TITLE

Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms

AUTHOR(S)
Lynch, A. G.; Dunning, M. J.; Iddawela, M.; Barbosa-Morais, N. L.; Ritchie, M. E.
PUB. DATE
October 2009
SOURCE
Statistical Methods in Medical Research;Oct2009, Vol. 18 Issue 5, p437
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Illumina's GoldenGate technology is a two-channel microarray platform that allows for the simultaneous interrogation of about 1 500 locations in the genome. GoldenGate has proved a flexible platform not only in the choice of those 1 500 locations, but also in the choice of the property being measured at them. It retains the desirable properties of Illumina's BeadArrays in that the probes (in this case 'beads') are randomly arranged across the microarray, there are multiple instances of each probe and many samples can be processed simultaneously. As for other Illumina technologies, however, these properties are not exploited as they might be. Here we review the various common adaptations of the GoldenGate platform, review the analysis methods that are associated with each adaptation and then, with the aid of a number of example data sets we illustrate some of the improvements that can be made over the default analysis.
ACCESSION #
44497181

 

Related Articles

  • Metal Nanoparticle-Based Detection for DNA Analysis. Moller, Robert; Fritzsche, Wolfgang // Current Pharmaceutical Biotechnology;Oct2007, Vol. 8 Issue 5, p274 

    In the last 20 years the practice of DNA sequence detection has gained more and more importance in a variety of fields like-genetics, food safety, pathology, and criminology. This has been driven by the growing knowledge about the human and other organism's genome. The development of...

  • Mapping Disease. Flora, Brad // EContent;Mar2007, Vol. 30 Issue 2, p12 

    The article looks at the progress made in developing deoxyribonucleic acid (DNA) microarrays, or gene chip. Both Affymetrix and Illumina released their 500,000-plus gene chips in 2006, and both companies have also announced first quarter 2007 releases for 1,000,000-plus chips. A microarray is a...

  • Microarrays for Methylation. Frederickson, Robert M. // Bio-IT World;Dec2006/Jan2007, Vol. 5 Issue 10, p13 

    The article focuses on the development of methods in detecting the methylation status of human genes. Gene methylation contributes to tumor development if its pattern is altered. MethylScope from Orion Genomics is a DNA array-based technology that can be used to monitor methylation patterns of...

  • DNA Microarray Technology for Pharmacogenomics Research. Claude E. Gagna; Lambert, W. Clark; Lambert, Peter // Drug Discovery & Development;Jul/Aug2012, Vol. 15 Issue 7, p26 

    The article discusses the importance of DNA microarray technology for conducting a study on pharmacogenomics. It asserts that novel nucleic acid-based microarrays play a significant role in the development of alternative molecular biological processes. It indicates that there are several...

  • A visual analytics approach for understanding biclustering results from microarray data. Santamaría, Rodrigo; Therón, Roberto; Quintales, Luis // BMC Bioinformatics;2008, Vol. 9, Special section p1 

    Background: Microarray analysis is an important area of bioinformatics. In the last few years, biclustering has become one of the most popular methods for classifying data from microarrays. Although biclustering can be used in any kind of classification problem, nowadays it is mostly used for...

  • The death of microarrays? Ledford, Heidi // Nature;10/16/2008, Vol. 455 Issue 7215, p847 

    The article reports on the effects of the efforts of the genome technology in creating genome sequencing on the condition of microarrays. It states that cheaper deoxyribonucleic acid (DNA) sequencing technology is revolutionizing the field of personal genomics. Despite the expensiveness of...

  • The Application of Single Nucleotide Polymorphism Microarrays in Cancer Research. Xueying Mao; Young, Bryan D.; Yong-Jie Lu // Current Genomics;Jul2007, Vol. 8 Issue 4, p219 

    The development of microarray technology has had a significant impact on the genetic analysis of human disease. The recently developed single nucleotide polymorphism (SNP) array can be used to measure both DNA polymorphism and dosage changes. Our laboratory has applied SNP microarray analysis to...

  • Current views of the origin and diversification of tetrapods. Kupriyanova, N. S. // Molecular Biology;Oct2009, Vol. 43 Issue 5, p819 

    In several recent decades, a wealth of evidence was obtained (including new fossils and new nucleotide sequences) that allows a revision of the current evolutionary theories. The primary structure was determined for orthologous regions from a variety of genomes. Complete genome sequences were...

  • A new African streak virus species from Nigeria. Oluwafemi, Sunday; Varsani, Arvind; Monjane, Adérito L.; Shepherd, Dionne N.; Owor, Betty E.; Rybicki, Edward P.; Martin, Darren P. // Archives of Virology;Jul2008, Vol. 153 Issue 7, p1407 

    The African streak viruses (AfSVs) are a diverse group of mastrevirus species (family Geminiviridae) that infect a wide variety of annual and perennial grass species across the African continent and its nearby Indian Ocean islands. Six AfSV species (of which maize streak virus is the best known)...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics