Open Access Research article

Generation of a non-small cell lung cancer transcriptome microarray

Austin Tanney1*, Gavin R Oliver1, Vadim Farztdinov1, Richard D Kennedy1, Jude M Mulligan1, Ciaran E Fulton1, Susan M Farragher1, John K Field2, Patrick G Johnston3, D Paul Harkin1, Vitali Proutski1 and Karl A Mulligan1

Author Affiliations

1 Almac Diagnostics Ltd, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK

2 Roy Castle Lung Cancer Research Programme, The University of Liverpool Cancer Research Centre, 200 London Road, Liverpool, L3 9TA, UK

3 Centre for Cancer Research and Cell Biology, Queen's University of Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK

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BMC Medical Genomics 2008, 1:20  doi:10.1186/1755-8794-1-20

Published: 30 May 2008

Abstract

Background

Non-small cell lung cancer (NSCLC) is the leading cause of cancer mortality worldwide. At present no reliable biomarkers are available to guide the management of this condition. Microarray technology may allow appropriate biomarkers to be identified but present platforms are lacking disease focus and are thus likely to miss potentially vital information contained in patient tissue samples.

Methods

A combination of large-scale in-house sequencing, gene expression profiling and public sequence and gene expression data mining were used to characterise the transcriptome of NSCLC and the data used to generate a disease-focused microarray – the Lung Cancer DSA research tool.

Results

Built on the Affymetrix GeneChip platform, the Lung Cancer DSA research tool allows for interrogation of ~60,000 transcripts relevant to Lung Cancer, tens of thousands of which are unavailable on leading commercial microarrays.

Conclusion

We have developed the first high-density disease specific transcriptome microarray. We present the array design process and the results of experiments carried out to demonstrate the array's utility. This approach serves as a template for the development of other disease transcriptome microarrays, including non-neoplastic diseases.