Готові списки джерел за темами / High-density genotyping microarray

Добірка наукової літератури з теми "High-density genotyping microarray"

Автор: Grafiati

Опубліковано: 10 грудня 2022

Оновлено: 28 січня 2023

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Статті в журналах з теми "High-density genotyping microarray"

Huang, Joe Xi, Dorothy Mehrens, Rick Wiese, Sandy Lee, Sun W. Tam, Steve Daniel, James Gilmore, Michael Shi, and Deval Lashkari. "High-Throughput Genomic and Proteomic Analysis Using Microarray Technology." Clinical Chemistry 47, no. 10 (October 1, 2001): 1912–16. http://dx.doi.org/10.1093/clinchem/47.10.1912.

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Abstract Background: High-density microarrays are ideally suited for analyzing thousands of genes against a small number of samples. The next step in the discovery process is to take the resulting genes of interest and rapidly screen them against thousands of patient samples, tissues, or cell lines to further investigate their involvement in disease risk or the response to medication. Methods: We used a microarray technology platform for both single-nucleotide polymorphisms (SNPs) and protein expression. Each microarray contains up to 250 elements that can be customized for each application. Slides contained either a 16- or 96-microarray format (4000–24 000 elements per slide), allowing the corresponding number of samples to be rapidly processed in parallel. Results: Results for SNP genotyping and protein profiling agreed with results of restriction fragment length polymorphism (RFLP) analysis or ELISA, respectively. Genotyping analyses, using the microarray technology, on large sample sets over multiple polymorphisms in the NAT2 gene were in full agreement with traditional methodologies, such as sequencing and RFLP analysis. The multiplexed protein microarray had correlation coefficients of 0.82–0.99 (depending on analyte) compared with ELISAs. Conclusions: The integrated microarray technology platform is adaptable and versatile, while offering the high-throughput capabilities needed for drug development and discovery applications.

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Sansaloni, Carolina P., César D. Petroli, Jason Carling, Corey J. Hudson, Dorothy A. Steane, Alexander A. Myburg, Dario Grattapaglia, René E. Vaillancourt, and Andrzej Kilian. "A high-density Diversity Arrays Technology (DArT) microarray for genome-wide genotyping in Eucalyptus." Plant Methods 6, no. 1 (2010): 16. http://dx.doi.org/10.1186/1746-4811-6-16.

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Dacheux, Laurent, Nicolas Berthet, Gabriel Dissard, Edward C. Holmes, Olivier Delmas, Florence Larrous, Ghislaine Guigon, et al. "Application of Broad-Spectrum Resequencing Microarray for Genotyping Rhabdoviruses." Journal of Virology 84, no. 18 (July 7, 2010): 9557–74. http://dx.doi.org/10.1128/jvi.00771-10.

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ABSTRACT The rapid and accurate identification of pathogens is critical in the control of infectious disease. To this end, we analyzed the capacity for viral detection and identification of a newly described high-density resequencing microarray (RMA), termed PathogenID, which was designed for multiple pathogen detection using database similarity searching. We focused on one of the largest and most diverse viral families described to date, the family Rhabdoviridae. We demonstrate that this approach has the potential to identify both known and related viruses for which precise sequence information is unavailable. In particular, we demonstrate that a strategy based on consensus sequence determination for analysis of RMA output data enabled successful detection of viruses exhibiting up to 26% nucleotide divergence with the closest sequence tiled on the array. Using clinical specimens obtained from rabid patients and animals, this method also shows a high species level concordance with standard reference assays, indicating that it is amenable for the development of diagnostic assays. Finally, 12 animal rhabdoviruses which were currently unclassified, unassigned, or assigned as tentative species within the family Rhabdoviridae were successfully detected. These new data allowed an unprecedented phylogenetic analysis of 106 rhabdoviruses and further suggest that the principles and methodology developed here may be used for the broad-spectrum surveillance and the broader-scale investigation of biodiversity in the viral world.

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Desjardins, Christopher A., Jürgen Gadau, Jacqueline A. Lopez, Oliver Niehuis, Amanda R. Avery, David W. Loehlin, Stephen Richards, John K. Colbourne, and John H. Werren. "Fine-Scale Mapping of the Nasonia Genome to Chromosomes Using a High-Density Genotyping Microarray." G3: Genes|Genomes|Genetics 3, no. 2 (February 2013): 205–15. http://dx.doi.org/10.1534/g3.112.004739.

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Jasmine, F., H. Ahsan, I. L. Andrulis, E. M. John, J. Chang-Claude, and M. G. Kibriya. "Whole-Genome Amplification Enables Accurate Genotyping for Microarray-Based High-Density Single Nucleotide Polymorphism Array." Cancer Epidemiology Biomarkers & Prevention 17, no. 12 (December 1, 2008): 3499–508. http://dx.doi.org/10.1158/1055-9965.epi-08-0482.

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Hans, Aymeric, Delphine Gaudaire, Jean-Claude Manuguerra, Albertine Leon, Antoine Gessain, Claire Laugier, Nicolas Berthet, and Stephan Zientara. "Combination of an Unbiased Amplification Method and a Resequencing Microarray for Detecting and Genotyping Equine Arteritis Virus." Journal of Clinical Microbiology 53, no. 1 (October 22, 2014): 287–91. http://dx.doi.org/10.1128/jcm.01935-14.

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This study shows that an unbiased amplification method applied to equine arteritis virus RNA significantly improves the sensitivity of the real-time reverse transcription-quantitative PCR (RT-qPCR) recommended by the World Organization for Animal Health. Twelve viral RNAs amplified using this method were hybridized on a high-density resequencing microarray for effective viral characterization.

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Li, Honghua, Hui-Yun Wang, Danielle Greenawalt, Xiangfeng Cui, IrinaV Tereshchenko, Minjie Luo, Qifeng Yang, et al. "Identification of possible genetic alterations in the breast cancer cell line MCF-7 using high-density SNP genotyping microarray." Journal of Carcinogenesis 8, no. 1 (2009): 6. http://dx.doi.org/10.4103/1477-3163.50886.

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Vogler, Amy J., Dawn Birdsell, Lance B. Price, Jolene R. Bowers, Stephen M. Beckstrom-Sternberg, Raymond K. Auerbach, James S. Beckstrom-Sternberg, et al. "Phylogeography of Francisella tularensis: Global Expansion of a Highly Fit Clone." Journal of Bacteriology 191, no. 8 (February 27, 2009): 2474–84. http://dx.doi.org/10.1128/jb.01786-08.

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ABSTRACT Francisella tularensis contains several highly pathogenic subspecies, including Francisella tularensis subsp. holarctica, whose distribution is circumpolar in the northern hemisphere. The phylogeography of these subspecies and their subclades was examined using whole-genome single nucleotide polymorphism (SNP) analysis, high-density microarray SNP genotyping, and real-time-PCR-based canonical SNP (canSNP) assays. Almost 30,000 SNPs were identified among 13 whole genomes for phylogenetic analysis. We selected 1,655 SNPs to genotype 95 isolates on a high-density microarray platform. Finally, 23 clade- and subclade-specific canSNPs were identified and used to genotype 496 isolates to establish global geographic genetic patterns. We confirm previous findings concerning the four subspecies and two Francisella tularensis subsp. tularensis subpopulations and identify additional structure within these groups. We identify 11 subclades within F. tularensis subsp. holarctica, including a new, genetically distinct subclade that appears intermediate between Japanese F. tularensis subsp. holarctica isolates and the common F. tularensis subsp. holarctica isolates associated with the radiation event (the B radiation) wherein this subspecies spread throughout the northern hemisphere. Phylogenetic analyses suggest a North American origin for this B-radiation clade and multiple dispersal events between North America and Eurasia. These findings indicate a complex transmission history for F. tularensis subsp. holarctica.

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Ohlson, Erik W., and Michael P. Timko. "Mapping and Validation of Alectra vogelii Resistance in the Cowpea Landrace B301." Agronomy 12, no. 11 (October 27, 2022): 2654. http://dx.doi.org/10.3390/agronomy12112654.

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Cowpea is the most important food legume in West and Central Africa and a valuable economic commodity in the region. Among the major biotic constraints to cowpea production are root parasitic weeds of which Alectra vogelii (Benth.) is of increasing importance. The cowpea landrace B301 was previously identified as a source of Alectra resistance, but neither the genes nor genomic loci conferring this resistance have been mapped. Therefore, to map and identify genetic markers linked to Alectra resistance for use in the molecular improvement of cowpea, we developed an F2 population from a cross of the susceptible variety 524B with B301. The population was phenotyped for resistance to A. vogelii and genotyped with a cowpea high density single nucleotide polymorphism (SNP) microarray. Putative resistance loci were mapped in F2 populations by categorical trait–multiple interval mapping and validated by selective genotyping. Selective genotyping indicated that the resistance loci on Vu04 (Rav1) and Vu11 (Rav2) were significantly associated with resistance (p ≤ 0.01). Using marker assisted backcrossing, the two resistance loci were introgressed independently into the susceptible 524B genetic background. Phenotyping and genotyping of the segregating backcross families delineated Rav1 to a 10 cM on chromosome 4 and Rav2 to a 6.7 cM interval in chromosome 11. These two loci are desirable for breeding Alectra resistant cowpea varieties due to their simple inheritance and ability to independently confer complete immunity to the parasite.

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Björkholm, Britta, Annelie Lundin, Anna Sillén, Karen Guillemin, Nina Salama, Carlos Rubio, Jeffrey I. Gordon, Per Falk, and Lars Engstrand. "Comparison of Genetic Divergence and Fitness between Two Subclones of Helicobacter pylori." Infection and Immunity 69, no. 12 (December 1, 2001): 7832–38. http://dx.doi.org/10.1128/iai.69.12.7832-7838.2001.

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ABSTRACT Helicobacter pylori has a very plastic genome, reflecting its high rate of recombination and point mutation. This plasticity promotes divergence of the population by the development of subclones and presumably enhances adaptation to host niches. We have investigated the genotypic and phenotypic characteristics of two such subclones isolated from one patient as well as the genetic evolution of these isolates during experimental infection. Whole-genome genotyping of the isolates using DNA microarrays revealed that they were more similar to each other than to a panel of other genotyped strains recovered from different hosts. Nonetheless, they still showed significant differences. For example, one isolate (67:21) contained the entire Cag pathogenicity island (PAI), whereas the other (67:20) had excised the PAI. Phenotypic studies disclosed that both isolates expressed adhesins that recognized human histo-blood group Lewisb glycan receptors produced by gastric pit and surface mucus cells. In addition, both isolates were able to colonize, to equivalent density and with similar efficiency, germ-free transgenic mice genetically engineered to synthesize Lewisb glycans in their pit cells (12 to 14 mice/isolate). Remarkably, the Cag PAI-negative isolate was unable to colonize conventionally raised Lewisb transgenic mice harboring a normal gastric microflora, whereas the Cag PAI-positive isolate colonized 74% of the animals (39 to 40 mice/isolate). The genomic evolution of both isolates during the infection of conventionally raised and germ-free mice was monitored over the course of 3 months. The Cag PAI-positive isolate was also surveyed after a 10 month colonization of conventionally raised transgenic animals (n = 9 mice). Microarray analysis of the Cag PAI and sequence analysis of the cagA,recA, and 16S rRNA genes disclosed no changes in recovered isolates. Together, these results reveal that the H. pyloripopulation infecting one individual can undergo significant divergence, creating stable subclones with substantial genotypic and phenotypic differences.

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Більше джерел

Дисертації з теми "High-density genotyping microarray"

Richards, Stephen Malone. "Investigation and application of methods for ancient DNA research." Thesis, 2015. http://hdl.handle.net/2440/100765.

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The introduction of high throughput sequencing (HTS) in 2005 caused a revolution in the field of ancient DNA (aDNA). Using the large sequencing capacity of HTS, researchers have overcome the abundant environmental contamination present in most aDNA extractions to reconstruct the genomes of long extinct organisms, such as an archaic horse that perished >500,000 years ago. The proliferation of genomes engendered by HTS has also led to the development of potential ancillary technologies for aDNA research such as genotyping microarrays. In this thesis, HTS and genotyping techniques were developed or refined to improve the application of aDNA to larger biological questions in evolution. This thesis successfully: a) describes an in-house hybridization capture system that uses RNA probes generated from long-range PCR amplicons, b) demonstrates that recombinase polymerase amplification is a less biased alternative to PCR in hybridization capture of aDNA, c) develops an analytical approach that improves phylogenies generated with data from the Illumina BovineSNP50 BeadChip (a commercially available genotyping microarray). In contrast, an attempt to determine the identity of modified nucleotides in aDNA with Pacific Bioscience’s Single Molecule Real-Time (SMRT) sequencing prove to be unsuccessful and genotyping of ancient bison aDNA with the BovineSNP50 BeadChip generated inconsistent results. Furthermore, a hybridization capture probe design was tested and found to be unsuitable for aDNA enrichment. For the larger biological aspect of this thesis, several of the methods developed were used to study bison, because these animals are ideal models of megafauna evolution. Using the in-house hybridization capture system, whole mitochondrial genomes were enriched from aDNA and used to help identify a new extinct species of bison. Furthermore, the new analytical approach for BovineSNP50 BeadChip data was used to demonstrate a significant genetic split between American woods and plains bison, which supports separating these animals at least at the subspecies level. This genetic split suggests that woods and plains bison should be conserved as separate species, which has considerable economic and political implications.
Thesis (Ph.D.) (Research by Publication) -- University of Adelaide,School of Earth and Environmental Sciences, 2015.

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