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

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

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

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

author email corresponding author email

BMC Medical Genomics 2008, 1:20doi: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.