TITLE

Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA

AUTHOR(S)
Gibbons, Brian; Datta, Parikkhit; Wu2, Ying; Chan, Alan; Armour, John AL
PUB. DATE
January 2006
SOURCE
BMC Genomics;2006, Vol. 7, p163
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Current methods for measurement of copy number do not combine all the desirable qualities of convenience, throughput, economy, accuracy and resolution. In this study, to improve the throughput associated with Multiplex Amplifiable Probe Hybridisation (MAPH) we aimed to develop a modification based on the 3-Dimensional, Flow-Through Microarray Platform from PamGene International. In this new method, electrophoretic analysis of amplified products is replaced with photometric analysis of a probed oligonucleotide array. Copy number analysis of hybridised probes is based on a dual-label approach by comparing the intensity of Cy3-labelled MAPH probes amplified from test samples co-hybridised with similarly amplified Cy5-labelled reference MAPH probes. The key feature of using a hybridisation-based end point with MAPH is that discrimination of amplified probes is based on sequence and not fragment length. Results: In this study we showed that microarray MAPH measurement of PMP22 gene dosage correlates well with PMP22 gene dosage determined by capillary MAPH and that copy number was accurately reported in analyses of DNA from 38 individuals, 12 of which were known to have Charcot-Marie-Tooth disease type 1A (CMT1A). Conclusion: Measurement of microarray-based endpoints for MAPH appears to be of comparable accuracy to electrophoretic methods, and holds the prospect of fully exploiting the potential multiplicity of MAPH. The technology has the potential to simplify copy number assays for genes with a large number of exons, or of expanded sets of probes from dispersed genomic locations.
ACCESSION #
28858675

 

Related Articles

  • TimeLogic Solutions For Sensitive, High-performance Oligonucleotide Searching.  // Pharmaceutical Discovery;Oct2005, Vol. 5 Issue 8, p30 

    The DeCypher® and CodeQuest™ bio-computing systems deliver the sensitivity and high-throughput searching required for microarray probe design, SNP mapping, and RNA interference. These systems process searches on the DeCypher Engine™ accelerator card to deliver performance of...

  • A comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray. Leiske, Danielle L; Karimpour-Fard, Anis; Hume, Patrick S; Fairbanks, Benjamin D; Gill, Ryan T // BMC Genomics;2006, Vol. 7, p72 

    Background: DNA microarrays have proven powerful for functional genomics studies. Several technologies exist for the generation of whole-genome arrays. It is well documented that 25mer probes directed against different regions of the same gene produce variable signal intensity values. However,...

  • Application of Equilibrium Models of Solution Hybridization to Microarray Design and Analysis. Gharaibeh, Raad Z.; Newton, Joshua M.; Weller, Jennifer W.; Gibas, Cynthia J. // PLoS ONE;2010, Vol. 5 Issue 6, p1 

    Background: The probe percent bound value, calculated using multi-state equilibrium models of solution hybridization, is shown to be useful in understanding the hybridization behavior of microarray probes having 50 nucleotides, with and without mismatches. These longer oligonucleotides are in...

  • An analysis of intra array repeats: the good, the bad and the non informative. Elbez, Yedid; Farkash-Amar, Shlomit; Simon, Itamar // BMC Genomics;2006, Vol. 7, p136 

    Background: On most common microarray platforms many genes are represented by multiple probes. Although this is quite common no one has systematically explored the concordance between probes mapped to the same gene. Results: Here we present an analysis of all the cases of multiple probe sets...

  • Relationship between gene co-expression and probe localization on microarray slides. Kluger, Yuval; Haiyuan Yu; Jiang Qian; Gerstein, Mark // BMC Genomics;2003, Vol. 4, p49 

    Background: Microarray technology allows simultaneous measurement of thousands of genes in a single experiment. This is a potentially useful tool for evaluating co-expression of genes and extraction of useful functional and chromosomal structural information about genes. Results: In this work we...

  • A fast and flexible approach to oligonucleotide probe design for genomes and gene families. Shengzhong Feng; Elisabeth R.M. Tillier // Bioinformatics;May2007, Vol. 23 Issue 10, p1195 

    Motivation: With hundreds of completely sequenced microbial genomes available, and advancements in DNA microarray technology, the detection of genes in microbial communities consisting of hundreds of thousands of sequences may be possible. The existing strategies developed for DNA probe design,...

  • Assessing probe-specific dye and slide biases in two-color microarray data. Ruixiao Lu; Geun-Cheol Lee; Shultz, Michael; Dardick, Chris; Kihong Jung; Phetsom, Jirapa; Yi Jia; Rice, Robert H.; Goldberg, Zelanna; Schnable, Patrick S.; Ronald, Pamela; Rocke, David M. // BMC Bioinformatics;2008, Vol. 9, Special section p1 

    Background: A primary reason for using two-color microarrays is that the use of two samples labeled with different dyes on the same slide, that bind to probes on the same spot, is supposed to adjust for many factors that introduce noise and errors into the analysis. Most users assume that any...

  • Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data. Hui Yu; Feng Wang; Kang Tu; Lu Xie; Yuan-Yuan Li; Yi-Xue Li // BMC Bioinformatics;2007, Vol. 8, p194 

    Background: The wide use of Affymetrix microarray in broadened fields of biological research has made the probeset annotation an important issue. Standard Affymetrix probeset annotation is at gene level, i.e. a probeset is precisely linked to a gene, and probeset intensity is interpreted as gene...

  • What length of probe is optimal for microarrays? Mir, Kalim U. // Nature Genetics;Nov99 Supplement, Vol. 23, p63 

    Presents an abstract for the article on the optimal length of probes for DNA microarrays.

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