Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA.

Circulating tumour DNA (ctDNA) can be used to detect and profile residual tumour cells persisting after curative intent therapy1. The study of large patient cohorts incorporating longitudinal plasma sampling and extended follow-up is required to determine the role of ctDNA as a phylogenetic biomarker of relapse in early-stage non-small-cell lung cancer (NSCLC). Here we developed ctDNA methods tracking a median of 200 mutations identified in resected NSCLC tissue across 1,069 plasma samples collected from 197 patients enrolled in the TRACERx study2. A lack of preoperative ctDNA detection distinguished biologically indolent lung adenocarcinoma with good clinical outcome. Postoperative plasma analyses were interpreted within the context of standard-of-care radiological surveillance and administration of cytotoxic adjuvant therapy. Landmark analyses of plasma samples collected within 120 days after surgery revealed ctDNA detection in 25% of patients, including 49% of all patients who experienced clinical relapse; 3 to 6 monthly ctDNA surveillance identified impending disease relapse in an additional 20% of landmark-negative patients. We developed a bioinformatic tool (ECLIPSE) for non-invasive tracking of subclonal architecture at low ctDNA levels. ECLIPSE identified patients with polyclonal metastatic dissemination, which was associated with a poor clinical outcome. By measuring subclone cancer cell fractions in preoperative plasma, we found that subclones seeding future metastases were significantly more expanded compared with non-metastatic subclones. Our findings will support (neo)adjuvant trial advances and provide insights into the process of metastatic dissemination using low-ctDNA-level liquid biopsy.

Artificial intelligence in cancer imaging: Clinical challenges and applications.

Judgement, as one of the core tenets of medicine, relies upon the integration of multilayered data with nuanced decision making. Cancer offers a unique context for medical decisions given not only its variegated forms with evolution of disease but also the need to take into account the individual condition of patients, their ability to receive treatment, and their responses to treatment. Challenges remain in the accurate detection, characterization, and monitoring of cancers despite improved technologies. Radiographic assessment of disease most commonly relies upon visual evaluations, the interpretations of which may be augmented by advanced computational analyses. In particular, artificial intelligence (AI) promises to make great strides in the qualitative interpretation of cancer imaging by expert clinicians, including volumetric delineation of tumors over time, extrapolation of the tumor genotype and biological course from its radiographic phenotype, prediction of clinical outcome, and assessment of the impact of disease and treatment on adjacent organs. AI may automate processes in the initial interpretation of images and shift the clinical workflow of radiographic detection, management decisions on whether or not to administer an intervention, and subsequent observation to a yet to be envisioned paradigm. Here, the authors review the current state of AI as applied to medical imaging of cancer and describe advances in 4 tumor types (lung, brain, breast, and prostate) to illustrate how common clinical problems are being addressed. Although most studies evaluating AI applications in oncology to date have not been vigorously validated for reproducibility and generalizability, the results do highlight increasingly concerted efforts in pushing AI technology to clinical use and to impact future directions in cancer care.

Deep Learning to Estimate Cardiovascular Risk From Chest Radiographs : A Risk Prediction Study.

BACKGROUND: Guidelines for primary prevention of atherosclerotic cardiovascular disease (ASCVD) recommend a risk calculator (ASCVD risk score) to estimate 10-year risk for major adverse cardiovascular events (MACE). Because the necessary inputs are often missing, complementary approaches for opportunistic risk assessment are desirable. OBJECTIVE: To develop and test a deep-learning model (CXR CVD-Risk) that estimates 10-year risk for MACE from a routine chest radiograph (CXR) and compare its performance with that of the traditional ASCVD risk score for implications for statin eligibility. DESIGN: Risk prediction study. SETTING: Outpatients potentially eligible for primary cardiovascular prevention. PARTICIPANTS: The CXR CVD-Risk model was developed using data from a cancer screening trial. It was externally validated in 8869 outpatients with unknown ASCVD risk because of missing inputs to calculate the ASCVD risk score and in 2132 outpatients with known risk whose ASCVD risk score could be calculated. MEASUREMENTS: 10-year MACE predicted by CXR CVD-Risk versus the ASCVD risk score. RESULTS: Among 8869 outpatients with unknown ASCVD risk, those with a risk of 7.5% or higher as predicted by CXR CVD-Risk had higher 10-year risk for MACE after adjustment for risk factors (adjusted hazard ratio [HR], 1.73 [95% CI, 1.47 to 2.03]). In the additional 2132 outpatients with known ASCVD risk, CXR CVD-Risk predicted MACE beyond the traditional ASCVD risk score (adjusted HR, 1.88 [CI, 1.24 to 2.85]). LIMITATION: Retrospective study design using electronic medical records. CONCLUSION: On the basis of a single CXR, CXR CVD-Risk predicts 10-year MACE beyond the clinical standard and may help identify individuals at high risk whose ASCVD risk score cannot be calculated because of missing data. PRIMARY FUNDING SOURCE: None.

Artificial Intelligence for Response Assessment in Neuro Oncology (AI-RANO), part 1: review of current advancements.

The development, application, and benchmarking of artificial intelligence (AI) tools to improve diagnosis, prognostication, and therapy in neuro-oncology are increasing at a rapid pace. This Policy Review provides an overview and critical assessment of the work to date in this field, focusing on diagnostic AI models of key genomic markers, predictive AI models of response before and after therapy, and differentiation of true disease progression from treatment-related changes, which is a considerable challenge based on current clinical care in neuro-oncology. Furthermore, promising future directions, including the use of AI for automated response assessment in neuro-oncology, are discussed.

Artificial Intelligence for Response Assessment in Neuro Oncology (AI-RANO), part 2: recommendations for standardisation, validation, and good clinical practice.

Technological advancements have enabled the extended investigation, development, and application of computational approaches in various domains, including health care. A burgeoning number of diagnostic, predictive, prognostic, and monitoring biomarkers are continuously being explored to improve clinical decision making in neuro-oncology. These advancements describe the increasing incorporation of artificial intelligence (AI) algorithms, including the use of radiomics. However, the broad applicability and clinical translation of AI are restricted by concerns about generalisability, reproducibility, scalability, and validation. This Policy Review intends to serve as the leading resource of recommendations for the standardisation and good clinical practice of AI approaches in health care, particularly in neuro-oncology. To this end, we investigate the repeatability, reproducibility, and stability of AI in response assessment in neuro-oncology in studies on factors affecting such computational approaches, and in publicly available open-source data and computational software tools facilitating these goals. The pathway for standardisation and validation of these approaches is discussed with the view of trustworthy AI enabling the next generation of clinical trials. We conclude with an outlook on the future of AI-enabled neuro-oncology.

National Cancer Institute Imaging Data Commons: Toward Transparency, Reproducibility, and Scalability in Imaging Artificial Intelligence.

The remarkable advances of artificial intelligence (AI) technology are revolutionizing established approaches to the acquisition, interpretation, and analysis of biomedical imaging data. Development, validation, and continuous refinement of AI tools requires easy access to large high-quality annotated datasets, which are both representative and diverse. The National Cancer Institute (NCI) Imaging Data Commons (IDC) hosts large and diverse publicly available cancer image data collections. By harmonizing all data based on industry standards and colocalizing it with analysis and exploration resources, the IDC aims to facilitate the development, validation, and clinical translation of AI tools and address the well-documented challenges of establishing reproducible and transparent AI processing pipelines. Balanced use of established commercial products with open-source solutions, interconnected by standard interfaces, provides value and performance, while preserving sufficient agility to address the evolving needs of the research community. Emphasis on the development of tools, use cases to demonstrate the utility of uniform data representation, and cloud-based analysis aim to ease adoption and help define best practices. Integration with other data in the broader NCI Cancer Research Data Commons infrastructure opens opportunities for multiomics studies incorporating imaging data to further empower the research community to accelerate breakthroughs in cancer detection, diagnosis, and treatment. Published under a CC BY 4.0 license.

What Does DALL-E 2 Know About Radiology?

Generative models, such as DALL-E 2 (OpenAI), could represent promising future tools for image generation, augmentation, and manipulation for artificial intelligence research in radiology, provided that these models have sufficient medical domain knowledge. Herein, we show that DALL-E 2 has learned relevant representations of x-ray images, with promising capabilities in terms of zero-shot text-to-image generation of new images, the continuation of an image beyond its original boundaries, and the removal of elements; however, its capabilities for the generation of images with pathological abnormalities (eg, tumors, fractures, and inflammation) or computed tomography, magnetic resonance imaging, or ultrasound images are still limited. The use of generative models for augmenting and generating radiological data thus seems feasible, even if the further fine-tuning and adaptation of these models to their respective domains are required first.

Small whole heart volume predicts cardiovascular events in patients with stable chest pain: insights from the PROMISE trial.

OBJECTIVES: The size of the heart may predict major cardiovascular events (MACE) in patients with stable chest pain. We aimed to evaluate the prognostic value of 3D whole heart volume (WHV) derived from non-contrast cardiac computed tomography (CT). METHODS: Among participants randomized to the CT arm of the Prospective Multicenter Imaging Study for Evaluation of Chest Pain (PROMISE), we used deep learning to extract WHV, defined as the volume of the pericardial sac. We compared the WHV across categories of cardiovascular risk factors and coronary artery disease (CAD) characteristics and determined the association of WHV with MACE (all-cause death, myocardial infarction, unstable angina; median follow-up: 26 months). RESULTS: In the 3798 included patients (60.5 ± 8.2 years; 51.5% women), the WHV was 351.9 ± 57.6 cm3/m2. We found smaller WHV in no- or non-obstructive CAD, women, people with diabetes, sedentary lifestyle, and metabolic syndrome. Larger WHV was found in obstructive CAD, men, and increased atherosclerosis cardiovascular disease (ASCVD) risk score (p < 0.05). In a time-to-event analysis, small WHV was associated with over 4.4-fold risk of MACE (HR (per one standard deviation) = 0.221; 95% CI: 0.068-0.721; p = 0.012) independent of ASCVD risk score and CT-derived CAD characteristics. In patients with non-obstructive CAD, but not in those with no- or obstructive CAD, WHV increased the discriminatory capacity of ASCVD and CT-derived CAD characteristics significantly. CONCLUSIONS: Small WHV may represent a novel imaging marker of MACE in stable chest pain. In particular, WHV may improve risk stratification in patients with non-obstructive CAD, a cohort with an unmet need for better risk stratification. KEY POINTS: • Heart volume is easily assessable from non-contrast cardiac computed tomography. • Small heart volume may be an imaging marker of major adverse cardiac events independent and incremental to traditional cardiovascular risk factors and established CT measures of CAD. • Heart volume may improve cardiovascular risk stratification in patients with non-obstructive CAD.

Deep Learning Using Chest Radiographs to Identify High-Risk Smokers for Lung Cancer Screening Computed Tomography: Development and Validation of a Prediction Model.

BACKGROUND: Lung cancer screening with chest computed tomography (CT) reduces lung cancer death. Centers for Medicare & Medicaid Services (CMS) eligibility criteria for lung cancer screening with CT require detailed smoking information and miss many incident lung cancers. An automated deep-learning approach based on chest radiograph images may identify more smokers at high risk for lung cancer who could benefit from screening with CT. OBJECTIVE: To develop and validate a convolutional neural network (CXR-LC) that predicts long-term incident lung cancer using data commonly available in the electronic medical record (EMR) (chest radiograph, age, sex, and whether currently smoking). DESIGN: Risk prediction study. SETTING: U.S. lung cancer screening trials. PARTICIPANTS: The CXR-LC model was developed in the PLCO (Prostate, Lung, Colorectal, and Ovarian) Cancer Screening Trial (n = 41 856). The final CXR-LC model was validated in additional PLCO smokers (n = 5615, 12-year follow-up) and NLST (National Lung Screening Trial) heavy smokers (n = 5493, 6-year follow-up). Results are reported for validation data sets only. MEASUREMENTS: Up to 12-year lung cancer incidence predicted by CXR-LC. RESULTS: The CXR-LC model had better discrimination (area under the receiver-operating characteristic curve [AUC]) for incident lung cancer than CMS eligibility (PLCO AUC, 0.755 vs. 0.634; P < 0.001). The CXR-LC model's performance was similar to that of PLCOM2012, a state-of-the-art risk score with 11 inputs, in both the PLCO data set (CXR-LC AUC of 0.755 vs. PLCOM2012 AUC of 0.751) and the NLST data set (0.659 vs. 0.650). When compared in equal-sized screening populations, CXR-LC was more sensitive than CMS eligibility in the PLCO data set (74.9% vs. 63.8%; P = 0.012) and missed 30.7% fewer incident lung cancers. On decision curve analysis, CXR-LC had higher net benefit than CMS eligibility and similar benefit to PLCOM2012. LIMITATION: Validation in lung cancer screening trials and not a clinical setting. CONCLUSION: The CXR-LC model identified smokers at high risk for incident lung cancer, beyond CMS eligibility and using information commonly available in the EMR. PRIMARY FUNDING SOURCE: None.

The Image Biomarker Standardization Initiative: Standardized Quantitative Radiomics for High-Throughput Image-based Phenotyping.

Background Radiomic features may quantify characteristics present in medical imaging. However, the lack of standardized definitions and validated reference values have hampered clinical use. Purpose To standardize a set of 174 radiomic features. Materials and Methods Radiomic features were assessed in three phases. In phase I, 487 features were derived from the basic set of 174 features. Twenty-five research teams with unique radiomics software implementations computed feature values directly from a digital phantom, without any additional image processing. In phase II, 15 teams computed values for 1347 derived features using a CT image of a patient with lung cancer and predefined image processing configurations. In both phases, consensus among the teams on the validity of tentative reference values was measured through the frequency of the modal value and classified as follows: less than three matches, weak; three to five matches, moderate; six to nine matches, strong; 10 or more matches, very strong. In the final phase (phase III), a public data set of multimodality images (CT, fluorine 18 fluorodeoxyglucose PET, and T1-weighted MRI) from 51 patients with soft-tissue sarcoma was used to prospectively assess reproducibility of standardized features. Results Consensus on reference values was initially weak for 232 of 302 features (76.8%) at phase I and 703 of 1075 features (65.4%) at phase II. At the final iteration, weak consensus remained for only two of 487 features (0.4%) at phase I and 19 of 1347 features (1.4%) at phase II. Strong or better consensus was achieved for 463 of 487 features (95.1%) at phase I and 1220 of 1347 features (90.6%) at phase II. Overall, 169 of 174 features were standardized in the first two phases. In the final validation phase (phase III), most of the 169 standardized features could be excellently reproduced (166 with CT; 164 with PET; and 164 with MRI). Conclusion A set of 169 radiomics features was standardized, which enabled verification and calibration of different radiomics software. © RSNA, 2020 Online supplemental material is available for this article. See also the editorial by Kuhl and Truhn in this issue.

Radiomics versus Visual and Histogram-based Assessment to Identify Atheromatous Lesions at Coronary CT Angiography: An ex Vivo Study.

Background Visual and histogram-based assessments of coronary CT angiography have limited accuracy in the identification of advanced lesions. Radiomics-based machine learning (ML) could provide a more accurate tool. Purpose To compare the diagnostic performance of radiomics-based ML with that of visual and histogram-based assessment of ex vivo coronary CT angiography cross sections to identify advanced atherosclerotic lesions defined with histologic examination. Materials and Methods In this prospective study, 21 coronary arteries from seven hearts obtained from male donors (mean age, 52.3 years ± 5.3) were imaged ex vivo with coronary CT angiography between February 23, 2009, and July 31, 2010. From 95 coronary plaques, 611 histologic cross sections were coregistered with coronary CT cross sections. Lesions were considered advanced if early fibroatheroma, late fibroatheroma, or thin-cap atheroma was present. CT cross sections were classified as showing homogeneous, heterogeneous, or napkin-ring sign plaques on the basis of visual assessment. The area of low attenuation (<30 HU) and the average Hounsfield unit were quantified. Radiomic parameters were extracted and used as inputs to ML algorithms. Eight radiomics-based ML models were trained on randomly selected cross sections (training set, 75% of the cross sections) to identify advanced lesions. Visual assessment, histogram-based assessment, and the best ML model were compared on the remaining 25% of the data (validation set) by using the area under the receiver operating characteristic curve (AUC) to identify advanced lesions. Results After excluding sections with no visible plaque (n = 134) and with heavy calcium (n = 32), 445 cross sections were analyzed. Of those 445 cross sections, 134 (30.1%) were advanced lesions. Visual assessment of the 445 cross sections indicated that 207 (46.5%) were homogeneous, 200 (44.9%) were heterogeneous, and 38 (8.5%) demonstrated the napkin-ring sign. A radiomics-based ML model incorporating 13 parameters outperformed visual assessment (AUC = 0.73 with 95% confidence interval [CI] of 0.63, 0.84 vs 0.65 with 95% CI of 0.56, 0.73, respectively; P = .04), area of low attenuation (AUC = 0.55 with 95% CI of 0.42, 0.68; P = .01), and average Hounsfield unit (AUC = 0.53 with 95% CI of 0.42, 0.65; P = .004) in the identification of advanced atheromatous lesions. Conclusion Radiomics-based machine learning analysis improves the discriminatory power of coronary CT angiography in the identification of advanced atherosclerotic lesions. Published under a CC BY 4.0 license.

Proceedings of the fourth international molecular pathological epidemiology (MPE) meeting.

An important premise of epidemiology is that individuals with the same disease share similar underlying etiologies and clinical outcomes. In the past few decades, our knowledge of disease pathogenesis has improved, and disease classification systems have evolved to the point where no complex disease processes are considered homogenous. As a result, pathology and epidemiology have been integrated into the single, unified field of molecular pathological epidemiology (MPE). Advancing integrative molecular and population-level health sciences and addressing the unique research challenges specific to the field of MPE necessitates assembling experts in diverse fields, including epidemiology, pathology, biostatistics, computational biology, bioinformatics, genomics, immunology, and nutritional and environmental sciences. Integrating these seemingly divergent fields can lead to a greater understanding of pathogenic processes. The International MPE Meeting Series fosters discussion that addresses the specific research questions and challenges in this emerging field. The purpose of the meeting series is to: discuss novel methods to integrate pathology and epidemiology; discuss studies that provide pathogenic insights into population impact; and educate next-generation scientists. Herein, we share the proceedings of the Fourth International MPE Meeting, held in Boston, MA, USA, on 30 May-1 June, 2018. Major themes of this meeting included 'integrated genetic and molecular pathologic epidemiology', 'immunology-MPE', and 'novel disease phenotyping'. The key priority areas for future research identified by meeting attendees included integration of tumor immunology and cancer disparities into epidemiologic studies, further collaboration between computational and population-level scientists to gain new insight on exposure-disease associations, and future pooling projects of studies with comparable data.

Density and morphology of coronary artery calcium for the prediction of cardiovascular events: insights from the Framingham Heart Study.

OBJECTIVES: To investigate the association between directly measured density and morphology of coronary artery calcium (CAC) with cardiovascular disease (CVD) events, using computed tomography (CT). METHODS: Framingham Heart Study (FHS) participants with CAC in noncontrast cardiac CT (2002-2005) were included and followed until 2016. Participants with known CVD or uninterpretable CT scans were excluded. We assessed and correlated (Spearman) CAC density, CAC volume, and the number of calcified segments. Moreover, we counted morphology features including shape (cylindrical, spherical, semi-tubular, and spotty), location (bifurcation, facing pericardium, or facing myocardium), and boundary regularity. In multivariate Cox regression analyses, we associated all CAC characteristics with CVD events (CVD-death, myocardial infarction, stroke). RESULTS: Among 1330 included participants (57.8 ± 11.7 years; 63% male), 73 (5.5%) experienced CVD events in a median follow-up of 9.1 (7.8-10.1) years. CAC density correlated strongly with CAC volume (Spearman's ρ = 0.75; p < 0.001) and lower number of calcified segments (ρ = - 0.86; p < 0.001; controlled for CAC volume). In the survival analysis, CAC density was associated with CVD events independent of Framingham risk score (HR (per SD) = 2.09; 95%CI, 1.30-3.34; p = 0.002) but not after adjustment for CAC volume (p = 0.648). The extent of spherically shaped and pericardially sided calcifications was associated with fewer CVD events accounting for the number of calcified segments (HR (per count) = 0.55; 95%CI, 0.31-0.98; p = 0.042 and HR = 0.66; 95%CI, 0.45-0.98; p = 0.039, respectively). CONCLUSIONS: Directly measured CAC density does not predict CVD events due to the strong correlation with CAC volume. The spherical shape and pericardial-sided location of CAC are associated with fewer CVD events and may represent morphological features related to stable coronary plaques. KEY POINTS: • Coronary calcium density may not be independently associated with cardiovascular events. • Coronary calcium density correlates strongly with calcium volume. • Spherical shape and pericardial-sided location of CAC are associated with fewer CVD events.

Inconsistency in large pharmacogenomic studies.

Two large-scale pharmacogenomic studies were published recently in this journal. Genomic data are well correlated between studies; however, the measured drug response data are highly discordant. Although the source of inconsistencies remains uncertain, it has potential implications for using these outcome measures to assess gene-drug associations or select potential anticancer drugs on the basis of their reported results.

Deep learning for lung cancer prognostication: A retrospective multi-cohort radiomics study.

BACKGROUND: Non-small-cell lung cancer (NSCLC) patients often demonstrate varying clinical courses and outcomes, even within the same tumor stage. This study explores deep learning applications in medical imaging allowing for the automated quantification of radiographic characteristics and potentially improving patient stratification. METHODS AND FINDINGS: We performed an integrative analysis on 7 independent datasets across 5 institutions totaling 1,194 NSCLC patients (age median = 68.3 years [range 32.5-93.3], survival median = 1.7 years [range 0.0-11.7]). Using external validation in computed tomography (CT) data, we identified prognostic signatures using a 3D convolutional neural network (CNN) for patients treated with radiotherapy (n = 771, age median = 68.0 years [range 32.5-93.3], survival median = 1.3 years [range 0.0-11.7]). We then employed a transfer learning approach to achieve the same for surgery patients (n = 391, age median = 69.1 years [range 37.2-88.0], survival median = 3.1 years [range 0.0-8.8]). We found that the CNN predictions were significantly associated with 2-year overall survival from the start of respective treatment for radiotherapy (area under the receiver operating characteristic curve [AUC] = 0.70 [95% CI 0.63-0.78], p < 0.001) and surgery (AUC = 0.71 [95% CI 0.60-0.82], p < 0.001) patients. The CNN was also able to significantly stratify patients into low and high mortality risk groups in both the radiotherapy (p < 0.001) and surgery (p = 0.03) datasets. Additionally, the CNN was found to significantly outperform random forest models built on clinical parameters-including age, sex, and tumor node metastasis stage-as well as demonstrate high robustness against test-retest (intraclass correlation coefficient = 0.91) and inter-reader (Spearman's rank-order correlation = 0.88) variations. To gain a better understanding of the characteristics captured by the CNN, we identified regions with the most contribution towards predictions and highlighted the importance of tumor-surrounding tissue in patient stratification. We also present preliminary findings on the biological basis of the captured phenotypes as being linked to cell cycle and transcriptional processes. Limitations include the retrospective nature of this study as well as the opaque black box nature of deep learning networks. CONCLUSIONS: Our results provide evidence that deep learning networks may be used for mortality risk stratification based on standard-of-care CT images from NSCLC patients. This evidence motivates future research into better deciphering the clinical and biological basis of deep learning networks as well as validation in prospective data.

Quantitative imaging of cancer in the postgenomic era: Radio(geno)mics, deep learning, and habitats.

Although cancer often is referred to as "a disease of the genes," it is indisputable that the (epi)genetic properties of individual cancer cells are highly variable, even within the same tumor. Hence, preexisting resistant clones will emerge and proliferate after therapeutic selection that targets sensitive clones. Herein, the authors propose that quantitative image analytics, known as "radiomics," can be used to quantify and characterize this heterogeneity. Virtually every patient with cancer is imaged radiologically. Radiomics is predicated on the beliefs that these images reflect underlying pathophysiologies, and that they can be converted into mineable data for improved diagnosis, prognosis, prediction, and therapy monitoring. In the last decade, the radiomics of cancer has grown from a few laboratories to a worldwide enterprise. During this growth, radiomics has established a convention, wherein a large set of annotated image features (1-2000 features) are extracted from segmented regions of interest and used to build classifier models to separate individual patients into their appropriate class (eg, indolent vs aggressive disease). An extension of this conventional radiomics is the application of "deep learning," wherein convolutional neural networks can be used to detect the most informative regions and features without human intervention. A further extension of radiomics involves automatically segmenting informative subregions ("habitats") within tumors, which can be linked to underlying tumor pathophysiology. The goal of the radiomics enterprise is to provide informed decision support for the practice of precision oncology.

PharmacoGx: an R package for analysis of large pharmacogenomic datasets.

UNLABELLED: Pharmacogenomics holds great promise for the development of biomarkers of drug response and the design of new therapeutic options, which are key challenges in precision medicine. However, such data are scattered and lack standards for efficient access and analysis, consequently preventing the realization of the full potential of pharmacogenomics. To address these issues, we implemented PharmacoGx, an easy-to-use, open source package for integrative analysis of multiple pharmacogenomic datasets. We demonstrate the utility of our package in comparing large drug sensitivity datasets, such as the Genomics of Drug Sensitivity in Cancer and the Cancer Cell Line Encyclopedia. Moreover, we show how to use our package to easily perform Connectivity Map analysis. With increasing availability of drug-related data, our package will open new avenues of research for meta-analysis of pharmacogenomic data. AVAILABILITY AND IMPLEMENTATION: PharmacoGx is implemented in R and can be easily installed on any system. The package is available from CRAN and its source code is available from GitHub. CONTACT: bhaibeka@uhnresearch.ca or benjamin.haibe.kains@utoronto.ca SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.