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Applications of microarray technology to Acute Myelogenous Leukemia.

Goswami RS, Sukhai MA, Thomas M, Reis PP, Kamel-Reid S - Cancer Inform (2008)

Bottom Line: Arrays have also been used extensively in elucidating the mechanism of and predicting therapeutic response in AML, as well as to further define the mechanism of AML pathogenesis.In this review, we discuss the major paradigms of gene expression array analysis, and provide insights into the use of software tools to annotate the array dataset and elucidate deregulated pathways and gene interaction networks.Finally, we discuss several new and emerging array technologies, and how they can be further utilized to improve our understanding of AML.

View Article: PubMed Central - PubMed

Affiliation: Division of Applied Molecular Oncology, Princess Margaret Hospital/Ontario Cancer Institute, University Health Network, Toronto, ON, Canada.

ABSTRACT
Microarray technology is a powerful tool, which has been applied to further the understanding of gene expression changes in disease. Array technology has been applied to the diagnosis and prognosis of Acute Myelogenous Leukemia (AML). Arrays have also been used extensively in elucidating the mechanism of and predicting therapeutic response in AML, as well as to further define the mechanism of AML pathogenesis. In this review, we discuss the major paradigms of gene expression array analysis, and provide insights into the use of software tools to annotate the array dataset and elucidate deregulated pathways and gene interaction networks. We present the application of gene expression array technology to questions in acute myelogenous leukemia; specifically, disease diagnosis, treatment and prognosis, and disease pathogenesis. Finally, we discuss several new and emerging array technologies, and how they can be further utilized to improve our understanding of AML.

No MeSH data available.


Related in: MedlinePlus

A ChIP-on-Chip workflow. Each step of the chromatin immunoprecipitation stage is optimized for every cell and tissue type. Enrichment analysis to determine successful immunoprecipitation is performed using quantitative real time PCR using primers against target DNA sequences known to be bound by the protein of interest. Large scale genome binding analyses are dependent on the array platform used in the study—these can include promoter arrays, whole genome tiling arrays, or custom made targeted tiling arrays.
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f2-cin-07-13: A ChIP-on-Chip workflow. Each step of the chromatin immunoprecipitation stage is optimized for every cell and tissue type. Enrichment analysis to determine successful immunoprecipitation is performed using quantitative real time PCR using primers against target DNA sequences known to be bound by the protein of interest. Large scale genome binding analyses are dependent on the array platform used in the study—these can include promoter arrays, whole genome tiling arrays, or custom made targeted tiling arrays.

Mentions: A summary of the ChIP-on-chip methodology is presented in Figure 2. Proteins are first fixed to capture cellular protein-DNA interactions by chemical fixation methods. Cells are then lysed, DNA fragmented and immunoprecipitated using antibodies against the target proteins. DNA associated with the targeted protein will be co-purified. The enriched DNA fragments are then labeled and applied to DNA microarrays to detect the enriched signals. Using a number of computational and bioinformatics analysis, a map of protein-genome occupancy is generated. Hybridized sequences can be annotated in silico using publicly available tools (including NCBI: www.ncbi.nlm.nih.gov/BLAST and the Transcription Element Search System software package [TESS]: http://www.cbil.upenn.edu/tess/) to determine the characteristics of identified sequences: promoter vs. enhancer/repressor function, as well as possible transcription factor binding sites recognized by the protein of interest. A number of array platforms are currently available for the hybridization of immunoprecipitated DNA. These include printed PCR amplicon arrays, and other commercial oligonucleotide arrays. The choice of array platform depends on the need for high performance, ease of use, cost, and resolution. Whole-genome oligonucleotide tiling arrays currently offer the highest resolution power with probes tiled at approximately 35-base pair intervals. These probes are selected at defined intervals through both coding and non-coding sequences of the entire genome. Base pair resolution describes the density of coverage of the genome on the arrays. High-resolution arrays allow for the more accurate detection of protein/DNA interaction. Other arrays that are commonly used in ChIP-on-Chip assays include promoter arrays, which contain sequences tiled though several thousand promoter regions, and CpG island arrays. In addition to determining transcription factor binding sites, ChIP-on-chip technology is also being applied to examine histone and DNA modifications including methylation, and acetylation, and distributions of chromatin modifying proteins, as well as interactions between proteins and RNA.


Applications of microarray technology to Acute Myelogenous Leukemia.

Goswami RS, Sukhai MA, Thomas M, Reis PP, Kamel-Reid S - Cancer Inform (2008)

A ChIP-on-Chip workflow. Each step of the chromatin immunoprecipitation stage is optimized for every cell and tissue type. Enrichment analysis to determine successful immunoprecipitation is performed using quantitative real time PCR using primers against target DNA sequences known to be bound by the protein of interest. Large scale genome binding analyses are dependent on the array platform used in the study—these can include promoter arrays, whole genome tiling arrays, or custom made targeted tiling arrays.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2664704&req=5

f2-cin-07-13: A ChIP-on-Chip workflow. Each step of the chromatin immunoprecipitation stage is optimized for every cell and tissue type. Enrichment analysis to determine successful immunoprecipitation is performed using quantitative real time PCR using primers against target DNA sequences known to be bound by the protein of interest. Large scale genome binding analyses are dependent on the array platform used in the study—these can include promoter arrays, whole genome tiling arrays, or custom made targeted tiling arrays.
Mentions: A summary of the ChIP-on-chip methodology is presented in Figure 2. Proteins are first fixed to capture cellular protein-DNA interactions by chemical fixation methods. Cells are then lysed, DNA fragmented and immunoprecipitated using antibodies against the target proteins. DNA associated with the targeted protein will be co-purified. The enriched DNA fragments are then labeled and applied to DNA microarrays to detect the enriched signals. Using a number of computational and bioinformatics analysis, a map of protein-genome occupancy is generated. Hybridized sequences can be annotated in silico using publicly available tools (including NCBI: www.ncbi.nlm.nih.gov/BLAST and the Transcription Element Search System software package [TESS]: http://www.cbil.upenn.edu/tess/) to determine the characteristics of identified sequences: promoter vs. enhancer/repressor function, as well as possible transcription factor binding sites recognized by the protein of interest. A number of array platforms are currently available for the hybridization of immunoprecipitated DNA. These include printed PCR amplicon arrays, and other commercial oligonucleotide arrays. The choice of array platform depends on the need for high performance, ease of use, cost, and resolution. Whole-genome oligonucleotide tiling arrays currently offer the highest resolution power with probes tiled at approximately 35-base pair intervals. These probes are selected at defined intervals through both coding and non-coding sequences of the entire genome. Base pair resolution describes the density of coverage of the genome on the arrays. High-resolution arrays allow for the more accurate detection of protein/DNA interaction. Other arrays that are commonly used in ChIP-on-Chip assays include promoter arrays, which contain sequences tiled though several thousand promoter regions, and CpG island arrays. In addition to determining transcription factor binding sites, ChIP-on-chip technology is also being applied to examine histone and DNA modifications including methylation, and acetylation, and distributions of chromatin modifying proteins, as well as interactions between proteins and RNA.

Bottom Line: Arrays have also been used extensively in elucidating the mechanism of and predicting therapeutic response in AML, as well as to further define the mechanism of AML pathogenesis.In this review, we discuss the major paradigms of gene expression array analysis, and provide insights into the use of software tools to annotate the array dataset and elucidate deregulated pathways and gene interaction networks.Finally, we discuss several new and emerging array technologies, and how they can be further utilized to improve our understanding of AML.

View Article: PubMed Central - PubMed

Affiliation: Division of Applied Molecular Oncology, Princess Margaret Hospital/Ontario Cancer Institute, University Health Network, Toronto, ON, Canada.

ABSTRACT
Microarray technology is a powerful tool, which has been applied to further the understanding of gene expression changes in disease. Array technology has been applied to the diagnosis and prognosis of Acute Myelogenous Leukemia (AML). Arrays have also been used extensively in elucidating the mechanism of and predicting therapeutic response in AML, as well as to further define the mechanism of AML pathogenesis. In this review, we discuss the major paradigms of gene expression array analysis, and provide insights into the use of software tools to annotate the array dataset and elucidate deregulated pathways and gene interaction networks. We present the application of gene expression array technology to questions in acute myelogenous leukemia; specifically, disease diagnosis, treatment and prognosis, and disease pathogenesis. Finally, we discuss several new and emerging array technologies, and how they can be further utilized to improve our understanding of AML.

No MeSH data available.


Related in: MedlinePlus