TitleAuthorsAbstractMethods SummaryReferencesMethodsPrimary lung specimensSNP array experimentsPrimary SNP array data analysisArray quality control analysisGISTIC analysisGISTIC analysis of large-scale regionsGISTIC analysis of focal regionsData visualizationChromosome arm analysisComparison between tertilesEstimation of stromal contaminationLOH analysisCorrelation analysisCorrelation of clinical features and NKX2-1 amplificationOverall survival of patients with NKX2-1 amplificationSequencingMutation validation by genotypingPTPRD mutation discovery and validationTissue microarray FISH (TMA-FISH)Cell lines and cell culture conditionsRNAi knockdownSoft agar anchorage-independent growth assayCell proliferation assaysMethods ReferencesFigure 1 Large-scale genomic events in lung adenocarcinoma.Figure 2 High-prevalence amplification of the MBIP/NKX2-1 locus on chromosome 14q.Figure 3 NKX2-1 RNAi leads to reduced anchorage-independent growth and viability of NCI-H2009 cells but not A549 cells.Table 1 Top focal regions of amplification and deletionLETTERSCharacterizing the cancer genome inlung adenocarcinomaBarbara A. Weir1,2*, Michele S. Woo1*, Gad Getz2*, Sven Perner3,4, Li Ding5, Rameen Beroukhim1,2, William M. Lin1,2,Michael A. Province6, Aldi Kraja6, Laura A. Johnson3, Kinjal Shah1,2, Mitsuo Sato8, Roman K. Thomas1,2,9,10,Justine A. Barletta3, Ingrid B. Borecki6, Stephen Broderick11,12, Andrew C. Chang14, Derek Y. Chiang1,2,Lucian R. Chirieac3,16, Jeonghee Cho1, Yoshitaka Fujii18, Adi F. Gazdar8, Thomas Giordano15, Heidi Greulich1,2,Megan Hanna1,2, Bruce E. Johnson1, Mark G. Kris11, Alex Lash11, Ling Lin5, Neal Lindeman3,16, Elaine R. Mardis5,John D. McPherson19, John D. Minna8, Margaret B. Morgan19, Mark Nadel1,2, Mark B. Orringer14, John R. Osborne5,Brad Ozenberger20, Alex H. Ramos1,2, James Robinson2, Jack A. Roth21, Valerie Rusch11, Hidefumi Sasaki18,Frances Shepherd25, Carrie Sougnez2, Margaret R. Spitz22, Ming-Sound Tsao25, David Twomey2,Roel G. W. Verhaak2, George M. Weinstock19, David A. Wheeler19, Wendy Winckler1,2, Akihiko Yoshizawa11,Soyoung Yu1, Maureen F. Zakowski11, Qunyuan Zhang6, David G. Beer14, Ignacio I. Wistuba23,24, Mark A. Watson7,Levi A. Garraway1,2, Marc Ladanyi11,12, William D. Travis11, William Pao11,12, Mark A. Rubin2,3, Stacey B. Gabriel2,Richard A. Gibbs19, Harold E. Varmus13, Richard K. Wilson5, Eric S. Lander2,17,26& Matthew Meyerson1,2,16Somatic alterations in cellular DNA underlie almost all humancancers1. The prospect of targeted therapies2and the developmentof high-resolution, genome-wide approaches3–8are now spurringsystematic efforts to characterize cancer genomes. Here we reporta large-scale project to characterize copy-number alterations inprimary lung adenocarcinomas. By analysis of a large collectionof tumours (n 5 371) using dense single nucleotide polymorphismarrays, we identify a total of 57 significantly recurrent events. Wefind that 26 of 39 autosomal chromosome arms show consistentlarge-scale copy-number gain or loss, of which only a handful havebeen linked to a specific gene. We also identify 31 recurrent focalevents, including 24 amplifications and 7 homozygous deletions.Only six of these focal events are currently associated with knownmutations in lung carcinomas. The most common event, amp-lification of chromosome 14q13.3, is found in12% of samples.On the basis of genomic and functional analyses, we identifyNKX2-1 (NK2 homeobox 1, also called TITF1), which lies in theminimal 14q13.3 amplification interval and encodes a lineage-specific transcription factor, as a novel candidate proto-oncogeneinvolved in a significant fraction of lung adenocarcinomas. Moregenerally, our results indicate that many of the genes that areinvolved in lung adenocarcinoma remain to be discovered.A collection of 528 snap-frozen lung adenocarcinoma resectionspecimens, with at least 70% estimated tumour content, was selectedby a panel of thoracic pathologists (Supplementary Table 1); sampleswere anonymized to protect patient privacy. Tumour and normalDNAs were hybridized to Affymetrix 250K Sty single nucleotidepolymorphism (SNP) arrays. Genomic copy number for each of over238,000 probe sets was determined by calculating the intensity ratiobetween the tumour DNA and the average of a set of normalDNAs9,10. Segmented copy numbers for each tumour were inferredwith the GLAD (gain and loss analysis of DNA) algorithm11andnormalized to a median of two copies. Each copy number profilewas then subjected to quality control, resulting in 371 high-qualitysamples used for further analysis, of which 242 had matched normalsamples (Methods).To identify regions of copy-number alteration, we applied GISTIC(genomic identification of significant targets in cancer)12, a statisticalmethod that calculates a score that is based on both the amplitude andfrequency of copy-number changes at each position in the genome,using permutation testing to determine significance (Methods).GISTIC identified 26 large-scale events and 31 focal events,reported below. Although the overall pattern is broadly consistentwith the literature on lung cancer8,13–15, our sample size and resolu-tion provide more power to accurately identify and localize bothlarge-scale and focal chromosomal alterations. With respect tolarge-scale events, no single previous study has identified more than5 of the gains or 11 of the losses13,14(Supplementary Table 2). Withrespect to focal events, three recent studies8,14,15report a total of ,200events, including 23 of the 31 recurrent focal events observed in ourstudy. The overlap among these three studies is limited to only fourevents (amplification of EGFR, CCNE1, MDM2 and 8p11, all seen*These authors contributed equally to this work.1Department of Medical Oncology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.2Cancer Program, Genetic AnalysisPlatform, and Genome Biology Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.3Department of Pathology, Brigham and Women’s Hospital,Boston, Massachusetts 02115, USA.4Institute of Pathology, University of Ulm, Ulm 89081, Germany.5Genome Sequencing Center,6Division of Statistical Genomics and7Departmentof Pathology and Immunology, Washington University in Saint Louis, Saint Louis, Missouri 63130, USA.8University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.9Max Planck Institute for Neurological Research with