A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response.

Cancer treatments can be highly toxic and frequently only a subset of the patient population will benefit from a given treatment. Tumour genetic makeup plays an important role in cancer drug sensitivity. We suspect that gene expression markers could be used as a decision aid for treatment selection or dosage tuning. Using in vitro cancer cell line dose-response and gene expression data from the Genomics of Drug Sensitivity in Cancer (GDSC) project, we build a dose-varying regression model. Unlike existing approaches, this allows us to estimate dosage-dependent associations with gene expression. We include the transcriptomic profiles as dose-invariant covariates into the regression model and assume that their effect varies smoothly over the dosage levels. A two-stage variable selection algorithm (variable screening followed by penalized regression) is used to identify genetic factors that are associated with drug response over the varying dosages. We evaluate the effectiveness of our method using simulation studies focusing on the choice of tuning parameters and cross-validation for predictive accuracy assessment. We further apply the model to data from five BRAF targeted compounds applied to different cancer cell lines under different dosage levels. We highlight the dosage-dependent dynamics of the associations between the selected genes and drug response, and we perform pathway enrichment analysis to show that the selected genes play an important role in pathways related to tumorigenesis and DNA damage response.

A hierarchical Bayesian approach for detecting global microbiome associations.

The human gut microbiome has been shown to be associated with a variety of human diseases, including cancer, metabolic conditions and inflammatory bowel disease. Current approaches for detecting microbiome associations are limited by relying on specific measures of ecological distance, or only allowing for the detection of associations with individual bacterial species, rather than the whole microbiome. In this work, we develop a novel hierarchical Bayesian model for detecting global microbiome associations. Our method is not dependent on a choice of distance measure, and is able to incorporate phylogenetic information about microbial species. We perform extensive simulation studies and show that our method allows for consistent estimation of global microbiome effects. Additionally, we investigate the performance of the model on two real-world microbiome studies: a study of microbiome-metabolome associations in inflammatory bowel disease, and a study of associations between diet and the gut microbiome in mice. We show that we can use the method to reliably detect associations in real-world datasets with varying numbers of samples and covariates.

The joint lasso: high-dimensional regression for group structured data.

We consider high-dimensional regression over subgroups of observations. Our work is motivated by biomedical problems, where subsets of samples, representing for example disease subtypes, may differ with respect to underlying regression models. In the high-dimensional setting, estimating a different model for each subgroup is challenging due to limited sample sizes. Focusing on the case in which subgroup-specific models may be expected to be similar but not necessarily identical, we treat subgroups as related problem instances and jointly estimate subgroup-specific regression coefficients. This is done in a penalized framework, combining an $\ell_1$ term with an additional term that penalizes differences between subgroup-specific coefficients. This gives solutions that are globally sparse but that allow information-sharing between the subgroups. We present algorithms for estimation and empirical results on simulated data and using Alzheimer's disease, amyotrophic lateral sclerosis, and cancer datasets. These examples demonstrate the gains joint estimation can offer in prediction as well as in providing subgroup-specific sparsity patterns.

Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study.

MOTIVATION: Molecular pathways and networks play a key role in basic and disease biology. An emerging notion is that networks encoding patterns of molecular interplay may themselves differ between contexts, such as cell type, tissue or disease (sub)type. However, while statistical testing of differences in mean expression levels has been extensively studied, testing of network differences remains challenging. Furthermore, since network differences could provide important and biologically interpretable information to identify molecular subgroups, there is a need to consider the unsupervised task of learning subgroups and networks that define them. This is a nontrivial clustering problem, with neither subgroups nor subgroup-specific networks known at the outset. RESULTS: We leverage recent ideas from high-dimensional statistics for testing and clustering in the network biology setting. The methods we describe can be applied directly to most continuous molecular measurements and networks do not need to be specified beforehand. We illustrate the ideas and methods in a case study using protein data from The Cancer Genome Atlas (TCGA). This provides evidence that patterns of interplay between signalling proteins differ significantly between cancer types. Furthermore, we show how the proposed approaches can be used to learn subtypes and the molecular networks that define them. AVAILABILITY AND IMPLEMENTATION: As the Bioconductor package nethet. CONTACT: staedler.n@gmail.com or sach.mukherjee@dzne.de. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Causal network inference using biochemical kinetics.

MOTIVATION: Networks are widely used as structural summaries of biochemical systems. Statistical estimation of networks is usually based on linear or discrete models. However, the dynamics of biochemical systems are generally non-linear, suggesting that suitable non-linear formulations may offer gains with respect to causal network inference and aid in associated prediction problems. RESULTS: We present a general framework for network inference and dynamical prediction using time course data that is rooted in non-linear biochemical kinetics. This is achieved by considering a dynamical system based on a chemical reaction graph with associated kinetic parameters. Both the graph and kinetic parameters are treated as unknown; inference is carried out within a Bayesian framework. This allows prediction of dynamical behavior even when the underlying reaction graph itself is unknown or uncertain. Results, based on (i) data simulated from a mechanistic model of mitogen-activated protein kinase signaling and (ii) phosphoproteomic data from cancer cell lines, demonstrate that non-linear formulations can yield gains in causal network inference and permit dynamical prediction and uncertainty quantification in the challenging setting where the reaction graph is unknown. AVAILABILITY AND IMPLEMENTATION: MATLAB R2014a software is available to download from warwick.ac.uk/chrisoates. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Assessment of Upper Extremity Function in Multiple Sclerosis: Feasibility of a Digital Pinching Test.

BACKGROUND: The development of touchscreen-based assessments of upper extremity function could benefit people with multiple sclerosis (MS) by allowing convenient, quantitative assessment of their condition. The Pinching Test forms a part of the Floodlight smartphone app (F. Hoffmann-La Roche Ltd, Basel, Switzerland) for people with MS and was designed to capture upper extremity function. OBJECTIVE: This study aimed to evaluate the Pinching Test as a tool for remotely assessing upper extremity function in people with MS. METHODS: Using data from the 24-week, prospective feasibility study investigating the Floodlight Proof-of-Concept app for remotely assessing MS, we examined 13 pinching, 11 inertial measurement unit (IMU)-based, and 13 fatigability features of the Pinching Test. We assessed the test-retest reliability using intraclass correlation coefficients [second model, first type; ICC(2,1)], age- and sex-adjusted cross-sectional Spearman rank correlation, and known-groups validity (data aggregation: median [all features], SD [fatigability features]). RESULTS: We evaluated data from 67 people with MS (mean Expanded Disability Status Scale [EDSS]: 2.4 [SD 1.4]) and 18 healthy controls. In this cohort of early MS, pinching features were reliable [ICC(2,1)=0.54-0.81]; correlated with standard clinical assessments, including the Nine-Hole Peg Test (9HPT) (|r|=0.26-0.54; 10/13 features), EDSS (|r|=0.25-0.36; 7/13 features), and the arm items of the 29-item Multiple Sclerosis Impact Scale (MSIS-29) (|r|=0.31-0.52; 7/13 features); and differentiated people with MS-Normal from people with MS-Abnormal (area under the curve: 0.68-0.78; 8/13 features). IMU-based features showed similar test-retest reliability [ICC(2,1)=0.47-0.84] but showed little correlations with standard clinical assessments. In contrast, fatigability features (SD aggregation) correlated with 9HPT time (|r|=0.26-0.61; 10/13 features), EDSS (|r|=0.26-0.41; 8/13 features), and MSIS-29 arm items (|r|=0.32-0.46; 7/13 features). CONCLUSIONS: The Pinching Test provides a remote, objective, and granular assessment of upper extremity function in people with MS that can potentially complement standard clinical evaluation. Future studies will validate it in more advanced MS. TRIAL REGISTRATION: ClinicalTrials.gov NCT02952911; https://clinicaltrials.gov/study/NCT02952911.

Preliminary validity of the Draw a Shape Test for upper extremity assessment in multiple sclerosis.

OBJECTIVE: To validate the smartphone sensor-based Draw a Shape Test - a part of the Floodlight Proof-of-Concept app for remotely assessing multiple sclerosis-related upper extremity impairment by tracing six different shapes. METHODS: People with multiple sclerosis, classified functionally normal/abnormal via their Nine-Hole Peg Test time, and healthy controls participated in a 24-week, nonrandomized study. Spatial (trace accuracy), temporal (mean and variability in linear, angular, and radial drawing velocities, and dwell time ratio), and spatiotemporal features (trace celerity) were cross-sectionally analyzed for correlation with standard clinical and brain magnetic resonance imaging (normalized brain volume and total lesion volume) disease burden measures, and for capacity to differentiate people with multiple sclerosis from healthy controls. RESULTS: Data from 69 people with multiple sclerosis and 18 healthy controls were analyzed. Trace accuracy (all shapes), linear velocity variability (circle, figure-of-8, spiral shapes), and radial velocity variability (spiral shape) had a mostly fair/moderate-to-good correlation (|r| = 0.14-0.66) with all disease burden measures. Trace celerity also had mostly fair/moderate-to-good correlation (|r| = 0.18-0.41) with Nine-Hole Peg Test performance, cerebellar functional system score, and brain magnetic resonance imaging. Furthermore, partial correlation analysis related these results to motor impairment. People with multiple sclerosis showed greater drawing velocity variability, though slower mean velocity, than healthy controls. Linear velocity (spiral shape) and angular velocity (circle shape) potentially differentiate functionally normal people with multiple sclerosis from healthy controls. INTERPRETATION: The Draw a Shape Test objectively assesses upper extremity impairment and correlates with all disease burden measures, thus aiding multiple sclerosis-related upper extremity impairment characterization.

Delay in loop ileostomy reversal surgery does not impact upon post-operative clinical outcomes. Complications are associated with an increased loss of microflora in the defunctioned intestine.

Loop ileostomy is a common surgical procedure to allow downstream tissue healing, with the aim of re-joining the bowel approximately 12 months later. The reversal procedure is associated with a substantial morbidity up to 40%. Our previous research demonstrated that defunctioned ileum becomes atrophied, with extensive microbial dysbiosis. This study sought to investigate the potential influence of delaying ileostomy reversal surgery upon both clinical and pathological outcomes. Post-operative clinical data was recorded, including routine blood test results, duration of hospital stay, length of time with stoma and incidence of post-operative complications. We measured ileal fibrosis and atrophy and assessed whether these, or dysbiosis, were impacted by the length of time a stoma was in place, or were linked to clinical outcomes. Associations between clinical data were investigated using scatterplot matrix analysis and t-tests. We found no differences in time between ileostomy formation and reversal in patients experiencing complications vs. individuals with no complications. Furthermore, there were no correlations between days with stoma and pathological measures, such as atrophy or fibrosis, and no ongoing increases in collagen production at the time of reversal surgery. This data suggests that the length of time a stoma is in place does not impact on the likelihood of complications. The incidence of complications is associated with increased loss of microbiota in the defunctioned ileum, but importantly, the decrease in bacteria is not linked to time with stoma. Microbiota diversity in the functional and defunctioned limb correlated within an individual, and was not significantly different between those who experienced complications following surgery vs. those that didn't. Microbiota diversity was also not significantly impacted through delay (>365 days) in stoma reversal. We propose that methods to restore intestinal microbiota numbers, and not necessarily their composition, prior to reversal should be explored to improve the clinical outcomes of ileostomy reversal surgery.

Personalized Longitudinal Assessment of Multiple Sclerosis Using Smartphones.

Personalized longitudinal disease assessment is central to quickly diagnosing, appropriately managing, and optimally adapting the therapeutic strategy of multiple sclerosis (MS). It is also important for identifying idiosyncratic subject-specific disease profiles. Here, we design a novel longitudinal model to map individual disease trajectories in an automated way using smartphone sensor data that may contain missing values. First, we collect digital measurements related to gait and balance, and upper extremity functions using sensor-based assessments administered on a smartphone. Next, we treat missing data via imputation. We then discover potential markers of MS by employing a generalized estimation equation. Subsequently, parameters learned from multiple training datasets are ensembled to form a simple, unified longitudinal predictive model to forecast MS over time in previously unseen people with MS. To mitigate potential underestimation for individuals with severe disease scores, the final model incorporates additional subject-specific fine-tuning using data from the first day. The results show that the proposed model is promising to achieve personalized longitudinal MS assessment; they also suggest that features related to gait and balance as well as upper extremity function, remotely collected from sensor-based assessments, may be useful digital markers for predicting MS over time.

An observational study to assess validity and reliability of smartphone sensor-based gait and balance assessments in multiple sclerosis: Floodlight GaitLab protocol.

Background: Gait and balance impairments are often present in people with multiple sclerosis (PwMS) and have a significant impact on quality of life and independence. Gold-standard quantitative tools for assessing gait and balance such as motion capture systems and force plates usually require complex technical setups. Wearable sensors, including those integrated into smartphones, offer a more frequent, convenient, and minimally burdensome assessment of functional disability in a home environment. We developed a novel smartphone sensor-based application (Floodlight) that is being used in multiple research and clinical contexts, but a complete validation of this technology is still lacking. Methods: This protocol describes an observational study designed to evaluate the analytical and clinical validity of Floodlight gait and balance tests. Approximately 100 PwMS and 35 healthy controls will perform multiple gait and balance tasks in both laboratory-based and real-world environments in order to explore the following properties: (a) concurrent validity of the Floodlight gait and balance tests against gold-standard assessments; (b) reliability of Floodlight digital measures derived under different controlled gait and balance conditions, and different on-body sensor locations; (c) ecological validity of the tests; and (d) construct validity compared with clinician- and patient-reported assessments. Conclusions: The Floodlight GaitLab study (ISRCTN15993728) represents a critical step in the technical validation of Floodlight technology to measure gait and balance in PwMS, and will also allow the development of new test designs and algorithms.