SEARCH · PubMed Health

Results for “simple sequence repeat”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 361 records · Page 20Linked to original sources

PubMed2004

Modification of breast cancer risk in young women by a polymorphic sequence in the egfr gene.

The regulation of the epidermal growth factor receptor (egfr) gene in human cancer is not yet fully understood. Recent data on a polymorphic CA repeat located at the 5'-regulatory sequence in intron 1 of the egfr gene [egfr CA simple sequence repeat (SSR) I] point to a possible inheritance of cancer risk associated with the egfr gene. Furthermore, we have detected frequent allelic imbalances restricted to the egfr CA SSR I in breast cancer tissue and nontumorous breast tissue adjacent to invasive and in situ breast cancer representing amplifications. Therefore, we conducted a population-based case-control study to assess the relationship between the egfr polymorphism and breast cancer risk. Cases with a first primary breast cancer by age 50 years and age-matched population controls provided information on known and suspected risk factors. The allelic length of the egfr CA SSR was determined in 616 cases and 1072 population-sampled controls. Genotypes were categorized for analysis by allele length. Multivariate logistic regression was used to compare genotype distributions, accounting for other risk factors, and to investigate gene-environment interactions. We found a modifying effect, albeit no main effect, of the allelic length of the egfr polymorphism on breast cancer risk. The presence of two long alleles (>/==" BORDER="0">19 CA) was associated with a significantly elevated odds ratio (OR) of 10.4 [95% confidence interval (CI), 1.85-58.70] among women with a first-degree family history of breast cancer (P = 0.015 for interaction). The risk increase associated with high red meat consumption (OR, 10.68; 95% CI, 1.57-72.58) and the protective effect of high vegetable intake (OR, 0.07; 95% CI, 0.004-1.07) was also most pronounced among carriers of two long alleles (>/==" BORDER="0">19 CA). The length of the egfr CA SSR may increase the risk for familial breast cancers, and its effect could be modulated by dietary factors.

Adult↗

PubMed1997

Identification and characterization of microsatellites in Norway spruce (Picea abies K.).

Norway spruce (Picea abies) genomic libraries were screened for presence of dinucleotide AC/GT and AG/CT microsatellites (or simple sequence repeats). On average, one (AG)n microsatellite every 194 kb and one (AC)n microsatellite every 406 kb were found. Forty-six positive clones were sequenced and primers flanking 24 AG microsatellites and 12 AC microsatellites diesigned. Only seven (20%) of them produced the expected single-locus polymorphic pattern when used to amplify Norway spruce DNAs. The other primer pairs gave either multiple bands or bad amplification, or a single monomorphic fragment. Such a small proportion of successful primer pairs was attributed to the high level of complexity of the Norway spruce genome. Dot blot analysis of the clones showed that many of them contained repetitive DNA and that those giving the single-locus polymorphic patterns usually corresponded to single-copy sequences. A family of repetitive DNA that contained AG repeats was identified and was present in about 40,000 copies per haploid genome. Simple Mendelian inheritance was observed for all the polymorphisms tested. The average number of alleles was 13, ranging from 6 to 22, and the expected heterozygosity was 0.79 when seven microsatellites were used to genotype a panel of 18 trees representing different populations. Compared with isozymes, microsatellites are about five times more informative and could provide an extremely valuable source of markers for genome mapping and genetic diversity studies.

Alleles↗

PubMed2001

Comparison of multilocus RFLPs and PCR-based marker systems for genetic analysis of the silkworm, Bombyx mori.

The utility of multilocus RFLPs and three PCR-based techniques, Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeat-PCR (ISSR-PCR) and simple sequence repeats (SSRs) for genetic characterization was examined using 13 diverse silkworm strains. All four approaches successfully discriminated the 13 silkworm varieties but differed in the amount of polymorphism detected. The usefulness of each system was examined in terms of number of loci revealed (effective multiplex ratio, EMR) and the amount of polymorphism detected (diversity index, DI). For example, the six multilocus RFLP probes produced 180 products of which 97% were polymorphic; 15 SSR loci gave rise to an average of 8 alleles each, of which 86% were polymorphic. The ISSR-PCR produced 39 fragments of which 76.98% were polymorphic. The highest diversity index was observed for ISSR-PCR (0.957) and the lowest for RAPDs (0.744). The RAPD, ISSR-PCR and RFLP assays clearly separated the diapausing and non-diapausing silkworm varieties. These results are discussed in terms of choice of appropriate marker technology for different aspects of silkworm genome analysis.

Animals↗

PubMed1992

Dinucleotide repeat polymorphism at the apolipoprotein AII locus--phenotyping from peripheral blood and hair.

The genomes of eukaryotes including humans contain very short simple sequence repeats such as (dA-dC)n and (dG-dT)n. Recently, these repeats have been reported to exhibit marked length polymorphism due to wide variation in their reiteration numbers. We report here dinucleotide repeat polymorphism at the apolipoprotein AII locus in Japanese subjects. The informativeness in Japanese was as high as in Caucasians (PIC value and heterozygosity of 0.67 and 0.72, respectively), but their allele frequencies were different with statistical significance. We also discuss the advantages of using dinucleotide repeat polymorphisms in forensic science, demonstrating determination of phenotype from not only a single hair root but also a short hair shaft.

Apolipoprotein A-II↗

PubMed1994

The Friedreich ataxia region: characterization of two novel genes and reduction of the critical region to 300 kb.

Friedreich ataxia is a severe neurodegenerative autosomal recessive disorder of unknown biochemical defect. The Friedreich ataxia locus (FRDA) is tightly linked to the centromeric side of the D9S5 locus. We have used 'exon-trapping' to identify two new genes, approximately 100 and 200 kb centromeric to D9S5, respectively. One gene appears ubiquitously expressed while the other is prominently expressed in muscle. The ubiquitous transcript codes for a protein containing a 20 aa repeat reminiscent of simple repeats found in several ribonucleoproteins. Using the single-strand conformation polymorphism (SSCP) procedure, we searched for mutations in affected patients in the coding sequence of the two genes, as well as in a gene that we had previously identified in the same region. Eight polymorphic DNA changes but no causative mutations were found, suggesting that the genes are not candidates for Friedreich ataxia. The discovery of a simple sequence repeat polymorphism in the most centromeric gene allowed the localization within that gene of the breakpoint of a previously described recombination in a Friedreich ataxia family, therefore excluding the two distal genes from the FRDA region. The lack of causative mutations in the three genes and the position of the recombination further delineate the FRDA locus to a 300 kb interval.

Amino Acid Sequence↗

PubMed2004

[Identification and registration of corn genotypes using molecular markers].

In plant genetics and breeding, second-generation molecular markers allow detailed characterization of plant genotypes. Unique genotypes at ten simple sequence repeat (SSR) loci were established for 40 maize accessions by means of PCR. For every locus, SSR analysis revealed heterozygotes among simple hybrids, which made it possible to identify the parental forms with a high probability of exclusion of nonparental forms. A system was proposed for registration of maize genotypes in the form of genetic formulas reflecting the allelic state of microsatellite loci, in order to catalog, preserve, and effectively employ the existing maize gene pool in breeding.

Base Sequence↗

PubMed1986

The simple repeat poly(dT-dG).poly(dC-dA) common to eukaryotes is absent from eubacteria and archaebacteria and rare in protozoans.

Genomic DNA from a wide variety of prokaryotic and eukaryotic organisms has been assayed for the simple repeat sequence poly(dT-dG).poly(dC-dA) by Southern blotting and DNA slot blot hybridizations. Consistent with findings of others, we have found the simple alternating sequence to be present in multiple copies in all organisms in the animal kingdom (e.g., mammals, reptiles, amphibians, fish, crustaceans, insects, jellyfish, nematodes). The TG element was also found in lower eukaryotes (Saccharomyces cerevisiae, Neurospora crassa, and Dictyostelium discoideum) and at a much lower frequency in protozoans (Oxytricha fallux and Tetrahymena thermophila). The sequence was also repeated in high copy number in a higher plant (Zea mays) as well as at very high levels in a unicellular green alga (Chlamydomonas reinhardi). Although the copy number of the repeat per haploid genome was generally proportional to genome size, there was a greater-than-1,000-fold variation in the number of (TG)25/100-kb genomic DNA. By contrast, no eu-or archaebacterium--including Myxococcus xanthus, whose life cycle is very similar to that of the slime mold Dictyostelium discoideum, and Halobacter volcanii, whose genome contains other repeated sequences--was found whose genomic DNA contained this sequence in detectable amounts. A computer search also failed to find the TG element in human mitochondrial DNA.

Animals↗

PubMed2000

Microsatellite repeats are not randomly distributed within Norway spruce (Picea abies K.) expressed sequences.

A Norway spruce (Picea abies K.) cDNA library obtained from vegetative bud tissue was screened for the presence of (AG)n and (AC)n microsatellite repeats. Ten (AG)n and six (AC)n microsatellites were found, with an average length of 25.5 repeat units. Most of the microsatellites are simple perfect repeats. The microsatellite distribution within the clones is clearly non-random, with different classes of repeats lying in different positions relative to the coding region and in a highly conserved orientation. An estimate of the frequency of dinucleotide microsatellites in expressed regions was obtained, showing that SSRs (simple sequence repeats) are found in genes about 20 times less frequently than in random genomic clones, with (AG)n repeats more frequent than (AC)n repeats. Potential applications of these sequences as expressed region-based molecular markers are shown by developing six SSR markers for the detection of natural variation in Norway spruce populations and testing two of them for the identification of illegitimate progenies from a mapping population.

DNA, Complementary↗

PubMed1999

Discrimination of DNA duplexes with matched and mismatched tandem repeats by T4 endonuclease VII.

A simple in situ method for scoring short tandem DNA repeat length has been developed using T4 endonuclease VII. This method measures tandem repeated simple sequences embedded in unique sequences. Single-stranded loops are formed on duplexes containing mismatched (different) numbers of tandem repeats. No single stranded loops are formed on structures containing matched (identical) numbers of tandem repeats. The matched and mismatched loop structures were distinguished and differentially labeled by enzymatic treatment with T4 endonuclease VII.

Bacteriophage T4↗

PubMed1995

Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size.

The distributions of allele sizes at eight simple-sequence repeat (SSR) or microsatellite loci in chimpanzees are found and compared with the distributions previously obtained from several human populations. At several loci, the differences in average allele size between chimpanzees and humans are sufficiently small that there might be a constraint on the evolution of average allele size. Furthermore, a model that allows for a bias in the mutation process shows that for some loci a weak bias can account for the observations. Several alleles at one of the loci (Mfd 59) were sequenced. Differences between alleles of different lengths were found to be more complex than previously assumed. An 8-base-pair deletion was present in the nonvariable region of the chimpanzee locus. This locus contains a previously unrecognized repeated region, which is imperfect in humans and perfect in chimpanzees. The apparently greater opportunity for mutation conferred by the two perfect repeat regions in chimpanzees is reflected in the higher variance in repeat number at Mfd 59 in chimpanzees than in humans. These data indicate that interspecific differences in allele length are not always attributable to simple changes in the number of repeats.

Alleles↗

PubMed2000

Microsatellites in different eukaryotic genomes: survey and analysis.

We examined the abundance of microsatellites with repeated unit lengths of 1-6 base pairs in several eukaryotic taxonomic groups: primates, rodents, other mammals, nonmammalian vertebrates, arthropods, Caenorhabditis elegans, plants, yeast, and other fungi. Distribution of simple sequence repeats was compared between exons, introns, and intergenic regions. Tri- and hexanucleotide repeats prevail in protein-coding exons of all taxa, whereas the dependence of repeat abundance on the length of the repeated unit shows a very different pattern as well as taxon-specific variation in intergenic regions and introns. Although it is known that coding and noncoding regions differ significantly in their microsatellite distribution, in addition we could demonstrate characteristic differences between intergenic regions and introns. We observed striking relative abundance of (CCG)(n)*(CGG)(n) trinucleotide repeats in intergenic regions of all vertebrates, in contrast to the almost complete lack of this motif from introns. Taxon-specific variation could also be detected in the frequency distributions of simple sequence motifs. Our results suggest that strand-slippage theories alone are insufficient to explain microsatellite distribution in the genome as a whole. Other possible factors contributing to the observed divergence are discussed.

Animals↗

PubMed2026

Evolutionary dynamics of the chloroplast genome in Abutilon (Malvoideae, Malvaceae).

The genus Abutilon Mill. (Malvaceae) comprises approximately 178 species distributed across tropical and subtropical regions, many of which hold significant ornamental, economic, and medicinal value; yet its taxonomic classification remains challenging. In this study, six species were sequenced from herbarium specimens, and the chloroplast (cp.) genomes of ten additional species were assembled de novo from publicly available raw data. Three previously reported cp. genomes were also incorporated to characterise cp. genome structure, identify polymorphic loci, and perform phylogenetic analyses. The cp. genomes ranged from 159,458 to 160,454 bp and exhibited the typical quadripartite structure, with each genome containing 112 unique genes (78 protein-coding, 30 tRNA, and 4 rRNA) that showed conserved content and organisation. These genomes exhibited high similarity in GC content, inverted repeat boundaries, relative synonymous codon usage, amino acid frequencies, and substitution patterns. However, notable variation was observed in the total number of simple sequence repeats, ranging from 70 to 97 per genome. Selection analyses indicated predominant purifying selection, with evidence of episodic positive selection detected in rpoC2, rbcL, and ycf1. Two codons in rbcL were clade-specific and provided phylogenetic signal distinguishing Australian and Old World pantropical species. Nucleotide diversity analysis identified six highly polymorphic intergenic spacers (trnH-psbA, rps19-rpl2, psbT-pbf1, psaC-ndhD, trnR-atpA, and ndhJ-ndhK) that may be suitable for taxonomic studies. The phylogeny from maximum likelihood (ML) and Bayesian inference (BI) resolved two major clades: one comprising an exclusively Australian lineage occurring predominantly in arid and semi-arid environments, and the other a pantropical lineage spanning multiple continents. Abutilon grandifolium was recovered as sister to the remaining sampled Abutilon taxa in both ML and BI analyses, although no biogeographic origin inference can be drawn from this placement pending broader taxon sampling and integration of nuclear genomic data. These findings provide insights into the evolutionary dynamics of the cp. genome in Abutilon and offer a foundational genomic framework for refining Abutilon taxonomy.

Genome, Chloroplast↗

PubMed1993

The topographic organization of repetitive DNA in the human nucleolus.

The nucleolus is a highly specialized nuclear domain where ribosomal DNA (rDNA) is transcribed and preribosomes are assembled. We investigated the molecular organization of the human lymphocyte nucleolus by fluorescence in situ hybridization and confocal laser scanning microscopy and found that transcribed rDNA and nontranscribed ribosomal intergenic spacer (IGS) sequences colocalized to discrete regions frequently on the nucleolar periphery of phytohemagglutinin-stimulated cells. The 5S rDNA gene cluster located on the long arm of chromosome 1 was not regularly associated with the nucleolus. Short interspersed (SINE) Alu elements detected by BLUR 11 were distributed diffusely throughout the nucleus but were severely underrepresented in the nucleolus, whereas an Alu element subcloned from the IGS detected sequences enriched in the nucleolus but sparsely represented in the remainder of the nucleus. In contrast, long interspersed (LINE) Kpn elements, which were located at the nucleolus, were not found in rDNA but were identified outside the ribosomal gene complex on the short arm of at least one acrocentric chromosome. A human chromosome 21-derived alphoid sequence that hybridized to the centromere was localized outside but near the nucleolus, and nonribosomal DNA consisting of a tandemly repeated simple sequence cluster derived from the short arm of chromosome 15 was organized in a compact fashion in the nucleolus. Our study provides new insight into the content and structure of the human nucleolus and illustrates that the unique organization of repetitive DNA on the acrocentric chromosome short arms is reflected in the topographic organization of the nucleolus.

Blotting, Southern↗

PubMed1995

Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome.

BACKGROUND: The study of plant populations is greatly facilitated by the deployment of chloroplast DNA markers. Asymmetric inheritance, lower effective population sizes and perceived lower mutation rates indicate that the chloroplast genome may have different patterns of genetic diversity compared to nuclear genomes. Convenient assays that would allow intraspecific chloroplast variability to be detected are required. RESULTS: Eukaryote nuclear genomes contain ubiquitous simple sequence repeat (microsatellite) loci that are highly polymorphic in length; these polymorphisms can be rapidly typed by the polymerase chain reaction (PCR). Using primers flanking simple mononucleotide repeat motifs in the chloroplast DNA of annual and perennial soybean species, we demonstrate that microsatellites in the chloroplast genome also exhibit length variation, and that this polymorphism is due to changes in the repeat region. Furthermore, we have observed a nonrandom geographic distribution of variations at these loci, and have examined the number and location of such repeats within the chloroplast genomes of other species. CONCLUSIONS: PCR-based analysis of mononucleotide repeats may be used to detect both intraspecific and interspecific variability in the chloroplast genomes of seed plants. The analysis of polymorphic microsatellites thus provides an important experimental tool to examine a range of issues in plant genetics.

Base Sequence↗

PubMed2001

Microsatellite-containing genes from the channel catfish brain: evidence of trinucleotide repeat expansion in the coding region of nucleotide excision repair gene RAD23B.

Expansion of trinucleotide repeats within genes is well known to cause pathological conditions in humans. Here we report a large number of genes containing simple sequence repeats (SSR) from the brain of channel catfish, of which a homologue of the RAD23B gene was found to include (CCA) trinucleotide repeats within its coding region. Because of the importance of the RAD23B gene in the nucleotide excision repair (NER) system, the catfish RAD23B locus was further characterized. The (ACC) repeats encode a polythreonine (T) tract within the catfish RAD23B gene that is absent from the previously cloned human and mouse genes. A survey of the allele variation at the locus indicated the existence of variable microsatellite repeats in the NER RAD23B gene, suggesting that the trinucleotide repeats are expanding or shrinking. The majority of individuals harbor 10 (ACC) repeats within the RAD23B gene, but alleles with 8 and 11 repeats were also detected. The (ACC) repeats are limited to only channel catfish and the closely related blue catfish, but are absent from flathead catfish and the cloned human and mouse genes, suggesting that the microsatellite invasion into the RAD23B gene is a recent event in evolution.

Alleles↗

PubMed1996

Microsatellites: evolution and mutational processes.

Microsatellites (simple sequence repeats) are ubiquitous in eukaryotic genomes, and they are highly polymorphic. They are currently the primary tools for most genetic mapping and for studies comparing the differentiation of human and other mammalian populations. More and more inherited human diseases are now recognized as resulting from mutations in particular microsatellites, and such microsatellite mutations can serve as markers for some cancers. The majority of microsatellite mutational changes probably consist of insertion or deletion of one or a few repeat units through replication slippage, whereas larger (much rarer) changes are important in producing observed allele distributions. Comparisons of microsatellite allele frequencies between humans and chimpanzees suggest that there are constraints on the overall length of microsatellites. Sequence analyses of microsatellites in diverse human and non-human populations indicate that the structure of many repeats may not be as simple as previously believed, in that alleles differ in base composition as well as in repeat length. Single base changes that result in long uninterrupted repeats may lead to increased mutation rates, including the extreme trinucleotide repeat instability responsible for several inherited diseases.

Animals↗

PubMed2000

Pooled genotyping of microsatellite markers in parent-offspring trios.

We studied the extent to which genotyping of simple sequence repeat polymorphisms (SSRs) in pooled DNA samples can be used to predict differences in allele frequencies between parents and their affected offspring. We also developed a simple method of correction for the effects of stutter and differential amplification on the analysis of SSRs in pooled DNA samples based on widely available software. We genotyped individually eight polymorphic microsatellite markers in 110 parent-offspring trios affected with bipolar affective disorder (BP). Analysis of pooled DNA samples predicted very accurately the differences in individual allele frequency distributions between children and their parents. The mean error was <1% (range 0%-3.2%) when marker-specific corrections for stutter and differential amplification were performed. We show that if an individual allele is significantly preferentially transmitted from parents to affected offspring, the difference in the frequency of that allele would be sufficiently large to be detected with pooling in most situations. We propose recommendations for disequilibrium mapping with pooling in which both case-control samples and trios are used in an initial screen and markers are genotyped individually only if they satisfy very relaxed criteria for statistical significance. The use of case-control samples should reduce the false-negative rate as the differences in allele frequencies between cases and controls are twice as high in the presence of the same genetic effect. The use of trios will confirm or reject any suggested differences, thus reducing the false-positive rate that can be created by hidden population stratification.

Bipolar Disorder↗

PubMed2003

A highly polymorphic STR locus in Cannabis sativa.

We report on the first short tandem repeat (STR) locus to be isolated from the plant Cannabis sativa. The STR locus, isolated by a hybrid-capture enrichment procedure, was found to contain a simple sequence repeat motif of 6 bp. This 6 bp repeat motif showed no variation in repeat length but with minor variations in repeat unit sequences. The data show the locus to be highly polymorphic with the number of repeat units ranging from 3 to 40 in 108 screened samples. The observed heterozygosity was approximately 87.04%. The forward and reverse primers (CS1F and CS1R) produced no PCR products in cross-reaction study from 20 species of plants, including highly related species such as Humulus japonicus and Nicotiana tabacum. This hexanucleotide repeat DNA locus could be used to identify cannabis samples and predict their genetic relationship as the test is specific to C. sativa and is highly reproducible.

Alleles↗