in the islands of the eastern Adriatic coast and one from the mainland. The purpose is to investigate the usefulness of these loci in detecting regional genetic differentiation in the studied populations. Significant heterogeneity among the island and mainland populations is revealed in the distributions of allele frequencies; however, the absolute magnitude of the coefficient of gene differentiation is small but significant. The summary measures of genetic variation, namely, heterozygosity, number of alleles, and allele size variance, do not indicate reduced genetic variation in the island populations compared to the mainland population. In contrast to the two measures of genetic variation, allele size variance and within-locus heterozygosity, the imbalance index (beta) indicates evidence of recent expansion of population sizes in all islands and in the mainland. High mutation rates of the studied loci together with local drift effects are likely explanations for interisland genetic variation and the observed lack of reduced genetic diversity among the island populations.

Alleles↗

PubMed2002

Association study of the short tandem repeat in the 5' upstream region of the cholecystokinin gene with mood disorders in the Japanese population.

We have recently identified a novel polymorphic short tandem repeat (STR) in the 5' upstream region of the cholecystokinin (CCK) gene and reported its association with panic disorder. A linkage study of affective disorder showed a modest linkage signal on the short arm of chromosome 3, the location of the CCK gene. Furthermore, clinical comorbidity of depression and anxiety disorders have been documented. In the present study, we examined a possible association of the CCK STR with mood disorders. We genotyped 165 subjects with mood disorders consisting of unipolar and bipolar disorders and 253 control samples. However, no significant allelic associations were detected between the STR and either the combined mood disorders (P = 0.885), the unipolar group (P = 0.296), or the bipolar group (P = 0.605). These data suggest that the CCK promoter STR is unlikely to have a major genetic effect on the development of mood disorders in the Japanese population.

Adult↗

PubMed1996

Validation of the Applied Biosystems Prism 377 automated sequencer for the forensic short tandem repeat analysis.

The Applied Biosystems (ABI) Prism 377 DNA sequencer has been evaluated in an attempt to increase the throughput of samples for short tandem repeat (STR) analysis, in both forensic casework and the UK National Criminal Intelligence DNA Database. The gel system assessed consisted of 0.2 mm, 4% acrylamide 6 M urea gels, with a well-to-read distance of 36 cm. Gels were run at a constant voltage of 3 kV and constant temperature of 51 degrees C. The run time of our second generation multiplex (SGM) STR system was achieved in less than 2 h. Rigorous validation has been performed on the instrument hardware and software. Complete resolution of 1 base differences was obtained, up to and beyond 350 bases; sizing precision across gels was more than 2-fold higher than the 373A and the sensitivity was increased by one third.

Autoanalysis↗

PubMed1997

Detection and quantitative characterization of artificial extra peaks following polymerase chain reaction amplification of 14 short tandem repeat systems used in forensic investigations.

Detection on automated DNA sequencers of polymerase chain reaction (PCR) products of tetra- and penta-nucleotide short tandem repeat (STR) loci frequently reveals one or more extra peaks along with the true, major allele peak. The most frequent extra peak pattern is a single smaller peak which is one repeat unit shorter than the true allele peak. The existence of such artificial peaks is of special importance when the methods are used for forensic investigations because the artificial extra peaks may simulate true alleles when samples containing mixtures of DNA from different individuals are analyzed. We have investigated the relative levels of formation of extra peaks in 14 STR marker systems. We found that not only the parameters of the PCR but also factors determining the stringency during the post-PCR and pre-electrophoresis handling of samples were of importance for the formation of extra peaks. In our hands, the amounts of extra peaks were reduced (i) if the samples were effectively denatured immediately before loading, (ii) if they contained substantial amounts of formamide (i.e. > or = 50%), and (iii) if the temperature of the electrophoresis gel was above a certain level (i.e. > or = 43 degrees C). The results suggest that extra peaks may in part be due to re-annealing of the PCR product under suboptimal conditions. When efforts had been made to reduce the post-PCR formation of extra peaks, the relative peak areas of the extra peaks ranged from 1% to 17% of those of the true alleles. Similar results were obtained when the PCR products were analyzed under native conditions. Low-copy genome analysis excluded that somatic heterogeneity of the STR regions caused the extra peaks. The systems HumVWA31A, HumFibra/FGA, and D21S11 were especially affected by low-stringency conditions, while Hum-TH01, HumCD4, and D12S391 were virtually unaffected by low-stringency conditions. Replacement of the Taq DNA polymerase with DNA polymerases with lower processivity resulted in higher levels of extra peaks. Our results support the hypothesis that extra peaks are produced due to slipped-strand mispairing.

DNA↗

PubMed1996

Structural variation in the alleles of a short tandem repeat system at the human alpha fibrinogen locus.

This paper reports the sequences of 22 alleles identified at the HumFGA (human alpha fibrinogen) short tandem repeat locus in the British Caucasian and Afro-Caribbean populations. Alleles at the lower end of the observed size range were found to increase in size by 4-bp increments with the repeat unit following the pattern TC(TCTT)n. However, 5 alleles were identified that differed in size by 2 bp from the 4 bp increment as a result of the deletion of a TC dinucleotide, or the addition of a TT dinucleotide, immediately prior to the 1st repeat unit. Alleles at the upper end of the observed size range were found to have a more complex repeat unit structure and also exhibited duplication of both 5' and 3' flanking sequences. A nomenclature for the designation of HumFGA alleles is proposed on the basis of this sequence data.

Base Sequence↗

PubMed1997

Analysis of short tandem repeat polymorphisms in human DNA by matrix-assisted laser desorption/ionization mass spectrometry.

The analysis of an important class of human genetic polymorphisms, short tandem repeats (STRs), using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is described. Several model STR systems have been investigated to evaluate MALDI-TOFMS as a realistic alternative to established electrophoresis procedures, and to develop rapid and generally applicable approaches to polymerase chain reaction (PCR) product purification for MALDI-TOFMS analysis. A purification/preconcentration method for PCR product preparation based on affinity capture of biotin-labeled PCR products is demonstrated to be directly compatible with MALDI-TOFMS analysis. The entire sample preparation for MALDI-TOFMS analysis immediately following PCR amplification from human DNA extracts can be accomplished routinely in under 12 min in a single Eppendorf tube. The simplicity of this approach essentially eliminates the sample preparation bottleneck encountered with MALDI-TOFMS analysis of PCR products using existing methods. Using this method, encouraging genotyping results are demonstrated for the THO1 and TPOxx STR systems using subpicomole quantities that represent a fraction of the original dsDNA from a single PCR reaction. The technique is also demonstrated to facilitate rapid sizing of PCR fragments larger than 200 bases using MALDI-TOFMS. As described here, the analysis of DNA can be accomplished in a manner that takes advantage of the rapid and accurate analysis capabilities offered by MALDI-TOFMS.

DNA↗

PubMed2000

Analysis of short tandem repeat polymorphisms by electrospray ion trap mass spectrometry.

The application of electrospray ionization (ESI) ion trap mass spectrometry (MS) to the analysis of short tandem repeats (STRs or microsatellites) is described. Several equine dinucleotide STR loci were chosen as a model system to evaluate ESI ion trap as a routine instrument for rapid and reliable genoytping. With the use of specific primers STR loci were amplified from different blood samples having allele sizes between 60 and 100 bp. A new purification method based on reversible binding of PCR products to magnetic particles has proven to be directly compatible with ESI ion trap MS analysis. The sense and antisense strands of the PCR products with concentrations of approximately 100 fmol/microliter were measured with a mass accuracy of 0.01%. The simplicity of the purification method and the capability for automated handling together with the precise sizing of PCR products by ESI ion trap MS facilitate the large scale analysis of polymorphic STRs. Moreover, mixtures of different allele length as obtained for heterozygous samples could accurately be assigned as well as a C-->G switch between the two strands of a PCR product.

Animals↗

PubMed2006

Genetics and genomics of core short tandem repeat loci used in human identity testing.

Over the past decade, the human identity testing community has settled on a set of core short tandem repeat (STR) loci that are widely used for DNA typing applications. A variety of commercial kits enable robust amplification of these core STR loci. A brief history is presented regarding the selection of core autosomal and Y-chromosomal STR markers. The physical location of each STR locus in the human genome is delineated and allele ranges and variants observed in human populations are summarized as are mutation rates observed from parentage testing. Internet resources for additional information on core STR loci are reviewed. Additional topics are also discussed, including potential linkage of STR loci to genetic disease-causing genes, probabilistic predictions of sample ethnicity, and desirable characteristics for additional STR loci that may be added in the future to the current core loci. These core STR loci, which form the basis for DNA databases worldwide, will continue to play an important role in forensic science for many years to come.

Alleles↗

PubMed1998

Tetranucleotide short tandem repeat polymorphisms and their possible mode of origin.

An analysis of three autosomal, one X-chromosomal, and one Y-chromosomal tetranucleotide short tandem repeat loci in a large southern German population sample (including family studies) and in several nonhuman primate species revealed remarkable similarities in structure of already known and some newly detected alleles and in allele frequency distributions. These similarities, which are briefly discussed, can best be explained by transspecific evolution, followed by gene-conversion-like mutational events.

Alleles↗

PubMed2005

[Study of genetic polymorphism of 6 short tandem repeat loci in Nongqu Mongolian of inner Mongolia Autonomous Region in China].

OBJECTIVE: To get the genotype and allele frequency distribution of 6 short tandem repeat (STR) loci VWA, FGA, PENTAE, D6S1043, D2S1772, D7S3048 in NongQu Mongolia of China. METHODS: Two hundred and ninety-three unrelated individuals from Nongqu Mongolian were investigated. Polymerase chain reaction and polyacrylamide gel electrophoresis were used. RESULTS: Eighty alleles and 335 genotypes were detected, with frequencies ranging from 0.0017 to 0.2828. All the 6 loci met Hardy-Weinberg equilibrium. The statistical analysis of 6 STR loci showed the heterozygosity (H) >/= 0.7945, the discrimination power (DP) >/= 0.9160, the probability of paternity exclusion (PPE) >/= 0.5919, and the polymorphic information content (PIC) >/= 0.7617. CONCLUSION: These results could serve as valuable data to enrich the Chinese genetic database and play an important role in Chinese population genetic forensic medical application.

Alleles↗

PubMed2006

[Genetic polymorphism of six short tandem repeat loci on the X chromosome in a Han race population in China].

OBJECTIVE: To investigate the alleles and genotype frequencies of 6 short tandem repeat (STR) loci DXS7130, DXS1214, DXS6799, DXS6804, DXS7424 and DXS7133 on the X chromosome in Chinese Han individuals living in Shaanxi province of Northwest China. METHODS: The 6 X-chromosomal STR loci were typed by PCR, denatured polyacylamide gel electrophoresis and silver stain. RESULTS: Among females from Xi'an Han population, the numbers of alleles in the 5 loci (DXS7130, DXS6799, DXS6804, DXS7424 and DXS7133) were detected to be 9, 6, 6, 7, and 7 respectively; the numbers of genotypes were 21, 14, 15, 17 and 12 respectively; and the number of alleles in the DXS1214 was 8. Exact tests demonstrated that genotype frequencies of females had no departure from Hardy-Weinberg equilibrium. CONCLUSION: The six loci of X-chromosomal STRs are appropriate for individual identification, paternity test involving in female child and for study in related disease.

Asian People↗

PubMed2025

Polygenic variants in DNA repair genes are associated with neurodevelopmental disorders, regression and increased burdens of somatic variants and short tandem repeat expansions.

PURPOSE: Developmental regression, characterized by the loss of acquired milestones, occurs in some individuals with neurodevelopmental disorders (NDDs); yet, its molecular basis remains unclear. Studies suggest that DNA damage repair (DDR) genes, such as FAN1, may protect against neurological dysfunction by modulating the somatic stability of short tandem repeats (STRs). This study explores the contribution of DDR gene variants in NDD cases presenting with regression. METHODS: We analyzed 1087 NDD patients, focusing on those carrying variants in DDR genes and presenting regression. We assessed the sensitivity to DNA damage using mitomycin C on lymphoblastoid cells. Somatic variants and STR expansions were evaluated through high-depth short-read genome sequencing. To further investigate the pathogenetic role of STR expansions, we performed long-read genome sequencing on the most severely affected proband. RESULTS: Probands with regression carried multiple DDR gene variants, several within the Fanconi anemia pathway. Their lymphoblastoid cells showed increased sensitivity to mitomycin C-induced cytotoxicity compared with parental and control samples. Probands with severe phenotypes and regression exhibited an accumulation of somatic variants and STR instability, enriched in neurodevelopmental genes. CONCLUSION: Our findings suggest that polygenic DDR gene variants may contribute to developmental regression in NDDs by promoting the accumulation of somatic variants and STR expansions.

Humans↗

PubMed2000

Comparison of automated short tandem repeat and manual variable number of tandem repeat analysis of chimerism in bone marrow transplant patients.

Hematopoietic chimerism can be monitored in bone marrow transplant patients at DNA polymorphic sites. In this study, allele detection and quantification by ethidium bromide-stained agarose gels were compared with automated fluorescent sizing on an artificially mixed system and on chimeric post-transplant whole blood and sorted cell populations. A panel of five variable number of tandem repeats (VNTRs) were amplified and quantified visually on an ethidium bromide-stained gel. The ten short tandem repeats (STRs) were amplified as a multiplex polymerase chain reaction (PCR) and fluorescently detected on a DNA sequencer. Fluorescent band intensities were converted to fluorescent peak areas for allele quantification. Using mixed DNA of different proportions, both STRs and VNTRs showed linearity and appeared equally sensitive. However, case studies showed STRs to be more sensitive (<5%) than VNTRs (<10%). The STRs more accurately quantified the minor DNA component at low concentrations.

Alleles↗

PubMed2024

Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes.

BACKGROUND: Great apes are a global conservation concern, with anthropogenic pressures threatening their survival. Genetic analysis can be used to assess the effects of reduced population sizes and the effectiveness of conservation measures. In humans, autosomal short tandem repeats (aSTRs) are widely used in population genetics and for forensic individual identification and kinship testing. Traditionally, genotyping is length-based via capillary electrophoresis (CE), but there is an increasing move to direct analysis by massively parallel sequencing (MPS). An example is the ForenSeq DNA Signature Prep Kit, which amplifies multiple loci including 27 aSTRs, prior to sequencing via Illumina technology. Here we assess the applicability of this human-based kit in African great apes. We ask whether cross-species genotyping of the orthologs of these loci can provide both individual and (sub)species identification. RESULTS: The ForenSeq kit was used to amplify and sequence aSTRs in 52 individuals (14 chimpanzees; 4 bonobos; 16 western lowland, 6 eastern lowland, and 12 mountain gorillas). The orthologs of 24/27 human aSTRs amplified across species, and a core set of thirteen loci could be genotyped in all individuals. Genotypes were individually and (sub)species identifying. Both allelic diversity and the power to discriminate (sub)species were greater when considering STR sequences rather than allele lengths. Comparing human and African great-ape STR sequences with an orangutan outgroup showed general conservation of repeat types and allele size ranges. Variation in repeat array structures and a weak relationship with the known phylogeny suggests stochastic origins of mutations giving rise to diverse imperfect repeat arrays. Interruptions within long repeat arrays in African great apes do not appear to reduce allelic diversity. CONCLUSIONS: Orthologs of most human aSTRs in the ForenSeq DNA Signature Prep Kit can be analysed in African great apes. Primer redesign would reduce observed variability in amplification across some loci. MPS of the orthologs of human loci provides better resolution for both individual and (sub)species identification in great apes than standard CE-based approaches, and has the further advantage that there is no need to limit the number and size ranges of analysed loci.

Animals↗

PubMed1999

Genealogy reconstruction from short tandem repeat genotypes in an Amazonian population.

We have reconstructed partial genealogies in a sample of 44 SW Amazonian Rondonian Surui, in which 45 dinucleotide short tandem repeat polymorphisms had previously been typed. The genotypes of 488 pairs of individuals having an age difference of 13 or greater were compared, and parentage was excluded if a pair failed to share an allele at more than one locus. In order to test the power of this method, we computed the expected distribution of the number of exclusionary loci for such pairs of unrelated individuals, as well as that for individuals with different degrees of relatedness, and compared it to the observed distribution. We estimated that the pairs compared contained approximately 20% of individual pairs with a first-cousin relation or closer. A total of 25 pairs were identified as possible parent-child. In three instances, we could identify two or more children having a common parent; we computed a relatedness coefficient in order to establish whether the children were full or half sibs. The genealogies inferred show that instances of polygyny and polyandry (or, alternatively, serial mating), in addition to apparent monogamy, can be found among the Surui. The Surui sample can be used as a model for paleoanthropological populations, in which the determination of relatedness can provide further insights into the social structure of past populations. We estimate that, depending on the history of the populations and the degree of inbreeding, 10-20 highly informative nuclear loci should be typed in order to infer genealogies with acceptable confidence.

Adolescent↗