Evaluation of reference-based two-color methods for measurement of gene expression ratios using spotted cDNA microarrays

BMC Genomics
Bernardo R PeixotoEduardo M Reis

Abstract

Spotted cDNA microarrays generally employ co-hybridization of fluorescently-labeled RNA targets to produce gene expression ratios for subsequent analysis. Direct comparison of two RNA samples in the same microarray provides the highest level of accuracy; however, due to the number of combinatorial pair-wise comparisons, the direct method is impractical for studies including large number of individual samples (e.g., tumor classification studies). For such studies, indirect comparisons using a common reference standard have been the preferred method. Here we evaluated the precision and accuracy of reconstructed ratios from three indirect methods relative to ratios obtained from direct hybridizations, herein considered as the gold-standard. We performed hybridizations using a fixed amount of Cy3-labeled reference oligonucleotide (RefOligo) against distinct Cy5-labeled targets from prostate, breast and kidney tumor samples. Reconstructed ratios between all tissue pairs were derived from ratios between each tissue sample and RefOligo. Reconstructed ratios were compared to (i) ratios obtained in parallel from direct pair-wise hybridizations of tissue samples, and to (ii) reconstructed ratios derived from hybridization of each tissue ...Continue Reading

References

Aug 30, 2000·Nature·C M PerouD Botstein
Nov 15, 2001·Proceedings of the National Academy of Sciences of the United States of America·M E GarberI Petersen
Feb 2, 2002·Nature·Laura J van 't VeerStephen H Friend
May 29, 2002·Proceedings of the National Academy of Sciences of the United States of America·Aimée M DudleyGeorge M Church
Aug 3, 2002·Nature Reviews. Genetics·Yee Hwa Yang, Terry Speed
Nov 1, 2002·Nucleic Acids Research·Ellen SterrenburgJohan T den Dunnen
Nov 28, 2002·Nature Genetics·Gary A Churchill
Nov 28, 2002·Nature Genetics·John Quackenbush
Dec 7, 2002·Nature Genetics·Sridhar RamaswamyTodd R Golub
Aug 23, 2003·Biostatistics·M K Kerr, G A Churchill
Feb 26, 2004·Nucleic Acids Research·Peter A C 't HoenJohan T den Dunnen
Mar 25, 2004·BioTechniques·Richard J RouseGary Hardiman
Jun 11, 2004·Nucleic Acids Research·Brian A WilliamsBarbara J Wold
Jun 24, 2004·BioTechniques·Francesco GorretaLuca Del Giacco
Nov 24, 2005·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Ricardo Z N Vêncio, Tie Koide

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Methods Mentioned

BETA
PCR
chip

Software Mentioned

Color
RefOligo
ArrayVision
Direct
One
R
LOWESS
RefPool
R scripts

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