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Query: UMLS:C0012872 (DNA marker)
 929 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Recurrence of trisomy 21 was observed in a family in which both parents had a normal chromosome complement. Mosaic trisomy 21 was found in a blood karyotype of the first child, a second pregnancy ended in spontaneous abortion, and a full trisomy 21 was found at prenatal diagnosis of the third pregnancy of this same couple. Although recurrent trisomy 21 may be due to chance, the possibility of germline mosaicism for trisomy 21 in one of the parents has important implications for recurrence risk. Molecular analysis was therefore undertaken in this family to determine the parental origin and the stage of nondisjunction of the extra chromosome 21 in both cases. Although a maternal origin of both instances of trisomy 21 was observed, the mosaic case showed homozygosity for all markers along the duplicated maternal chromosome. Such a finding would normally suggest a postzygotic origin of the trisomy 21. However, the diploid cell line in this same case showed maternal uniparental disomy 21, implying that it was the result of a trisomic conception. We suggest that a somatic nondisjunction in the maternal germ cells is the most likely explanation for these findings. The apparent meiotic II stage of nondisjunction of the nonmosaic trisomy 21 fetus was consistent with maternal mosaicism. A review of the literature for recurrent trisomy 21 cases studied by molecular means, suggests that mosaicism in germ cells may account for more cases than is detected cytogenetically. These results also show that DNA marker analysis does not provide a valuable tool for patient counseling in case of recurrent trisomy 21.
Am J Med Genet 2000 Sep 04
PMID:Recurrent trisomy 21 in a couple with a child presenting trisomy 21 mosaicism and maternal uniparental disomy for chromosome 21 in the euploid cell line. 1098 80

In-situ immunoassays do not allow the detection of the minute numbers of target molecules accessible with in-situ PCR. We developed a highly sensitive method, termed in-situ immuno-PCR, in which the DNA marker was linked to target molecules through an antibody-biotin-avidin bridge and amplified by in-situ PCR. Amplified DNA sequences were detected in situ by hybridisation. This technique may be the only one available to detect minute quantities of biological macromolecules such as proteins, carbohydrates, and lipids in intact cells or tissue sections.
Lancet 2000 Sep 16
PMID:In-situ immuno-PCR to detect antigens. 1104 6

Alu elements, the largest family of interspersed repeats, mobilize throughout the genomes of primates by retroposition. Alu are present in humans in an excess of 500 000 copies per haploid genome. Since some of the insertion alleles have not reached fixation, they remain polymorphic and can be used as biallelic DNA marker systems in investigations of human evolution. In this study, six polymorphic Alu insertional (PAI) loci were used as genetic markers. These markers are thought to be selectively neutral. The presence of these six PAIs was determined by a polymerase chain reaction (PCR)-based assay in 1646 individuals from 47 populations from around the world. Examination of the populations by plotting the first and second principal components, shows the expected segregation of populations according to geographical vicinity and established ethnic affinities. Centroid analysis demonstrated that sub-Sahara populations have experienced higher than average gene flow and/or represent larger populations as compared to groups in other parts of the globe and especially to known inbreed populations. This is consistent with greater heterogeneity and diversity expected of source groups. In addition, maximum likelihood (ML) analyses were performed with these 47 populations and a hypothetical ancestral group lacking the insertion in all six loci. Analysis of our data supports the Out of Africa hypothesis. African populations and admixed groups of African descent formed a single monophyletic group with a basal placement on the tree, which grouped closest to the hypothetical ancestor.
Electrophoresis 2002 Sep
PMID:Phylogenetics of worldwide human populations as determined by polymorphic Alu insertions. 1237 62

The optimum electrophoresis separation conditions of Lambda DNA/EcoR I + Hind III fragments were investigated using the capillary column DB-1 coated with polysiloxane. When hydroxyethylcellulose (HEC, 1.0%, mass percentage) was used as the only non-gel sieving medium solution, some Lambda DNA fragments could not be separated. After polyvinylpyrrolidone (PVP, 2%, mass percentage) being added into the medium solution, PVP and HEC formed a network colloidal solution in buffer, and changed the network hole size of sieving media. In addition, the results showed that PVP could restrain the adsorption of capillary to DNA, reduced electroosmotic flow, and improved the selectivity of separation. For the first time, all fragments of Lambda DNA marker was separated completely under the same condition of mixed sieving medium solution. The method was applied to separate two groups of DNA fragments of halobacterium halobium, and the base pair number was conjectured.
Se Pu 2001 Sep
PMID:[Separation of DNA fragments from halobacterium halobium by capillary electrophoresis with non-gel sieving media]. 1254 41

We report a genetic recombination map for Sorghum of 2512 loci spaced at average 0.4 cM ( approximately 300 kb) intervals based on 2050 RFLP probes, including 865 heterologous probes that foster comparative genomics of Saccharum (sugarcane), Zea (maize), Oryza (rice), Pennisetum (millet, buffelgrass), the Triticeae (wheat, barley, oat, rye), and Arabidopsis. Mapped loci identify 61.5% of the recombination events in this progeny set and reveal strong positive crossover interference acting across intervals of </=50 cM. Significant variations in DNA marker density are related to possible centromeric regions and to probable chromosome structural rearrangements between Sorghum bicolor and S. propinquum, but not to variation in levels of intraspecific allelic richness. While cDNA and genomic clones are similarly distributed across the genome, SSR-containing clones show different abundance patterns. Rapidly evolving hypomethylated DNA may contribute to intraspecific genomic differentiation. Nonrandom distribution patterns of multiple loci detected by 357 probes suggest ancient chromosomal duplication followed by extensive rearrangement and gene loss. Exemplifying the value of these data for comparative genomics, we support and extend prior findings regarding maize-sorghum synteny-in particular, 45% of comparative loci fall outside the inferred colinear/syntenic regions, suggesting that many small rearrangements have occurred since maize-sorghum divergence. These genetically anchored sequence-tagged sites will foster many structural, functional and evolutionary genomic studies in major food, feed, and biomass crops.
Genetics 2003 Sep
PMID:A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. 1450 43

Using a novel multilocus DNA marker analysis method, we studied the population genetic structure of Trypansoma brucei stocks and derived clones isolated from animal and rhodesiense sleeping sickness patients during a national sleeping sickness control program in Mukono district, Uganda. We then performed a cladistic analysis to trace relationships and evolution, using stocks and clones recovered from geographically and temporally matched hosts, including inter-strain comparisons with T. b. gambiense stocks and clones. Our results show that while there was close genetic relatedness among parasite populations from the same geographical region, micro-heterogeneities exist between different stocks. Data are presented that indicate that not every human sleeping sickness focus may be associated with a particular human-infective trypanosome strain responsible for long-term stability of the reference focus. We provide evidence of genetic sub-structuring among type 1 T. b. gambiense stocks, which has potentially important implications for molecular epidemiology of T. brucei.
Infect Genet Evol 2003 Sep
PMID:Population genetic structure and cladistic analysis of Trypanosoma brucei isolates. 1452 80

The progress made in DNA marker technology has been tremendous and exciting. DNA markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. The development of high-density molecular maps which has been facilitated by PCR-based markers, have made the mapping and tagging of almost any trait possible. Marker-assisted selection has the potential to deploy favorable gene combinations for disease control. Comparative studies between incompatible species using these markers has resulted in synteny maps which are useful not only in predicting genome organization and evolution but also have practical application in plant breeding. DNA marker technology has found application in fingerprinting genotypes, in determining seed purity, in systematic sampling of germplasm, and in phylogenetic analysis. This review discusses the use of this technology for the genetic improvement of plants.
Biotechnol Adv 1999 Sep
PMID:DNA markers in plant improvement: an overview. 1453 38

Hybridization between sympatric species provides unique opportunities to examine the contrast between mechanisms that promote hybridization and maintain species integrity. We surveyed hybridization between sympatric coastal steelhead (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki) from two streams in Washington State, Olsen Creek (256 individuals sampled) and Jansen Creek (431 individuals sampled), over a 3-year period. We applied 11 O. mykiss-specific nuclear markers, 11 O. c. clarki-specific nuclear markers and a mitochondrial DNA marker to assess spatial partitioning among species and hybrids and determine the directionality of hybridization. F1 and post-F1 hybrids, respectively, composed an average of 1.2% and 33.6% of the population sampled in Jansen Creek, and 5.9% and 30.4% of the population sampled in Olsen Creek. A modest level of habitat partitioning among species and hybrids was detected. Mitochondrial DNA analysis indicated that all F1 hybrids (15 from Olsen Creek and five from Jansen Creek) arose from matings between steelhead females and cutthroat males implicating a sneak spawning behaviour by cutthroat males. First-generation cutthroat backcrosses contained O. c. clarki mtDNA more often than expected suggesting natural selection against F1 hybrids. More hybrids were backcrossed toward cutthroat than steelhead and our results indicate recurrent hybridization within these creeks. Age analysis demonstrated that hybrids were between 1 and 4 years old. These results suggest that within sympatric salmonid hybrid zones, exogenous processes (environmentally dependent factors) help to maintain the distinction between parental types through reduced fitness of hybrids within parental environments while divergent natural selection promotes parental types through distinct adaptive advantages of parental phenotypes.
Mol Ecol 2004 Sep
PMID:Spatial partitioning and asymmetric hybridization among sympatric coastal steelhead trout (Oncorhynchus mykiss irideus), coastal cutthroat trout (O. clarki clarki) and interspecific hybrids. 1531 88

Dense coverage of the rice genome with polymorphic DNA markers is an invaluable tool for DNA marker-assisted breeding, positional cloning, and a wide range of evolutionary studies. We have aligned drafts of two rice subspecies, indica and japonica, and analyzed levels and patterns of genetic diversity. After filtering multiple copy and low quality sequence, 408,898 candidate DNA polymorphisms (SNPs/INDELs) were discerned between the two subspecies. These filters have the consequence that our data set includes only a subset of the available SNPs (in particular excluding large numbers of SNPs that may occur between repetitive DNA alleles) but increase the likelihood that this subset is useful: Direct sequencing suggests that 79.8% +/- 7.5% of the in silico SNPs are real. The SNP sample in our database is not randomly distributed across the genome. In fact, 566 rice genomic regions had unusually high (328 contigs/48.6 Mb/13.6% of genome) or low (237 contigs/64.7 Mb/18.1% of genome) polymorphism rates. Many SNP-poor regions were substantially longer than most SNP-rich regions, covering up to 4 Mb, and possibly reflecting introgression between the respective gene pools that may have occurred hundreds of years ago. Although 46.2% +/- 8.3% of the SNPs differentiate other pairs of japonica and indica genotypes, SNP rates in rice were not predictive of evolutionary rates for corresponding genes in another grass species, sorghum. The data set is freely available at http://www.plantgenome.uga.edu/snp.
Genome Res 2004 Sep
PMID:An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. 1534 64

Amplified Fragment Length Polymorphism (AFLP) screening is a genome-wide genotyping strategy that has been widely used in plants and bacteria, but little has been reported concerning its use in humans. We investigated if the AFLP procedure could be coupled with high-throughput capillary electrophoresis (CE) for use in tumor diagnosis and classification. Using CE-AFLP, a series of molecular 'fingerprints' were generated for a set of gastric tumor and normal genomic DNA samples. The CE-AFLP procedure was qualitatively and quantitatively robust, and a variety of clustering tools were used to identify a specific DNA marker 'pattern' of 20 features that classified the tumor and normal samples to reasonable degrees of accuracy (Sensitivity 95%, Specificity 80%). The CE-AFLP-based approach also correctly classified 16 tumor samples, which in a previous study had exhibited no detectable genomic aberrations by comparative genome hybridization (CGH). This is the first reported application of CE-AFLP screening in tumor diagnosis. As the procedure is relatively inexpensive and requires minimal prior sequence knowledge and biological material, we suggest that CE-AFLP-based protocols may represent a promising new approach for DNA-based cancer screening and diagnosis.
J Bioinform Comput Biol 2004 Sep
PMID:Identifying patterns of DNA for tumor diagnosis using capillary electrophoresis-amplified fragment length polymorphism (CE-AFLP) screening. 1535 27


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