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  • Oncogenomics
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Transcript map and complete genomic sequence for the 310 kb region of minimal allele loss on chromosome segment 11p15.5 in non-small-cell lung cancer

Oncogene volume 20, pages 8154–8164 (2001)Cite this article

Abstract

Molecular, functional, and clinical analyses strongly suggest that chromosome segment 11p15.5 contains a gene involved in lung cancer pathogenesis. The critical region of allele loss is 310 kb in size. We used our contig of P1-phage artificial chromosome (PAC) clones together with newly identified bacterial artificial chromosome (BAC) clones and the draft human genome sequence to complete a contiguous string of 380 407 bp. Three PAC clones that span the region were used to identify transcripts by exon trapping. Computational gene prediction algorithms were used to query the sequence for potential genes and exons. Screening for expression was performed with tissue-specific and cell line derived mRNA arrays. The region contains the complete SSA/Ro52 and RRM1 genes, exons 7–12 of the GOK gene, and the ψrad pseudo-gene. A cluster of six nearly identical genes with an intact open reading frame (ORF) of 585 bp that share 75% identity with the HSPC182 gene was found. In addition, five putative novel genes were identified. Sequence tagged sites (STS) and polymorphic markers were used to screen 117 lung cancer cell lines for homozygous deletions and none were identified. These data provide the basis for the identification of a lung cancer suppressor gene on 11p15.5.

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Acknowledgements

We thank David Chervinsky for allelotyping of the lung cancer cell lines and Drs Arvind Virmani and Adi Gazdar for providing DNA from lung cancer cell lines. We thank Drs John Cowell and Thomas Shows for helpful suggestions during the preparation of the manuscript. This work was supported by grants from the National Cancer Institute (5RO1 CA 70317) and the Roswell Park Cancer Center Support Grant (P30 CA 16056).

Accession Numbers

The DNA sequence was deposited in the EMBL database under Accession numbers AF391283, AF391284 and AF391285.

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  1. Departments of Medicine and Cancer Genetics, Lung Cancer Program, Roswell Park Cancer Institute, Buffalo, New York, USA

    Baohui Zhao & Gerold Bepler

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  1. Baohui Zhao
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  2. Gerold Bepler
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Correspondence to Gerold Bepler.

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Zhao, B., Bepler, G. Transcript map and complete genomic sequence for the 310 kb region of minimal allele loss on chromosome segment 11p15.5 in non-small-cell lung cancer. Oncogene 20, 8154–8164 (2001). https://doi.org/10.1038/sj.onc.1205027

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