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PubMed2005

Further tests of the association between schizophrenia and single nucleotide polymorphism markers at the catechol-O-methyltransferase locus in an Askenazi Jewish population using microsatellite markers.

Association studies are now primarily being conducted with single nucleotide polymorphisms because they are present everywhere in the genome and can be genotyped in "high throughput" formats. Microsatellite markers have a higher degree of polymorphism than single nucleotide polymorphisms and have been widely used in both linkage and association studies of disease. Polymorphic microsatellite markers with several alleles can readily detect linkage disequilibrium but at any given locus there may be differences between single nucleotide polymorphisms and microsatellites in their power to detect linkage disequilibrium because of the evolutionary history of the locus, especially the rate at which both the single nucleotide polymorphisms and microsatellite polymorphisms have mutated and the number of disease mutations and their history. In the current study, we examined the efficiency of microsatellite markers in association analysis by looking at all existent microsatellite markers in the catechol-O-methyltransferase gene region and by genotyping these microsatellites in a large cohort of schizophrenia patients and healthy controls, a subset of a sample where catechol-O-methyltransferase and schizophrenia were found to be associated. We also estimated the levels of linkage disequilibrium between these microsatellites and the previously reported single nucleotide polymorphisms (within the catechol-O-methyltransferase gene) found to be associated with schizophrenia. A modest allelic association of P=0.041 was found between schizophrenia and the microsatellite marker D22S944, which was not significant, however, when corrected for all microsatellites tested. Nevertheless, significant linkage disequilibrium was found between this marker and the three single nucleotide polymorphisms within the catechol-O-methyltransferase gene that displayed association with the disease in the previously published research on this sample. Significant linkage disequilibrium was also observed between microsatellites up to approximately 300 kb distant from those single nucleotide polymorphisms. Although significant, the extent of linkage disequilibrium in terms of r2 was small (in the order of 0.01).

Base Sequence↗
PubMed1997

Characterization of Alu repeats that are associated with trinucleotide and tetranucleotide repeat microsatellites.

The association of subclasses of Alu repetitive elements with various classes of trinucleotide and tetranucleotide microsatellites was characterized as a first step toward advancing our understanding of the evolution of microsatellite repeats. In addition, information regarding the association of specific classes of microsatellites with families of Alu elements was used to facilitate the development of genetic markers. Sequences containing Alu repeats were eliminated because unique primers could not be designed. Various classes of microsatellites are associated with different classes of Alu repeats. Very abundant and poly(A)-rich microsatellite classes (ATA, AATA) are frequently associated with an evolutionarily older subclass of Alu repeats, AluSx, whereas most of GATA and CA microsatellites are associated with a recent Alu subfamily, AluY. Our observations support all three possible mechanisms for the association of Alu repeats to microsatellites. Primers designed using a set of sequences from a particular microsatellite class showed higher homology with more sequences of that class than probes designed for other classes. We developed an efficient method of prescreening GGAA and ATA microsatellite clones for Alu repeats with probes designed in this study. We also showed that Alu probes labeled in a single reaction (multiplex labeling) could be used efficiently for prescreening of GGAA clones. Sequencing of these prescreened GGAA microsatellites revealed only 5% Alu repeats. Prescreening with primers designed for ATA microsatellite class resulted in the reduction of the loss of markers from approximately 50% to 10%. The new Alu probes that were designed have also proved to be useful in Alu-Alu fingerprinting.

Animals↗
PubMed1998

Telomerase activity and microsatellite instability in colorectal cancer and adenoma.

In order to examine their roles in carcinogenesis or in progression of colorectal carcinoma, we investigated telomerase activity and microsatellite instability in 67 non-familial colorectal cancers and in 18 adenomas. The incidence of detectable telomerase activity increased from 22% of normal colorectal mucosas adjacent to carcinoma, and 33% of adenomas, to 75% of carcinomas. On the other hand, the incidence of detectable microsatellite instability in carcinomas (30%) was almost the same as in adenomas (22%). No significant correlation was detected in the incidence of telomerase activity and microsatellite instability in carcinomas or in adenomas. Moreover, the incidence of telomerase activity and microsatellite instability did not increase during the progression of carcinomas. These results indicate that telomerase activity and microsatellite instability are independent events in colorectal carcinogenesis, and that telomerase activity and microsatellite instability are not correlated with the progression of colorectal carcinoma. However, in 13 multiple cancers, the incidence of telomerase activity (92%) and the incidence of microsatellite instability (54%) was higher than that of telomerase activity (70%) and that of microsatellite instability (24%) in 54 sporadic cancers. Moreover, the incidence of telomerase activity and that of microsatellite instability in adenomas with carcinomas (45% and 36% respectively) was higher than that of telomerase activity and microsatellite instability in adenomas without carcinomas (14% and 0% respectively). These results indicate that telomerase activity and microsatellite instability may play an important role in multicentric carcinogenesis in colorectal carcinoma.

Adenoma↗
PubMed1999

Long tomato microsatellites are predominantly associated with centromeric regions.

Microsatellites as genetic markers are used in many crop plants. Major criteria for their usability as molecular markers include that they are highly polymorphic and evenly spread throughout a genome. In tomato, it has been reported that long arrays of tetranucleotide microsatellites containing the motif GATA are highly clustered around the centromeres of all chromosomes. In this study, we have isolated tomato microsatellites containing long arrays (> 20 repeats) of the dinucleotide motifs GA, GT, AT, as well as GATA, assessed their variability within Lycopersicon esculentum varieties and mapped them onto a genetic map of tomato. The investigated microsatellite markers exhibited between 1 and 5 alleles in a diverse set of L. esculentum lines. Mapping of the microsatellites onto the genetic map of tomato demonstrates that, as previously shown, GATA microsatellites are highly clustered in the regions of the tomato centromeres. Interestingly, the same centromeric location was now found for long dinucleotide microsatellite markers. Because of this uneven distribution, genetic mapping of the entire tomato genome using long dinucleotide microsatellites will be very difficult to achieve and microsatellite markers with shorter arrays of microsatellites could be more suitable for mapping experiments albeit their lower level of polymorphism. Some microsatellite markers described in this study might provide a useful tool to study the molecular structure of tomato centromeric regions and for variety identification.

Base Sequence↗
PubMedDate not supplied

Two subtypes in colorectal mucinous carcinoma in relation to microsatellite instability.

BACKGROUND/AIMS: Although some investigators have attempted to divide colorectal mucinous adenocarcinoma into two entities, there have been few reports describing microsatellite instability of each subtype. In this study, we elucidated the clinicopathological features of subtypes in mucinous carcinoma, especially the relationship between microsatellite instability and each subtype. METHODOLOGY: The present study included 33 patients with mucinous colorectal cancer. The 33 patients were classified into two groups; the papillotubular type group (n = 22) and the mucocellular type group (n = 11). The clinicopathological aspects and microsatellite instability were examined. RESULTS: Significant differences were found between the papillotubular type group and the mucocellular type group regarding the following findings such as lymphatic invasion, lymph node metastasis, peritoneal metastasis, and Dukes stage. The mucocellular type group had 2 cases with high-frequency microsatellite instability, 7 cases with low-frequency microsatellite instability and 2 cases with microsatellite stability. Conversely, the papillotubular type group included 12 cases with high-frequency microsatellite instability, 3 cases with low-frequency microsatellite instability and 7 cases with microsatellite stability. The ratio of cases with high-frequency microsatellite instability in the mucocellular type group (18.1%) was significantly lower than that of the papillotubular type group (54.5%) (P = 0.0463). The 5-year survival rate of the mucocellular type group (29.1%) was significantly lower than that of the papillotubular type group (70.3%) (P = 0.0282). CONCLUSIONS: Colorectal mucinous carcinoma needs to be classified into two groups, papillotubular type and mucocellular type, because of significant differences in microsatellite instability and patients' survival.

Adenocarcinoma, Mucinous↗
PubMedDate not supplied

Molecular patterns of nuclear and mitochondrial microsatellite alterations in breast tumors.

The widespread distribution of microsatellite sequences within the human genome has allowed researchers to identify alternative patterns of microsatellite alterations in cancer cells. Among them, aneuploid patterns of nuclear microsatellites, pseudo-diploid microsatellite instability patterns, and also patterns of microsatellite instability within the mitochondrial genome. In this context, while aneuploid patterns of multiple genomic gains and losses had already been described in breast tumors, data on nuclear microsatellite instability still remain controversial and limited data on mitochondrial instability are available. In order to clarify this, we undertook an extensive analysis of nuclear and mitochondrial microsatellite alterations in breast ductal adenocarcinomas, stratified by grades. No instability was detected in any of the 40 dinucleotide microsatellites analysed nor in bat26 and APDelta3 mononucleotide repeats, clearly concluding that microsatellite instability is not a feature of ductal breast tumorigenesis. Instead, microsatellites defined a clear pattern of aneuploid genomic gains and losses among which, losses of BRCA1 at D17S855 and gains of plakoglobin at D17S846 significantly associated to grade III tumors and poor prognosis. On the other hand, mitochondrial instability at the transcription control region was also detected in 10.8% of cases. None of the new mitochondrial variants was found in the normal tissue counterparts, confirming that these new variants arise as sporadic somatic mutations in the tumor cells. Also, no association was found between heteroplasmy in the normal tissue and mitochondrial instability in the tumors. We therefore suggest that these new variants arise in tumors as a consequence of the progressive accumulation of slippage somatic mutations and the intrinsic instability of these microsatellite sequences. Finally, our results also confirm that mitochondrial instability does not associate with nuclear MSI.

Adult↗
PubMed1995

Abundance, variability and chromosomal location of microsatellites in wheat.

The potential of microsatellite sequences as genetic markers in hexaploid wheat (Triticum aestivum) was investigated with respect to their abundance, variability, chromosomal location and usefulness in related species. By screening a lambda phage library, the total number of (GA)n blocks was estimated to be 3.6 x 10(4) and the number of (GT)n blocks to be 2.3 x 10(4) per haploid wheat genome. This results in an average distance of approximately 270 kb between these two microsatellite types combined. Based on sequence analysis data from 70 isolated microsatellites, it was found that wheat microsatellites are relatively long containing up to 40 dinucleotide repeats. Of the tested primer pairs, 36% resulted in fragments with a size corresponding to the expected length of the sequenced microsatellite clone. The variability of 15 microsatellite markers was investigated on 18 wheat accessions. Significantly, more variation was detected with the microsatellite markers than with RFLP markers with, on average, 4.6 different alleles per microsatellite. The 15 PCR-amplified microsatellites were further localized on chromosome arms using cytogenetic stocks of Chinese Spring. Finally, the primers for the 15 wheat microsatellites were used for PCR amplification with rye (Secale cereale) and barley accessions (Hordeum vulgare, H. spontaneum). Amplified fragments were observed for ten primer pairs with barley DNA and for nine primer pairs with rye DNA as template. A microsatellite was found by dot blot analysis in the PCR products of barley and rye DNA for only one primer pair.

Base Sequence↗
PubMed1994

Genomic instability of microsatellite repeats and its association with the evolution of chronic myelogenous leukemia.

Tumorigenesis has been shown to proceed through a series of genetic alterations involving protooncogenes and tumor-suppressor genes. Investigation of genomic instability of microsatellites has indicated a new mechanism for human carcinogenesis in hereditary nonpolyposis colorectal cancer and sporadic cancer and this instability has been shown to be related to inherited predisposition to cancer. This study was conducted to determine whether such microsatellite instability is associated with the evolution of chronic myelogenous leukemia (CML) to the blast crisis. Nineteen CML patients clinically progressing from the chronic phase to accelerated phase or blast crisis and 20 other patients in the CML chronic phase were studied. By polymerase chain reaction assay, DNAs for genomic instability in five separate microsatellites in chromosome arms 5q (Mfd27), 17p (Mfd41), 18q (DCC), 3p (CI3-9), and 8p (LPL) were examined. Differences in unrelated microsatellites of chronic and blastic phase DNAs in 14 of 19 patients (73.7%) were demonstrated. Somatic instability in five microsatellites, Mfd27, Mfd41, DCC, CI3-9, and LPL, was detected in 2 of 19 (10.5%), 8 of 19 (42.1%), 11 of 19 (57.9%), 4 of 17 (23.5%), and 4 of 17 (23.5%) cases. In 10 of 19 cases (52.6%), genetic instability in at least two of five microsatellites was observed and was categorized as replication error (RER+) phenotype. CML evolution cases with myeloid, lymphoid, and mixed phenotypes and the blast crisis and accelerated phase showed somatic instability in a number of microsatellites. No alterations in leukemic cells at the chronic phase could be detected in any microsatellites. These data indicate instability of microsatellites (RER+) but not familial predisposition to possibly be a late genetic event in the evolution of CML to blast crisis. In the microsatellite of the DCC gene, complicated alterations in band patterns caused by instability as well as loss of heterozygosity (LOH) were observed in 13 of 19 cases (68.4%): instability in 9 cases, instability plus LOH in 2 cases, and only LOH in 2 cases. These highly frequent alterations in microsatellites, including instability and LOH, suggesting that secondary events due possibly to loss of fidelity in replication and repair machinery may be significantly associated with CML evolution.

Adult↗
PubMed2026

Genomic distribution characteristics and interspecific differences of microsatellite landscapes in Felidae.

BACKGROUND: Microsatellites within genomes play crucial roles in regulating gene expression, DNA replication, and chromosomal structure and function. Analyzing the composition and distribution patterns of microsatellites in closely related species not only reveals their evolutionary dynamics and adaptive mechanisms but also provides essential technical support for applications in genetic breeding, species conservation, and disease research. As one of the world's most captivating animal groups, the landscape patterns of microsatellites across feline genomes remain to be systematically characterized. RESULTS: This study utilized high-quality genomic data to conduct a systematic comparative analysis of microsatellite landscape distribution patterns across the genomes of 13 felid species. The findings revealed that microsatellite abundance and distribution exhibit species-specific characteristics, with a non-random genomic distribution and a negative correlation between microsatellite abundance and repeat length. The predominant distribution pattern followed the sequence: single > double > quadruple > triple > quintuple > sextuple nucleotide repeats. Microsatellite abundance peaked in intergenic regions, whereas trinucleotide repeats were more prevalent within exons. Coding regions showed a marked preference for trinucleotide and hexanucleotide repeats. Enrichment analysis of GO and KEGG pathways indicated that coding sequences containing microsatellites were primarily involved in transcription and translation processes. CONCLUSIONS: Our study elucidates the distribution patterns and characteristics of microsatellites across diverse feline species, providing significant insights into their evolutionary mechanisms and functional roles. Furthermore, these findings establish a valuable reference and foundational dataset for the future development of high-quality, species-specific microsatellite markers in felids.

Animals↗
PubMed2005

The role of microsatellites as a prognostic factor in primary malignant melanoma.

OBJECTIVE: To determine the impact of microsatellites as a prognostic factor in primary cutaneous melanoma. DESIGN: Retrospective cohort study. SETTING: Tertiary referral center. Patients A total of 504 patients with a history of primary melanoma observed for 2 years or having experienced a first relapse. MAIN OUTCOME MEASURES: Overall survival (OS) and relapse-free survival (RFS). RESULTS: Forty-five patients had evidence of microsatellites in their primary melanoma. Presence of microsatellites significantly correlated with the presence of several other histologic high-risk factors such as tumor thickness, ulceration, Clark level, vascular factors, and mitotic rate. Univariate analysis demonstrated decreased RFS and OS in patients with microsatellites. Presence of microsatellites was associated with increased locoregional metastasis but not distant metastasis. In multivariate analysis, with the inclusion of 6 other clinical and histologic factors, presence of microsatellites was a significant predictor of RFS but not OS. Patients with clinical macrosatellites had a trend toward worsening OS compared with those with microsatellites. CONCLUSIONS: The presence of microsatellites is intimately tied to other markers of melanoma aggressiveness. Microsatellites appear to predict locoregional relapse and RFS but neither distant metastasis nor OS. These results may have implications for patient care as well as the inclusion of microsatellites in stage III of the current classification.

Analysis of Variance↗
PubMed2005

Microsatellite distribution and indication for locoregional therapy in small hepatocellular carcinoma.

BACKGROUND: Intrahepatic disease recurrence is observed frequently after locoregional therapies for patients with hepatocellular carcinoma (HCC). However, the indication for locoregional therapy is still unclear. To clarify the indication for locoregional therapy for small HCC tumors, the authors measured the distance of microsatellites from the main tumor and analyzed the relation between this distance and clinicopathologic factors. METHODS: The authors retrospectively analyzed 100 patients with small HCC tumors (</= 5 cm in dimension) treated by curative hepatectomy. A microsatellite was defined as invasion into the portal vein or intrahepatic metastasis, and the distance from the main tumor to the most distant microsatellite was determined under light microscopy. The current study investigated the relation between microsatellite distance (0 mm if none present, </= 5 mm, and > 5 mm) and clinicopathologic factors, as well as overall and disease-free survival rates after hepatectomy. RESULTS: Of the 100 patients, 46 had microsatellites with a mean distance of 9.9 mm (median, 5.0 mm). Of the clinicopathologic factors investigated, tumor grade and preoperative alpha-fetoprotein level significantly correlated with the presence of a microsatellite. Tumor size and distance to the microsatellite were significantly correlated. All but 1 tumor associated with a microsatellite distance > 5 mm was a high-grade tumor > 25 mm in greatest dimension. The overall survival rate of patients with a microsatellite distance of > 5 mm was lower than that of patients with a microsatellite distance < 5 mm. CONCLUSIONS: Locoregional therapy, including limited resection and ablation therapies, was appropriate for patients with low-grade HCC tumors or with tumors < 25 mm in diameter.

Adult↗
PubMed2002

Microsatellite DNA and RAPD fingerprinting, identification and genetic relationships of hybrid poplar (Populus x canadensis) cultivars.

Microsatellite DNA markers of ten SSR loci and 248 RAPD loci (resolved by 26 RAPD primers) were used for DNA fingerprinting and differentiation of 17 widely grown Populus x canadensis syn. Populus x euramericana (interspecific Populus deltoides x Populus nigra hybrids) cultivars ("Baden 431", "Blanc du Poitou", "Canada Blanc", "Dorskamp 925", "Eugenei", "Gelrica", "Grandis", "Heidemij", "I-55/56", "I-132/56", "I-214", "Jacometti", "Ostia", "Regenerata", "Robusta", "Steckby" and "Zurich 03/3"), and determination of their genetic interrelationships. Informativeness of microsatellite and RAPD markers was also evaluated in comparison with allozyme markers for clone/cultivar identification in P. x canadensis. High microsatellite DNA and RAPD genetic diversity was observed in the sampled cultivars. All of the 17 P. x canadensis cultivars could be differentiated by their multilocus genotypes at four SSR loci, and were heterozygous for their parental species-specific alleles at the PTR6 SSR locus. Except for "Canada Blanc" and "Ostia", which had identical RAPD patterns, all cultivars could also be differentiated by RAPD fingerprints produced by each of the two RAPD primers, OPA07 and OPB15. For microsatellites, the mean number of alleles, polymorphic information content, observed heterozygosity, observed number of genotypes and the number of cultivars with unique genotypes per locus was 5.2, 0.64, 0.67, 5.7 and 2.2, respectively. For RAPD markers, the number of haplotypes per locus, and the number of cultivars with unique RAPD profiles per locus were 1.06 and 0.72, respectively. Overall, microsatellite DNA markers were the most informative for DNA fingerprinting of P. x canadensis cultivars. On the per locus basis, microsatellites were about six-times more informative than RAPD markers and about nine-times more informative than allozyme markers. However, on the per primer basis, RAPD markers were more informative. The UPGMA cluster plots separated the 17 cultivars into two major groups based on their microsatellite genotypic similarities, and into three major groups based on their RAPD fragment similarities. Both the microsatellite and RAPD data suggest that the cultivars "Baden 431", "Heidemij", "Robusta" and "Steckby" are genetically closely related. The inter-cultivar genetic relationships from microsatellite DNA and RAPD markers were consistent with those observed from allozyme markers, and were in general agreement with their speculated origin. Microsatellite DNA and RAPD markers could be used for clone and cultivar identification, varietal control and registration, and stock handling in P. x canadensis.

Alleles↗
PubMed2003

Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.).

A total of 150 microsatellite markers developed for common bean ( Phaseolus vulgaris L.) were tested for parental polymorphism and used to determine the positions of 100 genetic loci on an integrated genetic map of the species. The value of these single-copy markers was evident in their ability to link two existing RFLP-based genetic maps with a base map developed for the Mesoamerican x Andean population, DOR364 x G19833. Two types of microsatellites were mapped, based respectively on gene-coding and anonymous genomic-sequences. Gene-based microsatellites proved to be less polymorphic (46.3%) than anonymous genomic microsatellites (64.3%) between the parents of two inter-genepool crosses. The majority of the microsatellites produced single bands and detected single loci, however four of the gene-based and three of the genomic microsatellites produced consistent double or multiple banding patterns and detected more than one locus. Microsatellite loci were found on each of the 11 chromosomes of common bean, the number per chromosome ranging from 5 to 17 with an average of ten microsatellites each. Total map length for the base map was 1,720 cM and the average chromosome length was 156.4 cM, with an average distance between microsatellite loci of 19.5 cM. The development of new microsatellites from sequences in the Genbank database and the implication of these results for genetic mapping, quantitative trait locus analysis and marker-assisted selection in common bean are described.

Base Sequence↗
PubMed2006

Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.).

Paucity of polymorphic molecular markers in chickpea (Cicer arietinum L.) has been a major limitation in the improvement of this important legume. Hence, in an attempt to develop sequence-tagged microsatellite sites (STMS) markers from chickpea, a microsatellite enriched library from the C. arietinum cv. Pusa362 nuclear genome was constructed for the identification of (CA/GT)n and (CT/GA)n microsatellite motifs. A total of 92 new microsatellites were identified, of which 74 functional STMS primer pairs were developed. These markers were validated using 9 chickpea and one C. reticulatum accession. Of the STMS markers developed, 25 polymorphic markers were used to analyze the intraspecific genetic diversity within 36 geographically diverse chickpea accessions. The 25 primer pairs amplified single loci producing a minimum of 2 and maximum of 11 alleles. A total of 159 alleles were detected with an average of 6.4 alleles per locus. The observed and expected heterozygosity values averaged 0.32 (0.08-0.91) and 0.74 (0.23-0.89) respectively. The UPGMA based dendrogram was able to distinguish all the accessions except two accessions from Afghanistan establishing that microsatellites could successfully detect intraspecific genetic diversity in chickpea. Further, cloning and sequencing of size variant alleles at two microsatellite loci revealed that the variable numbers of AG repeats in different alleles were the major source of polymorphism. Point mutations were found to occur both within and immediately upstream of the long tracts of perfect repeats, thereby bringing about a conversion of perfect motifs into imperfect or compound motifs. Such events possibly occurred in order to limit the expansion of microsatellites and also lead to the birth of new microsatellites. The microsatellite markers developed in this study will be useful for genetic diversity analysis, linkage map construction as well as for depicting intraspecific microsatellite evolution.

Alleles↗
PubMed2006

Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana.

The level of variation and the mutation rate were investigated in an empirical study of 244 chloroplast microsatellites in 15 accessions of Arabidopsis thaliana. In contrast to SNP variation, microsatellite variation in the chloroplast was found to be common, although less common than microsatellite variation in the nucleus. No microsatellite variation was found in coding regions of the chloroplast. To evaluate different models of microsatellite evolution as possible explanations for the observed pattern of variation, the length distribution of microsatellites in the published DNA sequence of the A. thaliana chloroplast was subsequently used. By combining information from these two analyses we found that the mode of evolution of the chloroplast mononucleotide microsatellites was best described by a linear relation between repeat length and mutation rate, when the repeat lengths exceeded about 7 bp. This model can readily predict the variation observed in non-coding chloroplast DNA. It was found that the number of uninterrupted repeat units had a large impact on the level of chloroplast microsatellite variation. No other factors investigated--such as the position of a locus within the chromosome, or imperfect repeats--appeared to affect the variability of chloroplast microsatellites. By fitting the slippage models to the Genbank sequence of chromosome 1, we show that the difference between microsatellite variation in the nucleus and the chloroplast is largely due to differences in slippage rate.

Arabidopsis↗
PubMed2004

Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus).

Gene-derived markers are pivotal to the analysis of genome structure, organization, and evolution and necessary for comparative genomics. However, gene-derived markers are relatively difficult to develop. This project utilized the genomic resources of channel catfish expressed sequence tags (ESTs) to identify simple sequence repeats (SSRs), or microsatellites. It took the advantage of ESTs for the establishment of gene identities, and of microsatellites for the acquisition of high polymorphism. When microsatellites are tagged to genes, the microsatellites can then be used as gene markers. A bioinformatic analysis of 43,033 ESTs identified 4855 ESTs containing microsatellites. Cluster analysis indicated that 1312 of these ESTs fell into 569 contigs, and the remaining 3534 ESTs were singletons. A total of 4103 unique microsatellite-containing genes were identified. The dinucleotide CA/TG and GA/TC pairs were the most abundant microsatellites. AT-rich microsatellite types were predominant among trinucleotide and tetranucleotide microsatellites, consistent with our earlier estimation that the catfish genome is highly AT-rich. Our preliminary results indicated that the majority of the identified microsatellites were polymorphic and, therefore, useful for genetic linkage mapping of catfish. Mapping of these gene-derived markers is under way, which will set the foundation for comparative genome analysis in catfish.

Animals↗
PubMed2004

Microsatellite instability and expression of hMLH1 and hMSH2 proteins in ovarian endometrioid cancer.

Microsatellite instability and loss of heterozygosity has been implicated in ovarian carcinogenesis. The reported frequency of microsatellite instability in human ovarian cancer varies significantly owing to the use of heterogeneous tumor histotypes and various microsatellite markers in different laboratories. In this study, we determined the frequency of microsatellite instability in 74 ovarian endometrioid carcinomas using four microsatellite markers (BAT25, BAT26, D5S346, D17S250), and examined hMLH1 and hMSH2 protein expression. In all, 20% of the tumors were microsatellite instability high (two or more markers showing instability) and 12% were microsatellite instability low (one marker showed instability). Loss of hMLH1 and/or hMSH2 expression was found in nine of 15 microsatellite instability-high tumors. The microsatellite instability-high phenotype tended to occur more frequently in low-grade tumors (P=0.053), but did not correlate with clinical stage. Totally, 38% of cases also displayed loss of heterozygosity at D17S250; this loss of heterozygosity was associated with high clinical stage (P=0.097). Our results indicate that both microsatellite and loss of heterozygosity at D17S250 are involved in the development of ovarian endometrioid carcinoma.

Adaptor Proteins, Signal Transducing↗
PubMed2003

Differential expression of DOC-1 in microsatellite-unstable human colorectal cancer.

The precise genetic mechanism of malignant transformation in DNA mismatch repair deficient, microsatellite-unstable colorectal cancer (CRC) has yet to be elucidated. We employed cDNA microarray to identify patterns of gene expression among CRC cell lines and to compare directly lines with and without microsatellite instability. This study was undertaken to test the hypothesis that microsatellite-unstable CRC cell lines demonstrate specific patterns of gene expression that differ significantly from those observed among microsatellite-stable CRC. Multiple differential expression patterns were identified. Genes demonstrating differential expression included deleted-in-oral-cancer-1 (DOC-1), a highly conserved growth suppressor. DOC-1 expression correlated with microsatellite status, with significantly decreased expression in microsatellite-unstable cell lines and constitutive expression in microsatellite-stable cell lines. We also observed alterations in the biologic behavior of p12(DOC-1)-deficient cell lines, with increased S phase and decreased apoptosis compared to microsatellite-stable (DOC-1+) cell lines. Transfection of p12(DOC-1) into SW48, which lacks p12(DOC-1) expression, resulted in cell cycle and apoptosis profiles similar to other p12(DOC-1)+ cell lines. These results support the hypothesis that microsatellite-unstable CRC is characterized by novel patterns of gene expression different from those associated with microsatellite-stable CRC, and demonstrate that p12(DOC-1) has tumor suppressor potential in colon epithelial cells.

Apoptosis↗