Appraisal of Intraoperative Adverse Events to Improve Postoperative Care.

BACKGROUND: Intraoperative adverse events (iAEs) are associated with adverse postoperative outcomes and cause a significant healthcare burden. However, a critical appraisal of iAEs is lacking. Considering the details of iAEs could benefit postoperative care. We comprehensively analyzed iAEs in a large series including all types of operations and their relation to postoperative complications. METHODS: All patients enrolled in the multicenter ClassIntra® validation study (NCT03009929) were included in this analysis. The surgical and anesthesia team prospectively recorded all iAEs. Two researchers, blinded to each other's ratings, appraised all recorded iAEs according to their origin into four categories: surgery, anesthesia, organization, or other, including subcategories such as organ injury, arrhythmia, or instrument failure. They further descriptively analyzed subcategories of all iAEs. Postoperative complications were assessed using the Comprehensive Complication Index (CCI®), a weighted sum of all postoperative complications according to the Clavien-Dindo classification. The association of iAE origins in addition to the severity grade of ClassIntra® on CCI® was assessed with a multivariable mixed-effects generalized linear regression analysis. RESULTS: Of 2520 included patients, 778 iAEs were recorded in 610 patients. The origin was surgical in 420 (54%), anesthesia in 283 (36%), organizational in 34 (4%), and other in 41 (5%) events. Bleeding (n = 217, 28%), hypotension (n = 118, 15%), and organ injury (n = 98, 13%) were the three most frequent subcategories in surgery and anesthesia, respectively. In the multivariable mixed-effect analysis, no significant association between the origin and CCI® was observed. CONCLUSION: Analyzing the type and origin of an iAE offers individualized and contextualized information. This detailed descriptive information can be used for targeted surveillance of intra- and postoperative care, even though the overall predictive value for postoperative events was not improved by adding the origin in addition to the severity grade.

Genomic-transcriptomic evolution in lung cancer and metastasis.

Intratumour heterogeneity (ITH) fuels lung cancer evolution, which leads to immune evasion and resistance to therapy1. Here, using paired whole-exome and RNA sequencing data, we investigate intratumour transcriptomic diversity in 354 non-small cell lung cancer tumours from 347 out of the first 421 patients prospectively recruited into the TRACERx study2,3. Analyses of 947 tumour regions, representing both primary and metastatic disease, alongside 96 tumour-adjacent normal tissue samples implicate the transcriptome as a major source of phenotypic variation. Gene expression levels and ITH relate to patterns of positive and negative selection during tumour evolution. We observe frequent copy number-independent allele-specific expression that is linked to epigenomic dysfunction. Allele-specific expression can also result in genomic-transcriptomic parallel evolution, which converges on cancer gene disruption. We extract signatures of RNA single-base substitutions and link their aetiology to the activity of the RNA-editing enzymes ADAR and APOBEC3A, thereby revealing otherwise undetected ongoing APOBEC activity in tumours. Characterizing the transcriptomes of primary-metastatic tumour pairs, we combine multiple machine-learning approaches that leverage genomic and transcriptomic variables to link metastasis-seeding potential to the evolutionary context of mutations and increased proliferation within primary tumour regions. These results highlight the interplay between the genome and transcriptome in influencing ITH, lung cancer evolution and metastasis.

The evolution of lung cancer and impact of subclonal selection in TRACERx.

Lung cancer is the leading cause of cancer-associated mortality worldwide1. Here we analysed 1,644 tumour regions sampled at surgery or during follow-up from the first 421 patients with non-small cell lung cancer prospectively enrolled into the TRACERx study. This project aims to decipher lung cancer evolution and address the primary study endpoint: determining the relationship between intratumour heterogeneity and clinical outcome. In lung adenocarcinoma, mutations in 22 out of 40 common cancer genes were under significant subclonal selection, including classical tumour initiators such as TP53 and KRAS. We defined evolutionary dependencies between drivers, mutational processes and whole genome doubling (WGD) events. Despite patients having a history of smoking, 8% of lung adenocarcinomas lacked evidence of tobacco-induced mutagenesis. These tumours also had similar detection rates for EGFR mutations and for RET, ROS1, ALK and MET oncogenic isoforms compared with tumours in never-smokers, which suggests that they have a similar aetiology and pathogenesis. Large subclonal expansions were associated with positive subclonal selection. Patients with tumours harbouring recent subclonal expansions, on the terminus of a phylogenetic branch, had significantly shorter disease-free survival. Subclonal WGD was detected in 19% of tumours, and 10% of tumours harboured multiple subclonal WGDs in parallel. Subclonal, but not truncal, WGD was associated with shorter disease-free survival. Copy number heterogeneity was associated with extrathoracic relapse within 1 year after surgery. These data demonstrate the importance of clonal expansion, WGD and copy number instability in determining the timing and patterns of relapse in non-small cell lung cancer and provide a comprehensive clinical cancer evolutionary data resource.

Discrepancy in Reporting of Perioperative Complications: A Retrospective Observational Study.

OBJECTIVE: To assess the discrepancy between perioperative complications, prospectively recorded during a cohort study versus retrospectively from health records. BACKGROUND: Perioperative adverse events are relevant for patient outcome, but incomplete reporting is common. METHODS: Two physicians independently recorded all intraoperative adverse events according to ClassIntra and all postoperative complications according to the Clavien-Dindo classification based on all available health records. These retrospective assessments were compared with the number and severity of those prospectively assessed in the same patients during their inclusion in 1 center of a prospective multicenter cohort study. RESULTS: Interrater agreement between both physicians for retrospective recording was high [intraclass correlation coefficient: 0.89 (95% CI, 0.86, 0.91) for intraoperative and 0.88 (95% CI, 0.85, 0.90) for postoperative complications]. In 320 patients, the incidence rate was higher retrospectively than prospectively for any intraoperative complication (incidence rate ratio: 1.79; 95% CI, 1.50, 2.13) and for any postoperative complication (incidence rate ratio: 2.21; 95% CI, 1.90, 2.56). In 71 patients, the severity of the most severe intraoperative complication was higher in the retrospective than in the prospective data collection, whereas in 69 the grading was lower. In 106 patients, the severity of the most severe postoperative complication was higher in the retrospective than in the prospective data collection, whereas in 19 the grading was lower. CONCLUSIONS: There is a noticeable discrepancy in the number and severity of reported perioperative complications between these 2 data collection methods. On the basis of the double-blinded assessment of 2 independent raters, our study renders prospective underreporting more likely than retrospective overreporting.

Classification of intraoperative adverse events in visceral surgery.

BACKGROUND: Intraoperative adverse events (iAEs) are frequent in visceral surgery, but severity and related postoperative outcome are poorly investigated. A novel classification of intraoperative adverse events, ClassIntra, includes surgical and anesthesiologic intraoperative adverse events using 5 severity grades and showed a high criterion and construct validity across all surgical disciplines. ClassIntra was studied for reproducibility in a prespecified group of patients undergoing visceral surgery. METHODS: iAEs were recorded in all patients enrolled in the ClassIntra validation study (NCT03009929). Postoperative complications were assessed daily according to the Clavien-Dindo classification. Results of the visceral group were compared with those of the non-visceral group and the full cohort. The risk-adjusted association between most severe intra and postoperative complications was investigated in a multivariable proportional odds model. Second, risk-adjusted association between ClassIntra grade and Comprehensive Complication Index, and postoperative length of stay was investigated. RESULTS: In total, 1,270 out of 2,520 patients (50%) underwent visceral surgery. Compared with the nonvisceral group and full cohort, more intraoperative (337/1270 [27%] vs 273/1250 [22%] vs 610/2520 [24%] patients) and postoperative complications (457/1270 [36%] vs 381/1250 [30%] vs 838/2520 [33%] patients) occurred. The risk for a more severe postoperative complication increased with each ClassIntra grade (odds ratio [95% confidence interval] I vs 0 1.10 [0.73 to 1.66], II vs 0 1.69 [1.10 to 2.60], III vs 0 2.31 [1.21 to 4.41], IV vs 0 2.35 [0.69 to 8.06]). Accordingly, CCI and postoperative length of stay increased with each ClassIntra grade in the visceral group, comparable with the nonvisceral and full cohort. CONCLUSION: Consistent results for the association of intraoperative adverse events and patient outcomes render ClassIntra a valuable instrument in visceral surgery.

Using DNA sequencing data to quantify T cell fraction and therapy response.

The immune microenvironment influences tumour evolution and can be both prognostic and predict response to immunotherapy1,2. However, measurements of tumour infiltrating lymphocytes (TILs) are limited by a shortage of appropriate data. Whole-exome sequencing (WES) of DNA is frequently performed to calculate tumour mutational burden and identify actionable mutations. Here we develop T cell exome TREC tool (T cell ExTRECT), a method for estimation of T cell fraction from WES samples using a signal from T cell receptor excision circle (TREC) loss during V(D)J recombination of the T cell receptor-α gene (TCRA (also known as TRA)). TCRA T cell fraction correlates with orthogonal TIL estimates and is agnostic to sample type. Blood TCRA T cell fraction is higher in females than in males and correlates with both tumour immune infiltrate and presence of bacterial sequencing reads. Tumour TCRA T cell fraction is prognostic in lung adenocarcinoma. Using a meta-analysis of tumours treated with immunotherapy, we show that tumour TCRA T cell fraction predicts immunotherapy response, providing value beyond measuring tumour mutational burden. Applying T cell ExTRECT to a multi-sample pan-cancer cohort reveals a high diversity of the degree of immune infiltration within tumours. Subclonal loss of 12q24.31-32, encompassing SPPL3, is associated with reduced TCRA T cell fraction. T cell ExTRECT provides a cost-effective technique to characterize immune infiltrate alongside somatic changes.

Sex-Based Dimorphism of Anticancer Immune Response and Molecular Mechanisms of Immune Evasion.

PURPOSE: We previously demonstrated that sex influences response to immune checkpoint inhibitors. In this article, we investigate sex-based differences in the molecular mechanisms of anticancer immune response and immune evasion in patients with NSCLC. EXPERIMENTAL DESIGN: We analyzed (i) transcriptome data of 2,575 early-stage NSCLCs from seven different datasets; (ii) 327 tumor samples extensively characterized at the molecular level from the TRACERx lung study; (iii) two independent cohorts of 329 and 391 patients, respectively, with advanced NSCLC treated with anti-PD-1/anti-PD-L1 drugs. RESULTS: As compared with men, the tumor microenvironment (TME) of women was significantly enriched for a number of innate and adaptive immune cell types, including specific T-cell subpopulations. NSCLCs of men and women exploited different mechanisms of immune evasion. The TME of females was characterized by significantly greater T-cell dysfunction status, higher expression of inhibitory immune checkpoint molecules, and higher abundance of immune-suppressive cells, including cancer-associated fibroblasts, MDSCs, and regulatory T cells. In contrast, the TME of males was significantly enriched for a T-cell-excluded phenotype. We reported data supporting impaired neoantigens presentation to immune system in tumors of men, as molecular mechanism explaining the findings observed. Finally, in line with our results, we showed significant sex-based differences in the association between TMB and outcome of patients with advanced NSCLC treated with anti-PD-1/PD-L1 drugs. CONCLUSIONS: We demonstrated meaningful sex-based differences of anticancer immune response and immune evasion mechanisms, that may be exploited to improve immunotherapy efficacy for both women and men.

[Prospective Cohort Study of In-Hospital Patients Undergoing Ophthalmic Surgery for the Validation of ClassIntra: Classification of Intraoperative Adverse Events]. / Prospektive Kohortenstudie bei stationären augenchirurgischen Patienten für die Validierung der ClassIntra-Klassifikation für unerwünschte intraoperative Ereignisse.

BACKGROUND: To the best of our knowledge, there is no validated classification to assess intraoperative adverse events (iAEs) in ophthalmic surgery. ClassIntra is a newly developed classification for surgery- and anaesthesia-related iAEs that has been recently validated in various surgical disciplines, but not in ophthalmic surgery. We aim to assess the validity and practicability of ClassIntra in patients undergoing ophthalmic surgery. METHODS: A consecutive sample of in-hospital patients undergoing any type of ophthalmic surgery was included in this single-centre prospective cohort study. iAEs were classified using ClassIntra, consisting of 5 severity grades according to the symptoms of the patient and the required treatment. All patients were followed for two weeks to record all postoperative adverse events according to Clavien-Dindo. The primary endpoint was the risk-adjusted association between the most severe iAE and the weighted sum of all postoperative adverse events within the two-week follow-up using the Comprehensive Complication Index (CCI). In addition, ophthalmologists and anaesthesiologists were asked to complete an online survey assessing the severity of iAEs for 10 fictitious clinical case scenarios. Reliability was assessed by comparing the clinicians' ratings to the prespecified benchmark rating of the study team. RESULTS: In this study, 100 in-hospital patients with an average age of 64 years (SD 15) were included. The majority of all patients were ASA II (n = 53, 53%) or III (n = 42, 42%). Thirty-two iAEs were recorded in 22 patients (17 grade I, 12 grade II, 3 grade III). Ninety-four postoperative adverse events occurred in 50 patients (44 grade I, 36 grade II, 14 grade IIIa). We found a mean difference in CCI of 2,1 (95% confidence interval [CI] - 2,5 to 6,8) per one unit increase in severity grades of ClassIntra. Fifty ophthalmologists and anaesthesiologists completed the online survey (response rate 54%). The intraclass correlation coefficient was 0,79 (95% CI 0,64 to 0,94). CONCLUSIONS: The application of ClassIntra during daily routine in ophthalmic surgery showed the usefulness and practicability of this classification for the standardised assessment of intraoperative adverse events. Although construct validity could not be demonstrated, the good reliability in the survey's rating underlines the criterion validity of this newly developed classification in ophthalmic surgery.

Utilizing Computational Machine Learning Tools to Understand Immunogenic Breadth in the Context of a CD8 T-Cell Mediated HIV Response.

Predictive models are becoming more and more commonplace as tools for candidate antigen discovery to meet the challenges of enabling epitope mapping of cohorts with diverse HLA properties. Here we build on the concept of using two key parameters, diversity metric of the HLA profile of individuals within a population and consideration of sequence diversity in the context of an individual's CD8 T-cell immune repertoire to assess the HIV proteome for defined regions of immunogenicity. Using this approach, analysis of HLA adaptation and functional immunogenicity data enabled the identification of regions within the proteome that offer significant conservation, HLA recognition within a population, low prevalence of HLA adaptation and demonstrated immunogenicity. We believe this unique and novel approach to vaccine design as a supplement to vitro functional assays, offers a bespoke pipeline for expedited and rational CD8 T-cell vaccine design for HIV and potentially other pathogens with the potential for both global and local coverage.

Understanding the impact of immune-mediated selection on lung cancer evolution.

Understanding how a tumour evolves and avoids immune recognition is paramount to improving cancer immunotherapy and patient outcome. Here we examine our recent integration of multi-region genomic, transcriptomic, epigenomic, pathology, and clinical data, highlight the need for a systematic examination of immune escape mechanisms, and discuss implications for immunotherapy approaches.

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition.

Checkpoint inhibitors (CPIs) augment adaptive immunity. Systematic pan-tumor analyses may reveal the relative importance of tumor-cell-intrinsic and microenvironmental features underpinning CPI sensitization. Here, we collated whole-exome and transcriptomic data for >1,000 CPI-treated patients across seven tumor types, utilizing standardized bioinformatics workflows and clinical outcome criteria to validate multivariable predictors of CPI sensitization. Clonal tumor mutation burden (TMB) was the strongest predictor of CPI response, followed by total TMB and CXCL9 expression. Subclonal TMB, somatic copy alteration burden, and histocompatibility leukocyte antigen (HLA) evolutionary divergence failed to attain pan-cancer significance. Dinucleotide variants were identified as a source of immunogenic epitopes associated with radical amino acid substitutions and enhanced peptide hydrophobicity/immunogenicity. Copy-number analysis revealed two additional determinants of CPI outcome supported by prior functional evidence: 9q34 (TRAF2) loss associated with response and CCND1 amplification associated with resistance. Finally, single-cell RNA sequencing (RNA-seq) of clonal neoantigen-reactive CD8 tumor-infiltrating lymphocytes (TILs), combined with bulk RNA-seq analysis of CPI-responding tumors, identified CCR5 and CXCL13 as T-cell-intrinsic markers of CPI sensitivity.

Pervasive chromosomal instability and karyotype order in tumour evolution.

Chromosomal instability in cancer consists of dynamic changes to the number and structure of chromosomes1,2. The resulting diversity in somatic copy number alterations (SCNAs) may provide the variation necessary for tumour evolution1,3,4. Here we use multi-sample phasing and SCNA analysis of 1,421 samples from 394 tumours across 22 tumour types to show that continuous chromosomal instability results in pervasive SCNA heterogeneity. Parallel evolutionary events, which cause disruption in the same genes (such as BCL9, MCL1, ARNT (also known as HIF1B), TERT and MYC) within separate subclones, were present in 37% of tumours. Most recurrent losses probably occurred before whole-genome doubling, that was found as a clonal event in 49% of tumours. However, loss of heterozygosity at the human leukocyte antigen (HLA) locus and loss of chromosome 8p to a single haploid copy recurred at substantial subclonal frequencies, even in tumours with whole-genome doubling, indicating ongoing karyotype remodelling. Focal amplifications that affected chromosomes 1q21 (which encompasses BCL9, MCL1 and ARNT), 5p15.33 (TERT), 11q13.3 (CCND1), 19q12 (CCNE1) and 8q24.1 (MYC) were frequently subclonal yet appeared to be clonal within single samples. Analysis of an independent series of 1,024 metastatic samples revealed that 13 focal SCNAs were enriched in metastatic samples, including gains in chromosome 8q24.1 (encompassing MYC) in clear cell renal cell carcinoma and chromosome 11q13.3 (encompassing CCND1) in HER2+ breast cancer. Chromosomal instability may enable the continuous selection of SCNAs, which are established as ordered events that often occur in parallel, throughout tumour evolution.

Prospective validation of classification of intraoperative adverse events (ClassIntra): international, multicentre cohort study.

OBJECTIVE: To prospectively assess the construct and criterion validity of ClassIntra version 1.0, a newly developed classification for assessing intraoperative adverse events. DESIGN: International, multicentre cohort study. SETTING: 18 secondary and tertiary centres from 12 countries in Europe, Oceania, and North America. PARTICIPANTS: The cohort study included a representative sample of 2520 patients in hospital having any type of surgery, followed up until discharge. A follow-up to assess mortality at 30 days was performed in 2372 patients (94%). A survey was sent to a representative sample of 163 surgeons and anaesthetists from participating centres. MAIN OUTCOME MEASURES: Intraoperative complications were assessed according to ClassIntra. Postoperative complications were assessed daily until discharge from hospital with the Clavien-Dindo classification. The primary endpoint was construct validity by investigating the risk adjusted association between the most severe intraoperative and postoperative complications, measured in a multivariable hierarchical proportional odds model. For criterion validity, inter-rater reliability was evaluated in a survey of 10 fictitious case scenarios describing intraoperative complications. RESULTS: Of 2520 patients enrolled, 610 (24%) experienced at least one intraoperative adverse event and 838 (33%) at least one postoperative complication. Multivariable analysis showed a gradual increase in risk for a more severe postoperative complication with increasing grade of ClassIntra: ClassIntra grade I versus grade 0, odds ratio 0.99 (95% confidence interval 0.69 to 1.42); grade II versus grade 0, 1.39 (0.97 to 2.00); grade III versus grade 0, 2.62 (1.31 to 5.26); and grade IV versus grade 0, 3.81 (1.19 to 12.2). ClassIntra showed high criterion validity with an intraclass correlation coefficient of 0.76 (95% confidence interval 0.59 to 0.91) in the survey (response rate 83%). CONCLUSIONS: ClassIntra is the first prospectively validated classification for assessing intraoperative adverse events in a standardised way, linking them to postoperative complications with the well established Clavien-Dindo classification. ClassIntra can be incorporated into routine practice in perioperative surgical safety checklists, or used as a monitoring and outcome reporting tool for different surgical disciplines. Future studies should investigate whether the tool is useful to stratify patients to the appropriate postoperative care, to enhance the quality of surgical interventions, and to improve long term outcomes of surgical patients. TRIAL REGISTRATION: ClinicalTrials.gov NCT03009929.

The T cell differentiation landscape is shaped by tumour mutations in lung cancer.

Tumour mutational burden (TMB) predicts immunotherapy outcome in non-small cell lung cancer (NSCLC), consistent with immune recognition of tumour neoantigens. However, persistent antigen exposure is detrimental for T cell function. How TMB affects CD4 and CD8 T cell differentiation in untreated tumours, and whether this affects patient outcomes is unknown. Here we paired high-dimensional flow cytometry, exome, single-cell and bulk RNA sequencing from patients with resected, untreated NSCLC to examine these relationships. TMB was associated with compartment-wide T cell differentiation skewing, characterized by loss of TCF7-expressing progenitor-like CD4 T cells, and an increased abundance of dysfunctional CD8 and CD4 T cell subsets, with significant phenotypic and transcriptional similarity to neoantigen-reactive CD8 T cells. A gene signature of redistribution from progenitor-like to dysfunctional states associated with poor survival in lung and other cancer cohorts. Single-cell characterization of these populations informs potential strategies for therapeutic manipulation in NSCLC.

Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer.

Before squamous cell lung cancer develops, precancerous lesions can be found in the airways. From longitudinal monitoring, we know that only half of such lesions become cancer, whereas a third spontaneously regress. Although recent studies have described the presence of an active immune response in high-grade lesions, the mechanisms underpinning clinical regression of precancerous lesions remain unknown. Here, we show that host immune surveillance is strongly implicated in lesion regression. Using bronchoscopic biopsies from human subjects, we find that regressive carcinoma in situ lesions harbor more infiltrating immune cells than those that progress to cancer. Moreover, molecular profiling of these lesions identifies potential immune escape mechanisms specifically in those that progress to cancer: antigen presentation is impaired by genomic and epigenetic changes, CCL27-CCR10 signaling is upregulated, and the immunomodulator TNFSF9 is downregulated. Changes appear intrinsic to the carcinoma in situ lesions, as the adjacent stroma of progressive and regressive lesions are transcriptomically similar. SIGNIFICANCE: Immune evasion is a hallmark of cancer. For the first time, this study identifies mechanisms by which precancerous lesions evade immune detection during the earliest stages of carcinogenesis and forms a basis for new therapeutic strategies that treat or prevent early-stage lung cancer.See related commentary by Krysan et al., p. 1442.This article is highlighted in the In This Issue feature, p. 1426.

Publisher Correction: Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer.

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

Publisher Correction: A clonal expression biomarker associates with lung cancer mortality.

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

Geospatial immune variability illuminates differential evolution of lung adenocarcinoma.

Remarkable progress in molecular analyses has improved our understanding of the evolution of cancer cells toward immune escape1-5. However, the spatial configurations of immune and stromal cells, which may shed light on the evolution of immune escape across tumor geographical locations, remain unaddressed. We integrated multiregion exome and RNA-sequencing (RNA-seq) data with spatial histology mapped by deep learning in 100 patients with non-small cell lung cancer from the TRACERx cohort6. Cancer subclones derived from immune cold regions were more closely related in mutation space, diversifying more recently than subclones from immune hot regions. In TRACERx and in an independent multisample cohort of 970 patients with lung adenocarcinoma, tumors with more than one immune cold region had a higher risk of relapse, independently of tumor size, stage and number of samples per patient. In lung adenocarcinoma, but not lung squamous cell carcinoma, geometrical irregularity and complexity of the cancer-stromal cell interface significantly increased in tumor regions without disruption of antigen presentation. Decreased lymphocyte accumulation in adjacent stroma was observed in tumors with low clonal neoantigen burden. Collectively, immune geospatial variability elucidates tumor ecological constraints that may shape the emergence of immune-evading subclones and aggressive clinical phenotypes.

A clonal expression biomarker associates with lung cancer mortality.

An aim of molecular biomarkers is to stratify patients with cancer into disease subtypes predictive of outcome, improving diagnostic precision beyond clinical descriptors such as tumor stage1. Transcriptomic intratumor heterogeneity (RNA-ITH) has been shown to confound existing expression-based biomarkers across multiple cancer types2-6. Here, we analyze multi-region whole-exome and RNA sequencing data for 156 tumor regions from 48 patients enrolled in the TRACERx study to explore and control for RNA-ITH in non-small cell lung cancer. We find that chromosomal instability is a major driver of RNA-ITH, and existing prognostic gene expression signatures are vulnerable to tumor sampling bias. To address this, we identify genes expressed homogeneously within individual tumors that encode expression modules of cancer cell proliferation and are often driven by DNA copy-number gains selected early in tumor evolution. Clonal transcriptomic biomarkers overcome tumor sampling bias, associate with survival independent of clinicopathological risk factors, and may provide a general strategy to refine biomarker design across cancer types.