Analysis of treatment pathways for three chronic diseases using OMOP CDM.

The present study examined treatment pathways (the ordered sequence of medications that a patient is prescribed) for three chronic diseases (hypertension, type 2 diabetes, and depression), compared the pathways with recommendations from guidelines, discussed differences and standardization of medications in different medical institutions, explored population diversification and changes of clinical treatment, and provided clinical big data analysis-based data support for the development and study of drugs in China. In order to run the "Treatment Pathways in Chronic Disease" protocol in Chinese data sources,we have built a large data research and analysis platform for Chinese clinical medical data. Data sourced from the Clinical Data Repository (CDR) of the First Affiliated Hospital of Nanjing Medical University was extracted, transformed, and loaded into an observational medical outcomes partnership common data model (OMOP CDM) Ver. 5.0. Diagnosis and medication information for patients with hypertension, type 2 diabetes, and depression from 2005 to 2015 were extracted for observational research to obtain treatment pathways for the three diseases. The most common medications used to treat diabetes and hypertension were metformin and acarbose, respectively, at 28.5 and 20.9% as first-line medication. New drugs were emerging for depression; therefore, the favorite medication changed accordingly. Most patients with these three diseases had different treatment pathways from other patients with the same diseases. The proportions of monotherapy increased for the three diseases, especially in recent years. The recommendations presented in guidelines show some predominance. High-quality, effective guidelines incorporating domestic facts should be established to further guide medication and improve therapy at local hospitals. Medical institutions at all levels could improve the quality of medical services, and further standardize medications in the future. This research is the first application of the CDM model and OHDSI software in China, which were used to study, treatment pathways for three chronic diseases (hypertension, type 2 diabetes and depression), compare the pathways with recommendations from guidelines, discuss differences and standardization of medications in different medical institutions, demonstrate the urgent need for quality national guidelines, explores population diversification and changes of clinical treatment, and provide clinical big data analysis-based data support for the development and study of drugs in China.

Radiogenomics analysis reveals the associations of dynamic contrast-enhanced-MRI features with gene expression characteristics, PAM50 subtypes, and prognosis of breast cancer.

Background: To investigate reliable associations between dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) features and gene expression characteristics in breast cancer (BC) and to develop and validate classifiers for predicting PAM50 subtypes and prognosis from DCE-MRI non-invasively. Methods: Two radiogenomics cohorts with paired DCE-MRI and RNA-sequencing (RNA-seq) data were collected from local and public databases and divided into discovery (n = 174) and validation cohorts (n = 72). Six external datasets (n = 1,443) were used for prognostic validation. Spatial-temporal features of DCE-MRI were extracted, normalized properly, and associated with gene expression to identify the imaging features that can indicate subtypes and prognosis. Results: Expression of genes including RBP4, MYBL2, and LINC00993 correlated significantly with DCE-MRI features (q-value < 0.05). Importantly, genes in the cell cycle pathway exhibited a significant association with imaging features (p-value < 0.001). With eight imaging-associated genes (CHEK1, TTK, CDC45, BUB1B, PLK1, E2F1, CDC20, and CDC25A), we developed a radiogenomics prognostic signature that can distinguish BC outcomes in multiple datasets well. High expression of the signature indicated a poor prognosis (p-values < 0.01). Based on DCE-MRI features, we established classifiers to predict BC clinical receptors, PAM50 subtypes, and prognostic gene sets. The imaging-based machine learning classifiers performed well in the independent dataset (areas under the receiver operating characteristic curve (AUCs) of 0.8361, 0.809, 0.7742, and 0.7277 for estrogen receptor (ER), human epidermal growth factor receptor 2 (HER2)-enriched, basal-like, and obtained radiogenomics signature). Furthermore, we developed a prognostic model directly using DCE-MRI features (p-value < 0.0001). Conclusions: Our results identified the DCE-MRI features that are robust and associated with the gene expression in BC and displayed the possibility of using the features to predict clinical receptors and PAM50 subtypes and to indicate BC prognosis.

Concordance assessment of Watson for Oncology in breast cancer chemotherapy: first China experience.

BACKGROUND: IBM Watson for Oncology (WFO) is an artificial intelligence cognitive computing system that provides confidence-ranked, evidence-based treatment recommendations for cancer. We examine the level of agreement for breast cancer chemotherapy between WFO recommended and clinical use in a large population of breast cancer cases. METHODS: A total of 1,301 breast cancer patients were reviewed in The First Affiliated Hospital with Nanjing Medical University, China from June 2013 to December 2017. Patients' data were entered manually into WFO by the trained senior oncology fellows. Chemotherapy recommendations were provided in 3 categories, "Recommended", "For Consideration", and "Not Recommended". Concordance was achieved when oncologists' treatment suggestions were in the "Recommended" or "For Consideration" categories. RESULTS: The chemotherapy regimen concordance was 69.4% among all breast cancer cases, 65.0% among the cases in adjuvant chemotherapy (AC) group and 96.7% among the cases in neoadjuvant chemotherapy (NAC) group. The concordance varied greatly in subset analysis with respect to TNM stage and molecular subtype. AC recommendations were concordant in 92.3% of stage III breast cancer and 50.8% of stage I. However, the concordance varied by molecular subtype, which was higher for triple negative breast cancer (89.3%) than others. The chemotherapy regimen concordance declined significantly with increasing age, except for the age group 41-50 years. CONCLUSIONS: Chemotherapy regimens provided by WFO did not exhibit a high degree of agreement with those suggested by oncologists in clinical practice in the hospital in China. The current effort is underway to enhance WFO's capabilities as a cognitive decision support tool by incorporating regional guidelines, enabling oncologists and patients to benefit from WFO worldwide.