A small-cell lung cancer genome with complex signatures of tobacco exposure by Pleasance Erin D, Stephens Philip J, O'Meara Sarah, McBride David J, Meynert Alison, Jones David, Lin Meng-Lay, Beare David, Lau King Wai, Greenman Chris, Varela Ignacio, Nik-Zainal Serena, Davies Helen R, OrdoƱez Gonzalo R, Mudie Laura J, Latimer Calli, Edkins Sarah, Stebbings Lucy, Chen Lina, Jia Mingming, Leroy Catherine, Marshall John, Menzies Andrew, Butler Adam, Teague Jon W, Mangion Jonathon, Sun Yongming A, McLaughlin Stephen F, Peckham Heather E, Tsung Eric F, Costa Gina L, Lee Clarence C, Minna John D, Gazdar Adi, Birney Ewan, Rhodes Michael D, McKernan Kevin J, Stratton Michael R, Futreal P Andrew, Campbell Peter J in Nature (2010). PubMed

Abstract

Cancer is driven by mutation. Worldwide, tobacco smoking is the principal lifestyle exposure that causes cancer, exerting carcinogenicity through >60 chemicals that bind and mutate DNA. Using massively parallel sequencing technology, we sequenced a small-cell lung cancer cell line, NCI-H209, to explore the mutational burden associated with tobacco smoking. A total of 22,910 somatic substitutions were identified, including 134 in coding exons. Multiple mutation signatures testify to the cocktail of carcinogens in tobacco smoke and their proclivities for particular bases and surrounding sequence context. Effects of transcription-coupled repair and a second, more general, expression-linked repair pathway were evident. We identified a tandem duplication that duplicates exons 3-8 of CHD7 in frame, and another two lines carrying PVT1-CHD7 fusion genes, indicating that CHD7 may be recurrently rearranged in this disease. These findings illustrate the potential for next-generation sequencing to provide unprecedented insights into mutational processes, cellular repair pathways and gene networks associated with cancer.

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