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Published online 11 February 2004

Nucleic Acids Research, 2004, Vol. 32, No. 3 e27
© 2004 Oxford University Press

Genomic shotgun array: a procedure linking large-scale DNA sequencing with regional transcript mapping

Ling-Hui Li1, Jian-Chiuan Li1, Yung-Feng Lin1, Chung-Yen Lin2, Chung-Yung Chen1 and Shih-Feng Tsai*,1,3

1 Division of Molecular and Genomic Medicine, National Health Research Institutes, and 2 Division of Biostatistics and Bioinformatics, National Health Research Institutes, 128, Yen-Chiu-Yuan Road, Sec. 2, Taipei 115, Taiwan and 3 Institute of Genetics and Genome Research Center, National Yang-Ming University, 155, Li-Non Street, Sec. 2, Taipei 112, Taiwan

*To whom correspondence should be addressed. Tel: +886 2 26524120; Fax: +886 2 27890484; Email: petsai{at}nhri.org.tw

To facilitate transcript mapping and to investigate alterations in genomic structure and gene expression in a defined genomic target, we developed a novel microarray-based method to detect transcriptional activity of the human chromosome 4q22-24 region. Loss of heterozygosity of human 4q22-24 is frequently observed in hepatocellular carcinoma (HCC). One hundred and eighteen well-characterized genes have been identified from this region. We took previously sequenced shotgun subclones as templates to amplify overlapping sequences for the genomic segment and constructed a chromosome-region-specific microarray. Using genomic DNA fragments as probes, we detected transcriptional activity from within this region among five different tissues. The hybridization results indicate that there are new transcripts that have not yet been identified by other methods. The existence of new transcripts encoded by genes in this region was confirmed by PCR cloning or cDNA library screening. The procedure reported here allows coupling of shotgun sequencing with transcript mapping and, potentially, detailed analysis of gene expression and chromosomal copy of the genomic sequence for the putative HCC tumor suppressor gene(s) in the 4q candidate region.


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