Novel predictions of invasive breast cancer risk in mammography screening cohorts.

Mammography screening programs are aimed at reducing mortality due to breast cancer by detecting tumors at an early stage. There is currently interest in moving away from the age-based screening programs, and toward personalized screening based on individual risk factors. To accomplish this, risk prediction models for breast cancer are needed to determine who should be screened, and when. We develop a novel approach using a (random effects) continuous growth model, which we apply to a large population-based, Swedish screening cohort. Unlike existing breast cancer prediction models, this approach explicitly incorporates each woman's individual screening visits in the prediction. It jointly models invasive breast cancer tumor onset, tumor growth rate, symptomatic detection rate, and screening sensitivity. In addition to predicting the overall risk of invasive breast cancer, this model can make separate predictions regarding specific tumor sizes, and the mode of detection (eg, detected at screening, or through symptoms between screenings). It can also predict how these risks change depending on whether or not a woman will attend her next screening. In our study, we predict, given a future diagnosis, that the probability of having a tumor less than (as opposed to greater than) 10-mm diameter, at detection, will be, on average, 2.6 times higher if a woman in the cohort attends their next screening. This indicates that the model can be used to evaluate the short-term benefit of screening attendance, at an individual level.

A natural history and copula-based joint model for regional and distant breast cancer metastasis.

The few existing statistical models of breast cancer recurrence and progression to distant metastasis are predominantly based on multi-state modelling. While useful for summarising the risk of recurrence, these provide limited insight into the underlying biological mechanisms and have limited use for understanding the implications of population-level interventions. We develop an alternative, novel, and parsimonious approach for modelling latent tumour growth and spread to local and distant metastasis, based on a natural history model with biologically inspired components. We include marginal sub-models for local and distant breast cancer metastasis, jointly modelled using a copula function. Different formulations (and correlation shapes) are allowed, thus we can incorporate and directly model the correlation between local and distant metastasis flexibly and efficiently. Submodels for the latent cancer growth, the detection process, and screening sensitivity, together with random effects to account for between-patients heterogeneity, are included. Although relying on several parametric assumptions, the joint copula model can be useful for understanding - potentially latent - disease dynamics, obtaining patient-specific, model-based predictions, and studying interventions at a population level, for example, using microsimulation. We illustrate this approach using data from a Swedish population-based case-control study of postmenopausal breast cancer, including examples of useful model-based predictions.

Computable Phenotype of a Crohn's Disease Natural History Model.

BACKGROUND: Analytic tools to study important clinical issues in complex, chronic diseases such as Crohn's disease (CD) include randomized trials, claims database studies, or small longitudinal epidemiologic cohorts. Using natural language processing (NLP), we sought to define the computable phenotype health state of pediatric and adult CD and develop patient-level longitudinal histories for health outcomes. METHODS: We defined 6 health states for CD using a subjective symptom-based assessment (symptomatic/asymptomatic) and an objective disease state assessment (active/inactive/no testing). Gold standard for the 6 health states was derived using an iterative process during review by our CD experts. We calculated the transition probabilities to estimate the time to transitions between the various health states using nonparametric Kaplan-Meier estimation and a Markov model. Finally, we determined a standard utility measure from clinical patients assigned to different health states. RESULTS: The NLP computable phenotype health state model correctly ascertained the objective test results and symptoms 96% and 85% of the time, respectively, based on a blinded chart evaluation. In our model, >25% of patients who begin as asymptomatic/active transition to symptomatic/active over the following year. For both adult and pediatric CD health states, the utility assessments of a symptomatic/inactive health state closely resembled a symptomatic/active health state. CONCLUSIONS: Our methodology for a computable phenotype health state demonstrates the application of real-world data to define progression and optimal management of a chronic disease such as CD. The application of the model has the potential to lead to a better understanding of the true impact of a therapeutic intervention and can provide long-term cost-effectiveness analyses for a new therapy. HIGHLIGHTS: Using natural language processing, we defined the computable phenotype health state of Crohn's disease and developed patient-level longitudinal histories for health outcomes.Our methodology demonstrates the application of real-world data to define the progression of a chronic disease.The application of the model has the potential to provide better understanding of the true impact of a new therapy.

Estimating latent, dynamic processes of breast cancer tumour growth and distant metastatic spread from mammography screening data.

We propose a framework for jointly modelling tumour size at diagnosis and time to distant metastatic spread, from diagnosis, based on latent dynamic sub-models of growth of the primary tumour and of distant metastatic detection. The framework also includes a sub-model for screening sensitivity as a function of latent tumour size. Our approach connects post-diagnosis events to the natural history of cancer and, once refined, may prove useful for evaluating new interventions, such as personalised screening regimes. We evaluate our model-fitting procedure using Monte Carlo simulation, showing that the estimation algorithm can retrieve the correct model parameters, that key patterns in the data can be captured by the model even with misspecification of some structural assumptions, and that, still, with enough data it should be possible to detect strong misspecifications. Furthermore, we fit our model to observational data from an extension of a case-control study of post-menopausal breast cancer in Sweden, providing model-based estimates of the probability of being free from detected distant metastasis as a function of tumour size, mode of detection (of the primary tumour), and screening history. For women with screen-detected cancer and two previous negative screens, the probabilities of being free from detected distant metastases 5 years after detection and removal of the primary tumour are 0.97, 0.89 and 0.59 for tumours of diameter 5, 15 and 35 mm, respectively. We also study the probability of having latent/dormant metastases at detection of the primary tumour, estimating that 33% of patients in our study had such metastases.

Lung cancer screening by low-dose computed tomography: a cost-effectiveness analysis of alternative programmes in the UK using a newly developed natural history-based economic model.

BACKGROUND: A systematic review of economic evaluations for lung cancer identified no economic models of the UK setting based on disease natural history. We first sought to develop a new model of natural history for population screening, then sought to explore the cost-effectiveness of multiple alternative potential programmes. METHODS: An individual patient model (ENaBL) was constructed in MS Excel® and calibrated against data from the US National Lung Screening Trial. Costs were taken from the UK Lung Cancer Screening Trial and took the perspective of the NHS and PSS. Simulants were current or former smokers aged between 55 and 80 years and so at a higher risk of lung cancer relative to the general population. Subgroups were defined by further restricting age and risk of lung cancer as predicted by patient self-questionnaire. Programme designs were single, triple, annual and biennial arrangements of LDCT screens, thereby examining number and interval length. Forty-eight distinct screening strategies were compared to the current practice of no screening. The primary outcome was incremental cost-effectiveness of strategies (additional cost per QALY gained). RESULTS: LDCT screening is predicted to bring forward the stage distribution at diagnosis and reduce lung cancer mortality, with decreases versus no screening ranging from 4.2 to 7.7% depending on screen frequency. Overall healthcare costs are predicted to increase; treatment cost savings from earlier detection are outweighed by the costs of over-diagnosis. Single-screen programmes for people 55-75 or 60-75 years with ≥ 3% predicted lung cancer risk may be cost-effective at the £30,000 per QALY threshold (respective ICERs of £28,784 and £28,169 per QALY gained). Annual and biennial screening programmes were not predicted to be cost-effective at any cost-effectiveness threshold. LIMITATIONS: LDCT performance was unaffected by lung cancer type, stage or location and the impact of a national screening programme of smoking behaviour was not included. CONCLUSION: Lung cancer screening may not be cost-effective at the threshold of £20,000 per QALY commonly used in the UK but may be cost-effective at the higher threshold of £30,000 per QALY.

Modeling Disease Progression with Longitudinal Markers.

In this paper we propose a Bayesian natural history model for disease progression based on the joint modeling of longitudinal biomarker levels, age at clinical detection of disease and disease status at diagnosis. We establish a link between the longitudinal responses and the natural history of the disease by using an underlying latent disease process which describes the onset of the disease and models the transition to an advanced stage of the disease as dependent on the biomarker levels. We apply our model to the data from the Baltimore Longitudinal Study of Aging on prostate specific antigen (PSA) to investigate the natural history of prostate cancer.