Somatic DNA Copy Number Alterations Research Articles

A DNA copy number alteration classifier as a prognostic tool for prostate cancer patients.

Distinguishing between true indolent and potentially life-threatening prostate cancer is challenging in tumours displaying clinicopathologic features associated with low or intermediate risk of relapse. Several somatic DNA copy number alterations (CNAs) have been identified as potential prognostic biomarkers, but the standard cytogenetic method to assess them has a limited multiplexing capability. Multiplex ligation-dependent probe amplification (MLPA) targeting 14 genes was optimised to survey 448 tumours of patients with low or intermediaterisk (Grade Group 1-3, Gleason score ≤7) who underwent radical prostatectomy. A 6-gene CNA classifier was developed using random survival forest and Cox proportional hazard modelling to predict biochemical recurrence. The classifier score was significantly associated with biochemical recurrence after adjusting for standard clinicopathologic variables and the known prognostic index CAPRA-S score with a hazard ratio of 2.17 and 1.80, respectively (n = 406, P < 0.01). The prognostic value of this classifier was externally validated in published CNA data from three radical prostatectomy cohorts and one radiation therapy pre-treatment biopsy cohort. The 6-gene CNA classifier generated by a single MLPA assay compatible with the small quantities of DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue specimens has the potential to improve the clinical management of patients with low or intermediaterisk disease.

Abstract 1668: Development and characterization of a c-Myc-driven preclinical mouse model of osteosarcoma to investigate the tumor immune microenvironment

Abstract Osteosarcoma (OS) is the most common bone tumor in pediatric patients, particularly in adolescents and young adults. Currently, no effective molecular targeted therapies are available for the OS, however, many OS patients possess genetically defined somatic DNA copy number alterations, including amplification of chromosome 8q24, which harbors the oncogene Myc, and correlates with a worse prognosis. To better understand the molecular pathogenesis, and identify targeted therapy for OS, a robust and reliable preclinical model is needed both for the primary and metastatic disease. We have developed a novel conditional, osteoblast-specific Myc knock-in murine model to understand the mechanisms that underlie the ability of Myc to drive the development and progression of OS and utilize it for the identification of Myc-dependent intrinsic and extrinsic molecular vulnerabilities. A tissue-specific Myc-in genetically engineered murine model was generated by crossing Col2.3-Cre; TP53Flox/+ mice with LSL-MycT58A mice and characterized integrating RNA-seq and Mass Spectrometry. Syngeneic murine OS cell lines were also generated and characterized. The molecular characterization of the GEMM model was compared with high and low Myc expressing human tumors using the OS-TARGET dataset. Differential gene expression in Myc-driven and non-driven-tumor tissue samples were quantified by RNA sequencing. The immune landscape of OS was evaluated using SymphonyFACS and IHC staining. Murine OS tumor type was confirmed by H&amp;E staining. OS tumor was highly aggressive and metastatic in more than 60% of the mice. Myc expression was significantly higher both at the transcriptional and protein levels in the Myc-in tissue/cells compared to the non-Myc-driven model. Expression of 1479 genes (out of 13781 genes) were significantly altered in which 543 were upregulated and 936 were downregulated at transcriptional levels in Myc-in tumor tissue samples as compared to the low-Myc-driven OS tumor model analyzed by RNA sequencing. Myc-target-genes, splicing factor-related genes, E2F, G2M check-point, and DNA repair associated genes were significantly upregulated whereas the immune-related genes, oxidative phosphorylation, adipogenesis, and E2M transition genes were significantly downregulated when compared between two groups, which correlates to differential gene ontologies noted in high Myc human tumors. The total immune cell population, specifically the myeloid and macrophage populations were significantly diminished in the Myc-in tumor models, which could contribute to the poor prognosis in OS.Our murine model closely resembles human OS and will provide new opportunities for dissecting the molecular pathogenesis, identification of novel therapeutic strategies, and pre-clinical modeling for direct translational applications and targeting of Myc-driven OS. Citation Format: Bikesh K. Nirala, Lyazat Kurenbekova, Ryan L. Shuck, Tajhal Patel, Kimal Rajapakshe, Jason T. Yustein. Development and characterization of a c-Myc-driven preclinical mouse model of osteosarcoma to investigate the tumor immune microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1668.

Whole exome sequencing reveals BAP1 somatic abnormalities in mesothelioma in situ

ObjectivesWe have recently described the first cases of mesothelioma in situ, identified as a pure surface population of mesothelial cells that have lost BAP1 nuclear staining, in the setting of no clinically/radiologically demonstrable mesothelial tumor. These cases have a high propensity to develop invasive mesothelioma. The genetic events that lead to the development of mesothelioma in situ are unknown, nor is it known whether mesothelioma in situ cases carry somatic or germline mutations. Material and methodsWhole exome sequencing (WES) was performed on two cases of mesothelioma in situ (1 pleural, 1 peritoneal) and paired formalin fixed paraffin embedded normal tissue to characterize driver mutations and copy number alterations. ResultsThe analysis demonstrated somatic alterations in the BAP1 gene only. The pleural mesothelioma in situ showed copy number loss and LOH in the BAP1 locus on chromosome 3. The peritoneal mesothelioma in situ showed both a BAP1 somatic splice site mutation involving intron 5-exon 6 boundary (A126_splice) with an allelic fraction of 10%, and BAP1 copy number loss. No other driver point mutations, indels or somatic DNA copy number alterations reported to occur in invasive mesothelioma, or novel genetic alterations, were identified. ConclusionWhole exome sequencing confirms that mesothelioma in situ development is associated with BAP1 somatic mutations/deletions, and suggests that BAP1 mutation/deletion represents a very early event in the development of malignant mesothelioma. Whether BAP1 mutation/deletion alone is sufficient to lead to invasive mesothelioma or whether additional genetic alterations are required remains to be determined.

Feasibility and performance of a novel probe panel to detect somatic DNA copy number alterations in clinical specimens for predicting prostate cancer progression.

To assess the feasibility of a novel DNA-based probe panel to detect copy number alterations (CNAs) in prostate tumor DNA and its performance for predicting clinical progression. A probe panel was developed and optimized to measure CNAs in trace amounts of tumor DNA (2 ng) isolated from formalin-fixed paraffin-embedded tissues. Ten genes previously associated with aggressive disease were targeted. The panel's feasibility and performance were assessed in 175 prostate cancer (PCa) patients who underwent radical prostatectomy with a median 10-year follow-up, including 42 men who developed disease progression (either metastasis and/or PCa-specific death). Association with disease progression was tested using univariable and multivariable analyses. The probe panel detected CNAs in all 10 genes in tumor DNA isolated from either diagnostic biopsies or surgical specimens. A four-gene model (PTEN/MYC/BRCA2/CDKN1B) had the strongest association with disease progression; 64.3% of progressors and 22.5% of non-progressors had at least one CNA in these four genes, odds ratio (OR) (95% confidence interval) = 6.21 (2.77-13.87), P = 8.48E-06. The association with disease progression remained significant after adjusting for known clinicopathological variables. Among the seven progressors of the 65 patients with clinically low-risk disease, three (42.9%) had at least one CNA in these four genes. The probe panel can detect CNAs in trace amounts of tumor DNA from biopsies or surgical tissues at the time of diagnosis or surgery. CNAs independently predict metastatic/lethal cancer, particularly among men with clinically low-risk disease at diagnosis. If validated, this may improve current abilities to assess tumor aggressiveness.

Abstract 6147: Myc-driven osteosarcoma murine model for dissecting the molecular genetics and novel therapeutic strategies for OS

Abstract Osteosarcoma (OS) is the most common bone tumor in pediatric patients, particularly in adolescents and young adults. Unfortunately, over the past four decades, there has been minimal progress towards improving patient outcomes, especially for those with metastatic disease. Currently, no effective molecular targeted therapies are available for the OS, however many OS patients possess genetically defined somatic DNA copy number alterations (SCNAs), including amplification of chromosome 8q24. 8q24.2 region harbors the oncogene c-Myc, and the SCNA is associated with decreased overall survival rates. Furthermore, enhanced c-Myc transcript levels are significantly correlated with worse prognosis. There is a scarcity of reliable and reproducible in vivo animal models that mimic SCNAs and can be used to provide both intrinsic and extrinsic molecular insights into c-Myc-osteosarcoma biology. We have developed a novel conditional c- Myc knock-in mouse model to understand the mechanisms that underlie the ability of c-Myc to drive development and progression of OS and utilize for identification of c-Myc-dependent molecular vulnerabilities. A tissue-specific GEMM for osteosarcoma was developed by altering p53 (f/+) and c-Myc (c- Myc-in) genes in the osteoblast derived cells. Either c-Myc WT or the c-Myc T58A phosphorylation mutant was knocked-in from the constitutively active ROSA26 locus in response to Cre-recombinase. Differential gene expression in c-Myc-driven and non-driven-tumor tissue samples were quantified by RNA sequencing. The protein expression profiles were evaluated for both groups by comprehensive mass spectrometry (MS) analysis and reverse phase proteome analysis (RPPA). Osteosarcoma was confirmed for GEMM tumors by histopathological (H&amp;E) staining. The spontaneous tumor development was significantly accelerated and more aggressive in c-Myc- driven GEMMs as compared to the non-c-Myc-driven. c-Myc expression was significantly higher both at the transcriptional and protein levels in the c-Myc-driven tissue/cells. Expression of 1479 genes (out of 13781 genes) were significantly altered at transcriptional levels in c-Myc driven tumor tissue samples, analyzed by RNA sequencing. Myc-target, E2F, G2M check-point, KRAS and DNA repair associated genes were significantly upregulated whereas the protein secretion, oxidative phosphorylation, adipognenesis, myhogenesis, and E2M transition genes were significantly downregulated when compared with the non-c-Myc-driven group. A significant alteration was observed in the protein expression levels of ribosome biogenesis, DNA replication, nucleotide excision repair, mismatch repair and RNA degradation associated genes in MS data analysis. Our mouse model has high penetrance, short latency, closely resembles human OS and will provide new opportunities for dissecting the molecular genetics of OS and developing novel therapeutic strategies. This model has also provided syngeneic cell lines for future in vivo studies. Citation Format: Bikesh Kumar Nirala, Kurenbekova Lyazat, Tajhal Patel, Ryan Lane Shuck, Rajapakshe Kimal, Jason T. Yustein. Myc-driven osteosarcoma murine model for dissecting the molecular genetics and novel therapeutic strategies for OS [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6147.

Somatic DNA copy number alterations in non-dysplastic Barrett's esophagus.

The purpose of this study was to analyze non-dysplastic Barrett's esophagus (NDBE) biopsy tissue and compare the rate of somatic DNA copy number alterations (CNAs) in patients who subsequently progressed to high-grade dysplasia (HGD) or esophageal adenocarcinoma (EAC) to those patients who did not. A retrospectively collected database of Barrett's esophagus (BE) patients spanning a 16-year period was queried. Patients who progressed from NDBE to HGD or EAC were identified and compared to patients who did not. Initial biopsy specimens were microdissected and extracted DNA underwent Multiplex Ligation-dependent Probe Amplification (MLPA) for CNAs. Comparisons between progressors and non-progressors were made with Fisher's exact and two-sample t tests. Logistic regression assessed factors associated with progression. Of the 2459 patients in the BE database, 36 patients progressed from NDBE to either HGD or EAC. There were eight progressors who had biopsy specimens with adequate DNA for analysis. The progressor and non-progressor cohort had similar demographic information and medical history. The progressor group trended towards being older at diagnosis (72 ± 10 vs. 64 ± 13years, p = 0.097) and fewer progressors reported reflux symptoms (50 vs. 94.7%, p < 0.001). Progressor specimens had more overall CNAs (75% vs. 33.6%, p = 0.026). On univariable analysis, there was an association between progression and absence of GERD symptoms (OR 16.54 [3.42-80.03], p = 0.001), any CNA (OR 5.10 [1.18-23.30], p = 0.035), and CNA in GATA6 or ERBB2 (OR 6.72 [1.18-38.22], p = 0.032). Patients who progressed from NDBE to HGD or EAC were older at first diagnosis of BE and fewer of the progressors reported symptoms of reflux when compared to non-progressors. Progression was associated with the presence of any CNA and specific CNAs in GATA6 or ERBB2.

Abstract 2561: Integrated analysis of ESCC tumor/normal tissues and patient blood samples using expression, genotypes and DNA somatic change data

Abstract Esophageal cancer is the eighth most common and sixth most frequent fatal human cancer in the world, and the fourth most common incident cancer in China. Shanxi Province, a region in north central China, has among the highest esophageal cancer rates in China, and nearly all of these cases are esophageal squamous cell carcinoma (ESCC). Understanding the molecular mechanisms underlying esophageal carcinogenesis and its molecular pathology will facilitate the development of biomarkers for early detection to reduce ESCC mortality. Genome-wide association studies (GWAS) have found many loci associated with the development of ESCC, however, most of the significant SNPs identified by GWAS are noncoding variants with unknown functions located in intergenic regions far from genes and are difficult to study functionally. As an initial effort to identify causal variants for ESCC, we focused here on loci near genes with known biological functions. Our analysis consists of three steps. We identified some functional variants for ESCC in the second and third steps of the analysis. First, from the GWAS analysis we selected those loci in or around the genes in three important pathways - inflammation, immunity, and DNA repair - using information from KEGG, Biocarta, and GO databases. We selected loci which had their 95% confidence intervals of the odds ratios not including OR = 1 based on GWAS analysis. Second, we integrated the expression and genotype data from ESCC somatic and germline samples and computed eQTLs using the normal tissues for n = 100 cases which had both gene expression data and GWAS genotype data. We found some interesting results from the second step analysis. The top 20 most significant genes included XPC, TP73, CASP8, DAPK1, IGF1R and LEPR, which were implicated in different cancers (Cancer Genetics Web: http://www.cancer-genetics.org). CASP8 was known to be involved in apoptosis processes. It was significantly associated with early onset of esophageal adenocarcinoma (Wu et al, Neoplasia. 2011 Apr;13(4):386-92). It had been shown that IGF1R had a key role in malignant progression of esophageal cancer (Kalinina et al, Int J Cancer. 2010 Oct 15;127(8):1931-40; Doyle et al, Am J Gastroenterol. 2012 Feb;107(2):196-204). Finally, we further intersected these significant loci in the eQTL analysis with the loci that had significant association between genotype and the somatic DNA copy number alterations. One of the significant genes was ST6GAL1. It had been reported this gene may promote malignant progression by promoting the TGF-beta induced EMT through down-regulation of E-cadherin-mediated cell adhesion and up-regulation of integrin-mediated cell migration (J. Lu et al, J Biol Chem. 2014 Dec 12;289(50):34627-41). We also found some novel genes in the analyses and their relation to ESCC will be investigated in future. Citation Format: Howard H. Yang, Hua Su, Huaitian Liu, Nan Hu, Chaoyu Wang, Lemin Wang, Ti Ding, Carol Giffen, Alisa M. Goldstein, Philip R. Taylor, Maxwell P. Lee. Integrated analysis of ESCC tumor/normal tissues and patient blood samples using expression, genotypes and DNA somatic change data. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2561.

The sum of gains and losses of genes encoding the protein tyrosine kinase targets predicts response to multi-kinase inhibitor treatment: Characterization, validation, and prognostic value.

Validated predictive biomarkers for multi-tyrosine kinase inhibitors (MTKI) efficacy are lacking. We hypothesized that interindividual response variability is partially dependent on somatic DNA copy number alterations (SCNAs), particularly those of genes encoding the protein tyrosines targeted by MTKI (called target genes). Genomic alterations were investigated in MTKI responsive and non responsive patients with different histological subtypes included in the ProfiLER protocol (NCT 01774409). From March 2013 to August 2014, 58 patients with advanced cancer treated with one of 7 MTKIs were included in the ProfiLER trial and split into one discovery cohort (n = 13), and 2 validation cohorts (n = 12 and 33). An analysis of the copy number alterations of kinase-coding genes for each of 7 MTKIs was conducted. A prediction algorithm (SUMSCAN) based on the presence of specific gene gains (Tumor Target Charge, TTC) and losses (Tumor Target Losses, TTL) was conceived and validated in 2 independent validation cohorts. MTKI sensitive tumors present a characteristic SCNA profile including a global gain profile, and specific gains for target genes while MTKI resistant tumors present the opposite. SUMSCAN favorable patients achieved longer progression-free and overall survival. This work shows that the copy number sum of kinase-coding genes enables the prediction of response of cancer patients to MTKI, opening a novel paradigm for the treatment selection of these patients.

Somatic DNA copy number alterations and their potential clinical utility for predicting lethal prostate cancer.

Current clinicopathologic indicators are insufficient to distinguish the small percentage of aggressive prostate cancer (PCa) from the vast majority of indolent disease at diagnosis, leading to overtreatment of PCa. A recent study reported and confirmed a strong association of PCa-specific mortality with somatic DNA copy number alterations (CNAs) in primary prostate tumors. If a sensitive, robust and low-cost method can be developed to measure these CNAs in biopsy specimens, it may help to stratify patients for more appropriate management at the time of diagnosis; aggressive treatment or active surveillance for patients with or without these CNAs, respectively. A study on the association of somatic DNA copy number alterations (CNAs) in prostate tumors with lethal prostate cancer (PCa) by our collaborative group of Wake Forest University School of Medicine, the Brady Urological Institute of Johns Hopkins Medical Institutions, and the Karolinska Institute of Sweden was recently published in Cancer.1 Shortly after, two abstracts on the association of RNA expression of two different panels of genes with progression of PCa were presented by investigators from Mayo Clinic and University of California at San Francisco, respectively, in the 2013 American Urology Association Annual meeting.2,3 These studies all focused on the prognosis of PCa and received great attention in the scientific and clinical communities as well as in public, as evidenced by the news coverage. The excitement surrounding these studies is not surprising because distinguishing aggressive from indolent forms of PCa is probably the most important clinical task in managing and treating this heterogeneous disease. Most prostate tumors grow so slowly that they may never threaten a man's life; however, ∼15% are lethal if not treated appropriately. Currently used clinical predictors such as Gleason score and tumor stages are useful but insufficient to discriminate between the two types of PCa at the time of diagnosis. This inability leads to unnecessary and intensive treatment of many PCa patients, reducing their quality of life, and incurring financial burden to patients, families and society. Novel biomarkers are urgently needed to better identify aggressive PCa at the time of diagnosis for selection of treatment strategy; a choice of active surveillance for indolent PCa or intensive treatment for aggressive PCa. In this perspective piece, we highlight the key points of our Cancer paper on the association of CNAs with lethal PCa,1 discuss their advantages as markers for lethal PCa and describe the challenges for translating the genomic findings to clinics.

No evidence of somatic DNA copy number alterations in eutopic and ectopic endometrial tissue in endometriosis

De novo somatic copy number aberrations (SCNAs) in eutopic and ectopic endometria are thought to be involved in the pathogenesis of endometriosis. In this study we used, for the first time, high-density single nucleotide polymorphism-array technology for accurate detection of SCNAs, inherited DNA copy number variations (CNVs) and copy-neutral loss of heterozygosity (cn-LOH) patterns in patients with endometriosis. The Illumina HumanOmniExpress array was used to detect de novo somatic genomic alterations in eutopic and ectopic endometria from 11 women (eight with Stage I-II endometriosis and three with Stage III-IV endometriosis) by comparatively analysing DNA from peripheral blood, eutopic endometrium and a pure population of endometriotic cells harvested from endometriotic lesions by laser capture microdissection (LCM). The frequency of the CNV in 3p14.1 from blood DNA of 187 endometriosis patients (94 with Stage I-II endometriosis and 93 with Stage III-IV endometriosis) and 171 healthy women from the Estonian general population was evaluated. Analysis of array data showed that LCM DNA can be used successfully for detection of genetic changes as all inherited CNVs were identified in all tissues studied. No unique SCNAs or cases of cn-LOH were found in either eutopic or ectopic endometrium when compared with blood DNA. The frequency of the deletion allele in 3p14.1 did not differ between studied groups. In the present study no endometriosis-specific SCNAs or regions of cn-LOH in eutopic or ectopic endometrium were found. Nevertheless, as we studied only 17 endometriotic tissues derived from 11 patients we cannot entirely exclude the occurrence of rare SCNAs. Based on our results we suggest that molecular mechanisms other than chromosomal rearrangements most likely underlie the onset and progression of endometriosis.

Abstract A53: Genome-wide profile of somatic copy number alterations in Wilms tumor: Comparison between samples derived from patients with and without relapse

Abstract Wilms tumor (WT) is the most common kidney malignancy of childhood; nevertheless, its pathogenesis remains largely unknown. Although the majority of the WT occur sporadically, a strong genetic component is present at least in the many cases which are related to underlying syndromes. Tumor relapse occurs at a rate of approximately 15%, and molecular studies are focused in identifying markers to define the minimal therapy for limiting the late effects of treatment while maintaining high survival rate. Loss of heterozygosity of both 1p and 16q was already associated to an increased risk of relapse and death although detected in a very small subset of WT patients, making this feature a less sensitive prognostic factor. Somatic DNA copy number alterations (CNAs) are common genetic mutations in cancer, and often define key pathogenic events. This study was designed to assess the genome profile of CNAs in WT, aiming to identify genetic markers associated to relapse that could be of clinical and prognostic importance. We performed an array-CGH based survey of 48 WT samples, mainly tumors in stages III and IV, derived from patients with (17) and without (31) relapse in at least three years. Data was obtained using a high resolution oligoarray platform (180K - Agilent), with an average resolution &amp;gt;70 Kb, and analysis was performed on the software Nexus 6 (Biodiscovery). The analysis revealed high frequency of arm/whole chromosome alterations at 1q, 7q, and chromosomes 6 and 12 (gains), while losses were recurrent at 7p, 11 q, and 16q chromosome regions. WT derived from patients with relapse exhibited a distinctive pattern of genomic alterations, mainly characterized for an increased frequency of proximal 1q gain and low amplitude gain of chromosome 6. Additionally, analysis of small regions affected by recurrent focal alterations disclosed new genes that can be relevant for Wilms tumorigenesis and relapse. Financial support: FAPESP/CNPq Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr A53.

BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data

Identification of somatic DNA copy number alterations (CNAs) and significant consensus events (SCEs) in cancer genomes is a main task in discovering potential cancer-driving genes such as oncogenes and tumor suppressors. The recent development of SNP array technology has facilitated studies on copy number changes at a genome-wide scale with high resolution. However, existing copy number analysis methods are oblivious to normal cell contamination and cannot distinguish between contributions of cancerous and normal cells to the measured copy number signals. This contamination could significantly confound downstream analysis of CNAs and affect the power to detect SCEs in clinical samples. We report here a statistically principled in silico approach, Bayesian Analysis of COpy number Mixtures (BACOM), to accurately estimate genomic deletion type and normal tissue contamination, and accordingly recover the true copy number profile in cancer cells. We tested the proposed method on two simulated datasets, two prostate cancer datasets and The Cancer Genome Atlas high-grade ovarian dataset, and obtained very promising results supported by the ground truth and biological plausibility. Moreover, based on a large number of comparative simulation studies, the proposed method gives significantly improved power to detect SCEs after in silico correction of normal tissue contamination. We develop a cross-platform open-source Java application that implements the whole pipeline of copy number analysis of heterogeneous cancer tissues including relevant processing steps. We also provide an R interface, bacomR, for running BACOM within the R environment, making it straightforward to include in existing data pipelines. The cross-platform, stand-alone Java application, BACOM, the R interface, bacomR, all source code and the simulation data used in this article are freely available at authors' web site: http://www.cbil.ece.vt.edu/software.htm.

Arsenic-related DNA copy-number alterations in lung squamous cell carcinomas

Background:Lung squamous cell carcinomas (SqCCs) occur at higher rates following arsenic exposure. Somatic DNA copy-number alterations (CNAs) are understood to be critical drivers in several tumour types. We have assembled a rare panel of lung tumours from a population with chronic arsenic exposure, including SqCC tumours from patients with no smoking history.Methods:Fifty-two lung SqCCs were analysed by whole-genome tiling-set array comparative genomic hybridisation. Twenty-two were derived from arsenic-exposed patients from Northern Chile (10 never smokers and 12 smokers). Thirty additional cases were obtained for comparison from North American smokers without arsenic exposure. Twenty-two blood samples from healthy individuals from Northern Chile were examined to identify germline DNA copy-number variations (CNVs) that could be excluded from analysis.Results:We identified multiple CNAs associated with arsenic exposure. These alterations were not attributable to either smoking status or CNVs. DNA losses at chromosomes 1q21.1, 7p22.3, 9q12, and 19q13.31 represented the most recurrent events. An arsenic-associated gain at 19q13.33 contains genes previously identified as oncogene candidates.Conclusions:Our results provide a comprehensive approach to molecular characteristics of the arsenic-exposed lung cancer genome and the non-smoking lung SqCC genome. The distinct and recurrent arsenic-related alterations suggest that this group of tumours may be considered as a separate disease subclass.