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Characterizing the cancer genome in lung adenocarcinoma.

Weir BA | Woo MS | Getz G | Perner S | Ding L | Beroukhim R | Lin WM | Province MA | Kraja A | Johnson LA | Shah K | Sato M | Thomas RK | Barletta JA | Borecki IB | Broderick S | Chang AC | Chiang DY | Chirieac LR | Cho J | Fujii Y | Gazdar AF | Giordano T | Greulich H | Hanna M | Johnson BE | Kris MG | Lash A | Lin L | Lindeman N | Mardis ER | McPherson JD | Minna JD | Morgan MB | Nadel M | Orringer MB | Osborne JR | Ozenberger B | Ramos AH | Robinson J | Roth JA | Rusch V | Sasaki H | Shepherd F | Sougnez C | Spitz MR | Tsao MS | Twomey D | Verhaak RG | Weinstock GM | Wheeler DA | Winckler W | Yoshizawa A | Yu S | Zakowski MF | Zhang Q | Beer DG | Wistuba II | Watson MA | Garraway LA | Ladanyi M | Travis WD | Pao W | Rubin MA | Gabriel SB | Gibbs RA | Varmus HE | Wilson RK | Lander ES | Meyerson M
Nature | Dec 6, 2007

Somatic alterations in cellular DNA underlie almost all human cancers. The prospect of targeted therapies and the development of high-resolution, genome-wide approaches are now spurring systematic efforts to characterize cancer genomes. Here we report a large-scale project to characterize copy-number alterations in primary lung adenocarcinomas. By analysis of a large collection of tumours (n = 371) using dense single nucleotide polymorphism arrays, we identify a total of 57 significantly recurrent events. We find that 26 of 39 autosomal chromosome arms show consistent large-scale copy-number gain or loss, of which only a handful have been linked to a specific gene. We also identify 31 recurrent focal events, including 24 amplifications and 7 homozygous deletions. Only six of these focal events are currently associated with known mutations in lung carcinomas. The most common event, amplification of chromosome 14q13.3, is found in approximately 12% of samples. On the basis of genomic and functional analyses, we identify NKX2-1 (NK2 homeobox 1, also called TITF1), which lies in the minimal 14q13.3 amplification interval and encodes a lineage-specific transcription factor, as a novel candidate proto-oncogene involved in a significant fraction of lung adenocarcinomas. More generally, our results indicate that many of the genes that are involved in lung adenocarcinoma remain to be discovered.

Pubmed ID: 17982442 RIS Download

Mesh terms: Adenocarcinoma | Cell Line, Tumor | Chromosome Deletion | Chromosomes, Human, Pair 14 | Gene Amplification | Genome, Human | Genomics | Genotype | Humans | Intracellular Signaling Peptides and Proteins | Loss of Heterozygosity | Lung Neoplasms | Neoplasms | Nuclear Proteins | Polymorphism, Single Nucleotide | RNA Interference | Transcription Factors

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