Topic
Representation oligonucleotide microarray analysis
About: Representation oligonucleotide microarray analysis is a research topic. Over the lifetime, 9 publications have been published within this topic receiving 562 citations.
Papers
TL;DR: Alternative strategies for whole genome screening and high resolution breakpoint mapping of copy number changes by array-CGH are described, as well as tools available for accurate analysis of array- CGH experiments.
Abstract: Microarray-based Comparative Genomic Hybridization (array-CGH) has been applied for a decade to screen for submicroscopic DNA gains and losses in tumor and constitutional DNA samples. This method has become increasingly flexible with the integration of new biological resources generated by genome sequencing projects. In this chapter, we describe alternative strategies for whole genome screening and high resolution breakpoint mapping of copy number changes by array-CGH, as well as tools available for accurate analysis of array-CGH experiments. Although most methods listed here have been designed for microarrays composed of large-insert clones, they can be adapted easily to other types of microarray platforms, such as those constructed from printed or synthesized oligonucleotides.
26 citations
TL;DR: OligoArrayDb is a comprehensive database containing pangenomic oligonucleotide microarray probe sets designed for most of the sequenced genomes that are not covered by commercial catalog arrays.
Abstract: OligoArrayDb is a comprehensive database containing pangenomic oligonucleotide microarray probe sets designed for most of the sequenced genomes that are not covered by commercial catalog arrays. The availability of probe sequences, associated with custom microarray fabrication services offered by many companies and cores presents the unequalled possibility to perform microarray experiments on most of the sequenced organisms. OligoArrayDb contains more than 2.8 probes per gene in average for more than 600 organisms, mostly archaea and bacteria strains available from public database. On average, 98% of the annotated genes have at least one probe which is predicted to be specific to its intended target in >94% of the cases. OligoArrayDb is weekly updated as new sequenced genomes become available. Probe sequences, in addition to a comprehensive set of annotations can be downloaded from this database. OligoArrayDb is publicly accessible online at http://berry.engin.umich.edu/oligoarraydb.
12 citations
TL;DR: This chapter presents a validated protocol utilizing print-tip spotted HEEBO (Human Exonic Evidence Based Oligonucleotide) microarrays for conducting array-CGH using as little as 25 ng of genomic DNA from a wide variety of sources, including cultured cell lines and clinical specimens, with high spatial resolution and array-to-array reproducibility.
Abstract: Recent advances in DNA microarray technology have enabled researchers to comprehensively characterize the complex genomes of higher eukaryotic organisms at an unprecedented level of detail Array-based comparative genomic hybridization (Array-CGH) has been widely used for detecting DNA copy number alterations on a genomic scale, where the mapping resolution is limited only by the number of probes on the DNA microarray In this chapter, we present a validated protocol utilizing print-tip spotted HEEBO (Human Exonic Evidence Based Oligonucleotide) microarrays for conducting array-CGH using as little as 25 ng of genomic DNA from a wide variety of sources, including cultured cell lines and clinical specimens, with high spatial resolution and array-to-array reproducibility
11 citations
Journal Article•
TL;DR: This study determined the genome positions of all maize array probes to obtain current gene annotations and generated current Gene Ontology (GO) annotations, which allow tracing redundancy of the probe set and interfering cross-hybridizations, and doubled the number of genes with functional GO data.
Abstract: The microarray technology has become an established approach for large-scale gene expression analysis with mature protocols for sample, microarray, and data processing. The maize oligonucleotide array (maizearray) is one of the few microarray platforms designed for genome-wide gene expression analysis in Zea mays L. Many datasets addressing various genetic, physiological and developmental topics generated with this platform are available. The original 57,452 microarray probes were compiled based on expressed sequence tags (ESTs). Meanwhile the maize genome sequence became available providing the possibility for an improved annotation of the microarray probe set. In this study we determined the genome positions of all maize array probes to obtain current gene annotations and generated current Gene Ontology (GO) annotations. These new data allow tracing redundancy of the probe set and interfering cross-hybridizations, and doubled the number of genes with functional GO data. Our re-annotation will largely improve the functional analysis of available and future datasets generated on this microarray platform.
6 citations
1 Jan 2017
TL;DR: Two revolutionary advances in molecular biology have enabled scanning of the entire human genome for genetic variation: Array-comparative genomic hybridization-microarray analysis (aCGH, CMA, microarray analysis, referred to henceforth as aCGH) that identifies altered DNA dosage.
Abstract: Two revolutionary advances in molecular biology have enabled scanning of the entire human genome for genetic variation: 1. Array-comparative genomic hybridization-microarray analysis (aCGH, CMA, microarray analysis, referred to henceforth as aCGH) that identifies altered DNA dosage. 2. Whole genome or exome sequencing (WGS or WES) that identifies nucleotide sequence changes.
2 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2017 | 1 |
| 2015 | 1 |
| 2012 | 1 |
| 2009 | 3 |
| 2008 | 1 |
| 2004 | 1 |