Sensitivity analyses for the principal ignorability assumption using multiple imputation.

In the context of clinical trials, there is interest in the treatment effect for subpopulations of patients defined by intercurrent events, namely disease-related events occurring after treatment initiation that affect either the interpretation or the existence of endpoints. With the principal stratum strategy, the ICH E9(R1) guideline introduces a formal framework in drug development for defining treatment effects in such subpopulations. Statistical estimation of the treatment effect can be performed based on the principal ignorability assumption using multiple imputation approaches. Principal ignorability is a conditional independence assumption that cannot be directly verified; therefore, it is crucial to evaluate the robustness of results to deviations from this assumption. As a sensitivity analysis, we propose a joint model that multiply imputes the principal stratum membership and the outcome variable while allowing different levels of violation of the principal ignorability assumption. We illustrate with a simulation study that the joint imputation model-based approaches are superior to naive subpopulation analyses. Motivated by an oncology clinical trial, we implement the sensitivity analysis on a time-to-event outcome to assess the treatment effect in the subpopulation of patients who discontinued due to adverse events using a synthetic dataset. Finally, we explore the potential usage and provide interpretation of such analyses in clinical settings, as well as possible extension of such models in more general cases.

Gestational Age-Dependent Fetal Fluid Dynamics in the Ovine Developmental Model: Establishment of Surrogate Markers for the Differentiation of Stem Cell Origin.

The ovine developmental model represents the standard in vivo model for studies involving maternofetal physiology, amniotic fluid (AF) research, and fetal cell therapy prior to human clinical use. Although being close to the human fetal anatomy, 2 separate extraembryonic fluid compartments remain during gestation, known as the amnion and the allantois. A clear distinction between AF versus allantoic fluid (AL) is therefore indispensable for correct scientific conclusions with regard to human translation. In the presented study, the biochemical composition of AF and AL was evaluated in ovine gravid uteri postmortem (n = 31) over the entire gestation. Four parameters, consisting of Na+, Cl-, Mg2+, and total protein, have been found to allow for specific discrimination of the 2 fetal fluids at all gestational phases and therefore as potential surrogate parameters for gestational age. In addition, volumetric changes of the developing fetus and the 2 fetal fluid cavities were analyzed by contrast-enhanced computed tomography (n = 12). AF showed a significant, linear volumetric increase over gestation, whereas AL volume maintained relatively static independent of gestational age. These results serve as a basis for future studies by providing surrogate markers enabling a reliable distinction of isolated fetal fluids and contained cells in the ovine developmental model over the entire gestation.

Evidence synthesis from aggregate recurrent event data for clinical trial design and analysis.

Information from historical trials is important for the design, interim monitoring, analysis, and interpretation of clinical trials. Meta-analytic models can be used to synthesize the evidence from historical data, which are often only available in aggregate form. We consider evidence synthesis methods for trials with recurrent event endpoints, which are common in many therapeutic areas. Such endpoints are typically analyzed by negative binomial regression. However, the individual patient data necessary to fit such a model are usually unavailable for historical trials reported in the medical literature. We describe approaches for back-calculating model parameter estimates and their standard errors from available summary statistics with various techniques, including approximate Bayesian computation. We propose to use a quadratic approximation to the log-likelihood for each historical trial based on 2 independent terms for the log mean rate and the log of the dispersion parameter. A Bayesian hierarchical meta-analysis model then provides the posterior predictive distribution for these parameters. Simulations show this approach with back-calculated parameter estimates results in very similar inference as using parameter estimates from individual patient data as an input. We illustrate how to design and analyze a new randomized placebo-controlled exacerbation trial in severe eosinophilic asthma using data from 11 historical trials.

Methodology for Good Machine Learning with Multi-Omics Data.

In 2020, Novartis Pharmaceuticals Corporation and the U.S. Food and Drug Administration (FDA) started a 4-year scientific collaboration to approach complex new data modalities and advanced analytics. The scientific question was to find novel radio-genomics-based prognostic and predictive factors for HR+/HER- metastatic breast cancer under a Research Collaboration Agreement. This collaboration has been providing valuable insights to help successfully implement future scientific projects, particularly using artificial intelligence and machine learning. This tutorial aims to provide tangible guidelines for a multi-omics project that includes multidisciplinary expert teams, spanning across different institutions. We cover key ideas, such as "maintaining effective communication" and "following good data science practices," followed by the four steps of exploratory projects, namely (1) plan, (2) design, (3) develop, and (4) disseminate. We break each step into smaller concepts with strategies for implementation and provide illustrations from our collaboration to further give the readers actionable guidance.

Updated Overall Survival of Ribociclib plus Endocrine Therapy versus Endocrine Therapy Alone in Pre- and Perimenopausal Patients with HR+/HER2- Advanced Breast Cancer in MONALEESA-7: A Phase III Randomized Clinical Trial.

PURPOSE: Ribociclib plus endocrine therapy (ET) demonstrated a statistically significant progression-free survival and overall survival (OS) benefit in the phase III MONALEESA-7 trial of pre-/perimenopausal patients with hormone receptor (HR)-positive (HR+), HER2-negative (HER2-) advanced breast cancer (ABC). The median OS was not reached in the ribociclib arm in the protocol-specified final analysis; we hence performed an exploratory OS and additional outcomes analysis with an extended follow-up (median, 53.5 months). PATIENTS AND METHODS: Patients were randomized to receive ET [goserelin plus nonsteroidal aromatase inhibitor (NSAI) or tamoxifen] with ribociclib or placebo. OS was evaluated with a stratified Cox proportional hazard model and summarized with Kaplan-Meier methods. RESULTS: The intent-to-treat population included 672 patients. Median OS was 58.7 months with ribociclib versus 48.0 months with placebo [hazard ratio = 0.76; 95% confidence interval (CI), 0.61-0.96]. Kaplan-Meier estimated OS at 48 months was 60% and 50% with ribociclib and placebo, respectively. Subgroup analyses were generally consistent with the OS benefit, including patients who received NSAI and patients aged less than 40 years. Subsequent antineoplastic therapies following discontinuation were balanced between the ribociclib (77%) and placebo (78%) groups. Use of cyclin-dependent kinase 4/6 inhibitors after discontinuation was higher with placebo (26%) versus ribociclib (13%). Time to first chemotherapy was significantly delayed with ribociclib versus placebo. No drug-drug interactions were observed between ribociclib and either NSAI. CONCLUSIONS: Ribociclib plus ET continued to show significantly longer OS than ET alone in pre-/perimenopausal patients, including patients aged less than 40 years, with HR+/HER2- ABC with 53.5 months of median follow-up (ClinicalTrials.gov, NCT02278120).

Epidemic cystic and alveolar echinococcosis in Kyrgyzstan: an analysis of national surveillance data.

BACKGROUND: Human cystic and alveolar echinococcosis are among the priority neglected zoonotic diseases for which WHO advocates control. The incidence of both cystic echinococcosis and alveolar echinococcosis has increased substantially in the past 30 years in Kyrgyzstan. Given the scarcity of adequate data on the local geographical variation of these focal diseases, we aimed to investigate within-country incidence and geographical variation of cystic echinococcosis and alveolar echinococcosis at a high spatial resolution in Kyrgyzstan. METHODS: We mapped all confirmed surgical cases of cystic echinococcosis and alveolar echinococcosis reported through the national echinococcosis surveillance system in Kyrgyzstan between Jan 1, 2014, and Dec 31, 2016, from nine regional databases. We then estimated crude surgical incidence, standardised incidence, and standardised incidence ratios (SIRs) of primary cases (ie, excluding relapses) based on age and sex at country, region, district, and local community levels. Finally, we tested the SIRs for global and local spatial autocorrelation to identify disease hotspots at the local community level. All incidence estimates were calculated per 100 000 population and averaged across the 3-year study period to obtain annual estimates. FINDINGS: The surveillance system reported 2359 primary surgical cases of cystic echinococcosis and 546 primary surgical cases of alveolar echinococcosis. Country-level crude surgical incidence was 13·1 per 100 000 population per year for cystic echinococcosis and 3·02 per 100 000 population per year for alveolar echinococcosis. At the local community level, we found annual crude surgical incidences up to 176 per 100 000 population in Sary-Kamysh (Jalal-Abad region) for cystic echinococcosis and 246 per 100 000 population in Uch-Dobo (Alay district, Osh region) for alveolar echinococcosis. Significant hotspots of cystic echinococcosis were found in four regions: Osh (five local communities in Uzgen district and four in Alay district), Naryn (three local communities in Jumgal district and one in Naryn district), Talas (three local communities in Talas district), and Chuy (one local community in Jayyl district). Significant alveolar echinococcosis hotspots were detected in the Osh region (11 communities in Alay district, including the local community of Sary Mogol, and one in Chong-Alay district) and in the Naryn region (five communities in Jumgal district and three in At-Bashy district), in the southwest and centre of the country. INTERPRETATION: Our analyses reveal remarkable within-country variation in the surgical incidence of cystic echinococcosis and alveolar echinococcosis in Kyrgyzstan. These high-resolution maps identify precise locations where interventions and epidemiological research should be targeted to reduce the burden of human cystic echinococcosis and alveolar echinococcosis. FUNDING: Swiss National Science Foundation.

Increase in Airway Obstruction between 1993 and 2012 in Switzerland. An Observational Study.

Rationale: Most studies determining the prevalence of airway obstruction are limited to short time periods.Objectives: Because temporal trends of obstruction in populations are largely unknown, we determined the prevalence of airway obstruction over 20 years in yearly general population samples in Switzerland between 1993 and 2012.Methods: We analyzed data of 85,789 participants aged 35 years and older who provided spirometric measurements as part of the LuftiBus lung function campaign. We linked data from the 2003-2012 period to the Swiss National Cohort to adjust for annual population differences. Spirometry was performed without bronchodilation, according to American Thoracic Society guidelines. We used Global Lung Initiative (GLI) and Hankinson reference equations to identify obstruction.Results: Obstruction prevalence increased between 1993 and 2012 from 6.1% (95% confidence interval [CI], 5.5 to 6.7) to 15.6% (95% CI, 13.8 to 17.3) based on GLI estimates and from 5.3% (95% CI, 4.7 to 5.9) to 15.4% (95% CI, 13.6 to 17.1) based on Hankinson estimates. When adjusted for participant demographics, air pollutant and occupational exposures, altitude, and season, the prevalence ratios of obstruction were 1.54 (95% CI, 1.22 to 1.93) and 1.65 (95% CI, 1.33 to 2.04) for GLI- and Hankinson-defined airway obstruction, respectively, for 2012 compared with 2003.Conclusions: Though prebronchodilator measurements likely overestimate the prevalence of airway obstruction in absolute terms compared with post-bronchodilator measurements, we found an increase in airway obstruction prevalence. Even with adjustment for several well-known risk factors for obstruction to make the populations across the years more comparable, we still saw a statistically significant increase in prevalence over this time period.

Modelling anthelmintic resistance by extending eggCounts package to allow individual efficacy.

The same anthelmintic treatment can have variable efficacy on individual animals even if the parasite population is homogenously susceptible. An extension of the R package eggCounts is proposed to take individual efficacy into account using a Bayesian hierarchical model. A simulation study is conducted to compare the performance of five different methods on estimating faecal egg count reduction and its uncertainty interval. Simulation results showed the individual efficacy model offered robust inference to two different data simulation procedures with low root mean squared error on the reduction estimate and appropriate uncertainty estimates. Different methods were used to evaluate the anthelmintic resistance in a dataset from USA with sheep and cattle faecal egg counts, where a strong anthelmintic resistance was detected. Open-source statistical tools were updated to include the proposed model.

Zero-inflated hierarchical models for faecal egg counts to assess anthelmintic efficacy.

The prevalence of anthelmintic resistance has increased in recent years, as a result of the extensive use of anthelmintic drugs to reduce the infection of parasitic worms in livestock. In order to detect the resistance, the number of parasite eggs in animal faeces is counted. Typically a subsample of the diluted faeces is examined, and the mean egg counts from both untreated and treated animals are compared. However, the conventional method ignores the variabilities introduced by the counting process and by different infection levels across animals. In addition, there can be extra zero counts, which arise as a result of the unexposed animals in an infected population or animals. In this paper, we propose the zero-inflated Bayesian hierarchical models to estimate the reduction in faecal egg counts. The simulation study compares the Bayesian models with the conventional faecal egg count reduction test and other methods such as bootstrap and quasi-Poisson regression. The results show the Bayesian models are more robust and they perform well in terms of both the bias and the coverage. We further illustrate the advantages of our proposed model using a case study about the anthelmintic resistance in Swedish sheep flocks.

Combined Inactivation of MYC and K-Ras oncogenes reverses tumorigenesis in lung adenocarcinomas and lymphomas.

BACKGROUND: Conditional transgenic models have established that tumors require sustained oncogene activation for tumor maintenance, exhibiting the phenomenon known as "oncogene-addiction." However, most cancers are caused by multiple genetic events making it difficult to determine which oncogenes or combination of oncogenes will be the most effective targets for their treatment. METHODOLOGY/PRINCIPAL FINDINGS: To examine how the MYC and K-ras(G12D) oncogenes cooperate for the initiation and maintenance of tumorigenesis, we generated double conditional transgenic tumor models of lung adenocarcinoma and lymphoma. The ability of MYC and K-ras(G12D) to cooperate for tumorigenesis and the ability of the inactivation of these oncogenes to result in tumor regression depended upon the specific tissue context. MYC-, K-ras(G12D)- or MYC/K-ras(G12D)-induced lymphomas exhibited sustained regression upon the inactivation of either or both oncogenes. However, in marked contrast, MYC-induced lung tumors failed to regress completely upon oncogene inactivation; whereas K-ras(G12D)-induced lung tumors regressed completely. Importantly, the combined inactivation of both MYC and K-ras(G12D) resulted more frequently in complete lung tumor regression. To account for the different roles of MYC and K-ras(G12D) in maintenance of lung tumors, we found that the down-stream mediators of K-ras(G12D) signaling, Stat3 and Stat5, are dephosphorylated following conditional K-ras(G12D) but not MYC inactivation. In contrast, Stat3 becomes dephosphorylated in lymphoma cells upon inactivation of MYC and/or K-ras(G12D). Interestingly, MYC-induced lung tumors that failed to regress upon MYC inactivation were found to have persistent Stat3 and Stat5 phosphorylation. CONCLUSIONS/SIGNIFICANCE: Taken together, our findings point to the importance of the K-Ras and associated down-stream Stat effector pathways in the initiation and maintenance of lymphomas and lung tumors. We suggest that combined targeting of oncogenic pathways is more likely to be effective in the treatment of lung cancers and lymphomas.