Gene expression profiling in mitochondrial disease: Assessment of microarray accuracy by high-throughput Q-PCR

Kenneth B. Beckman, Kathleen Y. Lee, Tamara Golden, Simon Melov

Research output: Contribution to journalArticlepeer-review

24 Scopus citations

Abstract

Mitochondrial diseases are a heterogenous array of disorders with a complex etiology. Use of microarrays as a tool to investigate complex human disease is increasingly common, however, a principle drawback of microarrays is their limited dynamic range, due to the poor quantification of weak signals. Although it is generally understood that low-intensity microarray 'spots' may be unreliable, there exists little documentation of their accuracy. Quantitative PCR (Q-PCR) is frequently used to validate microarray data, yet few Q-PCR validation studies have focused on the accuracy of low-intensity microarray signals. Hence, we have used Q-PCR to systematically assess microarray accuracy as a function of signal strength in a mouse model of mitochondrial disease, the superoxide dismutase 2 (SOD2) nullizygous mouse. We have focused on a unique category of data- spots with only one weak signal in a two-dye comparative hybridization - and show that such 'high-low' signal intensities are common for differentially expressed genes. This category of differential expression may be more important in mitochondrial disease in which there are often mosaic expression patterns due to the idiosyncratic distribution of mutant mtDNA in heteroplasmic individuals. Using RNA from the SOD2 mouse, we found that when spotted cDNA microarray data are filtered for quality (low variance between many technical replicates) and spot intensity (above a negative control threshold in both channels), there is an excellent quantitative concordance with Q-PCR (R2=0.94). The accuracy of gene expression ratios from low-intensity spots (R2=0.27) and 'high-low' spots (R2=0.32) is considerably lower. Our results should serve as guidelines for microarray interpretation and the selection of genes for validation in mitochondrial disorders.

Original languageEnglish (US)
Pages (from-to)453-470
Number of pages18
JournalMitochondrion
Volume4
Issue number5-6 SPEC. ISS.
DOIs
StatePublished - Sep 2004

Bibliographical note

Funding Information:
KBB would like to thank Russ Higuchi, Terry Speed, and John Quackenbush for discussion and encouragement, and Alan Kimmel for useful critiques of draft versions of the manuscript. KBB would like to thank the following individuals for their support in the preparation of this manuscript, including Joe Butler, Jiggs Davis, Sharon Draemel, Mike Hunter, Yurah Kang, Deepak Maganti, Ricardo Mancebo, Sepp Saljoughi, Aaron Schohn, Nico Tuason, and David Tyler. SM is indebted to Tamara Golden, Krysta Felkey and Lawreen Asuncion at the Buck Institute for invaluable practical help in generation of the data. This work was partially supported by National Institutes of Health grant AG18679, and a Senior Scholar award from the Ellison Medical Foundation, both awarded to SM.

Copyright:
Copyright 2008 Elsevier B.V., All rights reserved.

Keywords

  • Mitochondrial disorders
  • Real-time quantitative PCR
  • Validation

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