The Inclusion of Practical Urology Skills in Intern Induction: A Pilot Programme

Introduction Intern is the first postgraduate year of training and gives interns the opportunity to practice skills in real-life settings. We aim to examine the undergraduate exposure to urology across all Irish Medical Schools and assess the impact of a mandatory urology training skills session delivered during induction on the preparedness of interns ahead of starting their intern year. Methods In July 2020 all interns mandated to attend the Dublin/Mid-Leinster (DML) network intern induction underwent a 120-minute urology teaching session. The session comprised of formal teaching, followed by practical training and an informal question and answer session. All interns were asked to complete a survey before and after the session that examined undergraduate urology exposure and confidence around practical skills. Results All interns (n=74) who attended induction completed the survey. Less than half [43% (n=32]) reported a compulsory urology placement in medical school and 57% (n=42) reported previous practical training sessions in urology. There was low level of confidence in the management of urological scenarios with only 45 % (n = 33) reporting confidence in the management of urosepsis and 26 % (n = 19) in the insertion of a male catheter. There was a significant increase in self-reported confidence following the teaching session with 78 % (n = 58) interns reporting confidence in the management of urosepsis and 81 % (n = 60) in the insertion of a male catheter. Conclusion To ensure best patient care interns need to be trained in the management of common urology presentations, but our results suggest the current undergraduate curriculum is not sufficient. A dedicated theory and practical urology teaching session during intern induction was able to improve self-reported confidence and better prepare interns. Therefore we support inclusion of practical urology skills session in network intern induction.

Technology Feature | Small images, big picture: Artificial intelligence to revolutionize microscopy

Researchers hope that bringing deep learning techniques to cell imaging and analysis could turn messy biological problems into solvable computations.

Bladder cancer in Ireland: a 21-year review

INTRODUCTION

Bladder carcinoma is one of the most commonly diagnosed cancers worldwide; however, various studies have reported on marked international variation in incidence and mortality rates. The aim of this study was to report national figures on incidence, survival and risk factors of bladder cancer. This retrospective review is the first to offer a comprehensive analysis of incidence rates, mortality and potential risk factors in the Irish population from 1994 to 2015.

METHODS

This was a retrospective study of incidence and survival trends in bladder cancer in the Irish population from 1994 to 2014 based on data from the National Cancer Registry of Ireland (NCRI). Patient demographics, pathology and survival data, as well as potential contributing factors, were studied.

RESULTS

A total of 9656 cases of bladder cancer were diagnosed from 1994 to 2015, with majority of cases occurring in males (71%). Survival decreased with increasing age, higher grade and higher stage. Bladder cancer is more common in those with a smoking history and with a higher deprivation score. Urothelial cell carcinoma was the most common pathology (95%), with the majority of patients being stage 1 or 2 (44.7%).

CONCLUSION

The overall incidence of bladder cancer in Ireland has fallen, in line with reducing smoking rates. Our data reflects international trends in incidence, survival and contributing risk factors.

Author Correction: The evolutionary history of lethal metastatic prostate cancer

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Technology Feature | The road to reducing traffic accidents in China

Biomarkers for neurological diseases used to be few and far between, but better technology is making it easier for researchers to track brain health by measuring molecules. This means less invasive testing, earlier diagnosis, faster drug development, and—hopefully—more effective treatments.

Augmented exercise in hospital improves physical performance and reduces negative post hospitalization events: a randomized controlled trial

BACKGROUND

To measure the effects of an augmented prescribed exercise programme versus usual care, on physical performance, quality of life and healthcare utilisation for frail older medical patients in the acute setting.

METHODS

This was a parallel single-blinded randomised controlled trial. Within 2 days of admission, older medical inpatients with an anticipated length of stay ≥3 days, needing assistance/aid to walk, were blindly randomly allocated to the intervention or control group. Until discharge, both groups received twice daily, Monday-to-Friday half-hour assisted exercises, assisted by a staff physiotherapist. The intervention group completed tailored strengthening and balance exercises; the control group performed stretching and relaxation exercises. Length of stay was the primary outcome measure. Blindly assessed secondary measures included readmissions within 3 months, and physical performance (Short Physical Performance Battery) and quality of life (EuroQOL-5D-5 L) at discharge and at 3 months. Time-to-event analysis was used to measure differences in length of stay, and regression models were used to measure differences in physical performance, quality of life, adverse events (falls, deaths) and negative events (prolonged hospitalisation, institutionalisation).

RESULTS

Of the 199 patients allocated, 190 patients' (aged 80 ± 7.5 years) data were analysed. Groups were comparable at baseline. In intention-to-treat analysis, length of stay did not differ between groups (HR 1.09 (95% CI, 0.77-1.56) p = 0.6). Physical performance was better in the intervention group at discharge (difference 0.88 (95% CI, 0.20-1.57) p = 0.01), but lost at follow-up (difference 0.45 (95% CI, - 0.43 - 1.33) p = 0.3). An improvement in quality of life was detected at follow-up in the intervention group (difference 0.28 (95% CI, 0.9-0.47) p = 0.004). Overall, fewer negative events occurred in the intervention group (OR 0.46 (95% CI 0.23-0.92) p = 0.03).

CONCLUSION

Improvements in physical performance, quality of life and fewer negative events suggest that this intervention is of value to frail medical inpatients. Its effect on length of stay remains unclear.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT02463864, registered prospectively 26.05.2015.

Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

Multiple signatures of somatic mutations have been identified in cancer genomes. Exome sequences of 1,001 human cancer cell lines and 577 xenografts revealed most common mutational signatures, indicating past activity of the underlying processes, usually in appropriate cancer types. To investigate ongoing patterns of mutational-signature generation, cell lines were cultured for extended periods and subsequently DNA sequenced. Signatures of discontinued exposures, including tobacco smoke and ultraviolet light, were not generated in vitro. Signatures of normal and defective DNA repair and replication continued to be generated at roughly stable mutation rates. Signatures of APOBEC cytidine deaminase DNA-editing exhibited substantial fluctuations in mutation rate over time with episodic bursts of mutations. The initiating factors for the bursts are unclear, although retrotransposon mobilization may contribute. The examined cell lines constitute a resource of live experimental models of mutational processes, which potentially retain patterns of activity and regulation operative in primary human cancers.

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Annotation of mutational signatures across 1,001 cancer cell lines and 577 PDXs

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Activities of mutational processes determined over time in cancer cell lines

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APOBEC-associated mutagenesis is often ongoing and can be episodic

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Detection of mutational signatures by single-cell sequencing

Classification and Personalized Prognosis in Myeloproliferative Neoplasms

BACKGROUND

Myeloproliferative neoplasms, such as polycythemia vera, essential thrombocythemia, and myelofibrosis, are chronic hematologic cancers with varied progression rates. The genomic characterization of patients with myeloproliferative neoplasms offers the potential for personalized diagnosis, risk stratification, and treatment.

METHODS

We sequenced coding exons from 69 myeloid cancer genes in patients with myeloproliferative neoplasms, comprehensively annotating driver mutations and copy-number changes. We developed a genomic classification for myeloproliferative neoplasms and multistage prognostic models for predicting outcomes in individual patients. Classification and prognostic models were validated in an external cohort.

RESULTS

A total of 2035 patients were included in the analysis. A total of 33 genes had driver mutations in at least 5 patients, with mutations in JAK2, CALR, or MPL being the sole abnormality in 45% of the patients. The numbers of driver mutations increased with age and advanced disease. Driver mutations, germline polymorphisms, and demographic variables independently predicted whether patients received a diagnosis of essential thrombocythemia as compared with polycythemia vera or a diagnosis of chronic-phase disease as compared with myelofibrosis. We defined eight genomic subgroups that showed distinct clinical phenotypes, including blood counts, risk of leukemic transformation, and event-free survival. Integrating 63 clinical and genomic variables, we created prognostic models capable of generating personally tailored predictions of clinical outcomes in patients with chronic-phase myeloproliferative neoplasms and myelofibrosis. The predicted and observed outcomes correlated well in internal cross-validation of a training cohort and in an independent external cohort. Even within individual categories of existing prognostic schemas, our models substantially improved predictive accuracy.

CONCLUSIONS

Comprehensive genomic characterization identified distinct genetic subgroups and provided a classification of myeloproliferative neoplasms on the basis of causal biologic mechanisms. Integration of genomic data with clinical variables enabled the personalized predictions of patients' outcomes and may support the treatment of patients with myeloproliferative neoplasms. (Funded by the Wellcome Trust and others.).

Analysis of the genomic landscape of multiple myeloma highlights novel prognostic markers and disease subgroups

In multiple myeloma, next-generation sequencing (NGS) has expanded our knowledge of genomic lesions, and highlighted a dynamic and heterogeneous composition of the tumor. Here we used NGS to characterize the genomic landscape of 418 multiple myeloma cases at diagnosis and correlate this with prognosis and classification. Translocations and copy number abnormalities (CNAs) had a preponderant contribution over gene mutations in defining the genotype and prognosis of each case. Known and novel independent prognostic markers were identified in our cohort of proteasome inhibitor and immunomodulatory drug-treated patients with long follow-up, including events with context-specific prognostic value, such as deletions of the PRDM1 gene. Taking advantage of the comprehensive genomic annotation of each case, we used innovative statistical approaches to identify potential novel myeloma subgroups. We observed clusters of patients stratified based on the overall number of mutations and number/type of CNAs, with distinct effects on survival, suggesting that extended genotype of multiple myeloma at diagnosis may lead to improved disease classification and prognostication.

Satisfaction rates with the current Special Type Consultation (STC) reimbursement scheme among General Practitioners - A Mixed Methods Study

The Special Type Consultation (STC) scheme is a fee-for-service reimbursement scheme for General Practitioners (GPs) in Ireland. Introduced in 1989, the scheme includes specified patient services involving the application of a learned skill, e.g. suturing. This study aims to establish the extent to which GPs believe this scheme is appropriate for current General Practice. This is an embedded mixed-methods study combining quantitative data on GPs working experience of and qualitative data on GPs attitudes towards the scheme. Data were collected by means of an anonymous postal questionnaire. The response rate was 60.4% (n=159.) Twenty-nine percent (n=46) disagreed and 65% (n=104) strongly disagreed that the current list of special items is satisfactory. Two overriding themes were identified: economics and advancement of the STC process. This study demonstrates an overwhelming consensus among GPs that the current STC scheme is outdated and in urgent need of revision to reflect modern General Practice.

Genomic Classification and Prognosis in Acute Myeloid Leukemia

BACKGROUND

Recent studies have provided a detailed census of genes that are mutated in acute myeloid leukemia (AML). Our next challenge is to understand how this genetic diversity defines the pathophysiology of AML and informs clinical practice.

METHODS

We enrolled a total of 1540 patients in three prospective trials of intensive therapy. Combining driver mutations in 111 cancer genes with cytogenetic and clinical data, we defined AML genomic subgroups and their relevance to clinical outcomes.

RESULTS

We identified 5234 driver mutations across 76 genes or genomic regions, with 2 or more drivers identified in 86% of the patients. Patterns of co-mutation compartmentalized the cohort into 11 classes, each with distinct diagnostic features and clinical outcomes. In addition to currently defined AML subgroups, three heterogeneous genomic categories emerged: AML with mutations in genes encoding chromatin, RNA-splicing regulators, or both (in 18% of patients); AML with TP53 mutations, chromosomal aneuploidies, or both (in 13%); and, provisionally, AML with IDH2(R172) mutations (in 1%). Patients with chromatin-spliceosome and TP53-aneuploidy AML had poor outcomes, with the various class-defining mutations contributing independently and additively to the outcome. In addition to class-defining lesions, other co-occurring driver mutations also had a substantial effect on overall survival. The prognostic effects of individual mutations were often significantly altered by the presence or absence of other driver mutations. Such gene-gene interactions were especially pronounced for NPM1-mutated AML, in which patterns of co-mutation identified groups with a favorable or adverse prognosis. These predictions require validation in prospective clinical trials.

CONCLUSIONS

The driver landscape in AML reveals distinct molecular subgroups that reflect discrete paths in the evolution of AML, informing disease classification and prognostic stratification. (Funded by the Wellcome Trust and others; ClinicalTrials.gov number, NCT00146120.).

A study protocol of a randomised controlled trial to measure the effects of an augmented prescribed exercise programme (APEP) for frail older medical patients in the acute setting

Background

Older adults experience functional decline in hospital leading to increased healthcare burden and morbidity. The benefits of augmented exercise in hospital remain uncertain. The aim of this trial is to measure the short and longer-term effects of augmented exercise for older medical in-patients on their physical performance, quality of life and health care utilisation.

Design & Methods

Two hundred and twenty older medical patients will be blindly randomly allocated to the intervention or sham groups. Both groups will receive usual care (including routine physiotherapy care) augmented by two daily exercise sessions. The sham group will receive stretching and relaxation exercises while the intervention group will receive tailored strengthening and balance exercises. Differences between groups will be measured at baseline, discharge, and three months. The primary outcome measure will be length of stay. The secondary outcome measures will be healthcare utilisation, activity (accelerometry), physical performance (Short Physical Performance Battery), falls history in hospital and quality of life (EQ-5D-5 L).

Discussion

This simple intervention has the potential to transform the outcomes of the older patient in the acute setting.

Trial registration

ClinicalTrials.gov Identifier: NCT02463864, registered 26.05.2015.

Abstract 956: The evolutionary history of lethal metastatic prostate cancer

Cancers emerge from an on-going Darwinian evolutionary process, often leading to multiple competing subclones within a single primary tumour. This evolutionary process culminates in the formation of metastases, which is the cause of 90% of cancer-related deaths. However, despite its clinical importance, little is known about the principles governing the dissemination of cancer cells to distant organs. Although the hypothesis that each metastasis originates from a single tumour cell is generally supported, recent studies using mouse models of cancer demonstrated the existence of polyclonal seeding from and inter-clonal cooperation between multiple subclones. In this study, we sought definitive evidence for the existence of polyclonal seeding in human malignancy and to establish the clonal relationship among different metastases in the context of androgen-deprived metastatic prostate cancer. Using whole genome sequencing, we characterised multiple metastases arising from prostate tumours in ten patients. Integrated analyses of subclonal architecture revealed the patterns of metastatic spread in unprecedented detail. Metastasis-to-metastasis spread was found to be common, either through de novo monoclonal seeding of daughter metastases or, in five cases, through the transfer of multiple tumour clones between metastatic sites. Lesions affecting tumour suppressor genes usually occur as single events, whereas mutations in genes involved in androgen receptor signalling commonly involve multiple, convergent events in different metastases. Our results elucidate in detail the complex patterns of metastatic spread and further our understanding of the development of resistance to androgen deprivation therapy in prostate cancer.

Citation Format: Gunes Gundem, Peter Van Loo, Barbara Kremeyer, Ludmil B. Alexandrov, Jose M.C. Tubio, Elli Papaemmanuil, Daniel S. Brewer, Heini Kallio, Gunilla Högnäs, Matti Annala, Kati Kivinummi, Victoria Goody, Calli Latimer, Sarah O'Meara, Kevin J. Dawson, William Isaacs, Michael R. Emmert-Buck, Matti Nykter, Christopher Foster, Zsofia Kote-Jarai, Douglas Easton, Hayley C. Whitaker, David E. Neal, Colin S. Cooper, Rosalind A. Eeles, Tapio Visakorpi, Peter J. Campbell, Ultan McDermott, David C. Wedge, G. S. Bova. The evolutionary history of lethal metastatic prostate cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 956. doi:10.1158/1538-7445.AM2015-956

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue

Genome-wide DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men. Mutations were present at high levels in morphologically normal tissue distant from the cancer, reflecting clonal expansions, and the underlying mutational processes at work in morphologically normal tissue were also at work in cancer. Our observations demonstrate the existence of ongoing abnormal mutational processes, consistent with field effects, underlying carcinogenesis. This mechanism gives rise to extensive branching evolution and cancer clone mixing, as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule. Subsets of mutations were shared either by morphologically normal and malignant tissues or between different ERG lineages, indicating earlier or separate clonal cell expansions. Our observations inform on the origin of multifocal disease and have implications for prostate cancer therapy in individual cases.

Polygenic in vivo validation of cancer mutations using transposons

The in vivo validation of cancer mutations and genes identified in cancer genomics is resource-intensive because of the low throughput of animal experiments. We describe a mouse model that allows multiple cancer mutations to be validated in each animal line. Animal lines are generated with multiple candidate cancer mutations using transposons. The candidate cancer genes are tagged and randomly expressed in somatic cells, allowing easy identification of the cancer genes involved in the generated tumours. This system presents a useful, generalised and efficient means for animal validation of cancer genes.

The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models

Background

Melanoma is the most deadly form of skin cancer. Expression of oncogenic BRAF or NRAS, which are frequently mutated in human melanomas, promote the formation of nevi but are not sufficient for tumorigenesis. Even with germline mutated p53, these engineered melanomas present with variable onset and pathology, implicating additional somatic mutations in a multi-hit tumorigenic process.

Results

To decipher the genetics of these melanomas, we sequence the protein coding exons of 53 primary melanomas generated from several BRAF^V600E or NRAS^Q61K driven transgenic zebrafish lines. We find that engineered zebrafish melanomas show an overall low mutation burden, which has a strong, inverse association with the number of initiating germline drivers. Although tumors reveal distinct mutation spectrums, they show mostly C > T transitions without UV light exposure, and enrichment of mutations in melanogenesis, p53 and MAPK signaling. Importantly, a recurrent amplification occurring with pre-configured drivers BRAF^V600E and p53^-/- suggests a novel path of BRAF cooperativity through the protein kinase A pathway.

Conclusion

This is the first analysis of a melanoma mutational landscape in the absence of UV light, where tumors manifest with remarkably low mutation burden and high heterogeneity. Genotype specific amplification of protein kinase A in cooperation with BRAF and p53 mutation suggests the involvement of melanogenesis in these tumors. This work is important for defining the spectrum of events in BRAF or NRAS driven melanoma in the absence of UV light, and for informed exploitation of models such as transgenic zebrafish to better understand mechanisms leading to human melanoma formation.

Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes

Long interspersed nuclear element-1 (L1) retrotransposons are mobile repetitive elements that are abundant in the human genome. L1 elements propagate through RNA intermediates. In the germ line, neighboring, nonrepetitive sequences are occasionally mobilized by the L1 machinery, a process called 3' transduction. Because 3' transductions are potentially mutagenic, we explored the extent to which they occur somatically during tumorigenesis. Studying cancer genomes from 244 patients, we found that tumors from 53% of the patients had somatic retrotranspositions, of which 24% were 3' transductions. Fingerprinting of donor L1s revealed that a handful of source L1 elements in a tumor can spawn from tens to hundreds of 3' transductions, which can themselves seed further retrotranspositions. The activity of individual L1 elements fluctuated during tumor evolution and correlated with L1 promoter hypomethylation. The 3' transductions disseminated genes, exons, and regulatory elements to new locations, most often to heterochromatic regions of the genome.

Somatic CALR mutations in myeloproliferative neoplasms with nonmutated JAK2

BACKGROUND

Somatic mutations in the Janus kinase 2 gene (JAK2) occur in many myeloproliferative neoplasms, but the molecular pathogenesis of myeloproliferative neoplasms with nonmutated JAK2 is obscure, and the diagnosis of these neoplasms remains a challenge.

METHODS

We performed exome sequencing of samples obtained from 151 patients with myeloproliferative neoplasms. The mutation status of the gene encoding calreticulin (CALR) was assessed in an additional 1345 hematologic cancers, 1517 other cancers, and 550 controls. We established phylogenetic trees using hematopoietic colonies. We assessed calreticulin subcellular localization using immunofluorescence and flow cytometry.

RESULTS

Exome sequencing identified 1498 mutations in 151 patients, with medians of 6.5, 6.5, and 13.0 mutations per patient in samples of polycythemia vera, essential thrombocythemia, and myelofibrosis, respectively. Somatic CALR mutations were found in 70 to 84% of samples of myeloproliferative neoplasms with nonmutated JAK2, in 8% of myelodysplasia samples, in occasional samples of other myeloid cancers, and in none of the other cancers. A total of 148 CALR mutations were identified with 19 distinct variants. Mutations were located in exon 9 and generated a +1 base-pair frameshift, which would result in a mutant protein with a novel C-terminal. Mutant calreticulin was observed in the endoplasmic reticulum without increased cell-surface or Golgi accumulation. Patients with myeloproliferative neoplasms carrying CALR mutations presented with higher platelet counts and lower hemoglobin levels than patients with mutated JAK2. Mutation of CALR was detected in hematopoietic stem and progenitor cells. Clonal analyses showed CALR mutations in the earliest phylogenetic node, a finding consistent with its role as an initiating mutation in some patients.

CONCLUSIONS

Somatic mutations in the endoplasmic reticulum chaperone CALR were found in a majority of patients with myeloproliferative neoplasms with nonmutated JAK2. (Funded by the Kay Kendall Leukaemia Fund and others.).

Whole exome sequencing of adenoid cystic carcinoma

Adenoid cystic carcinoma (ACC) is a rare malignancy that can occur in multiple organ sites and is primarily found in the salivary gland. While the identification of recurrent fusions of the MYB-NFIB genes have begun to shed light on the molecular underpinnings, little else is known about the molecular genetics of this frequently fatal cancer. We have undertaken exome sequencing in a series of 24 ACC to further delineate the genetics of the disease. We identified multiple mutated genes that, combined, implicate chromatin deregulation in half of cases. Further, mutations were identified in known cancer genes, including PIK3CA, ATM, CDKN2A, SF3B1, SUFU, TSC1, and CYLD. Mutations in NOTCH1/2 were identified in 3 cases, and we identify the negative NOTCH signaling regulator, SPEN, as a new cancer gene in ACC with mutations in 5 cases. Finally, the identification of 3 likely activating mutations in the tyrosine kinase receptor FGFR2, analogous to those reported in ovarian and endometrial carcinoma, point to potential therapeutic avenues for a subset of cases.

Systematic review and mixed treatment comparison: dressings to heal diabetic foot ulcers

AIMS/HYPOTHESIS

Foot ulcers in people with diabetes are a common and serious global health issue. Dressings form a key part of ulcer treatment. Existing systematic reviews are limited by the lack of head-to-head comparisons of alternative dressings in a field where there are several different dressing options. We aimed to determine the relative effects of alternative wound dressings on the healing of diabetic foot ulcers.

METHODS

This study was a systematic review involving Bayesian mixed treatment comparison. We included randomised controlled trials evaluating the effects on diabetic foot ulcer healing of one or more wound dressings. There were no restrictions based on language or publication status.

RESULTS

Fifteen eligible studies, evaluating nine dressing types, were included. Ten direct treatment comparisons were made. Whilst there was increased healing associated with hydrogel and foam dressings compared with basic wound contact materials, these findings were based on data from small studies at unclear or high risk of bias. The mixed treatment comparison suggested that hydrocolloid-matrix dressings were associated with higher odds of ulcer healing than all other dressing types; there was a high degree of uncertainty around these estimates, which were deemed to be of very low quality.

CONCLUSIONS/INTERPRETATION

These findings summarise all available trial evidence regarding the use of dressings to heal diabetic foot ulcers. More expensive dressings may offer no advantages in terms of healing than cheaper basic dressings. In addition, evidence pointing to a difference in favour of 'advanced' dressing types over basic wound contact materials is of low or very low quality.

A small-cell lung cancer genome with complex signatures of tobacco exposure

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.