Using big data to retrospectively validate the COMPASS-CAT risk assessment model: considerations on methodology.

External validation is a prerequisite in order for a prediction model to be introduced into clinical practice. Nonetheless, methodologically intact external validation studies are a scarce finding. Utilization of big datasets can help overcome several causes of methodological failure. However, transparent reporting is needed to standardize the methods, assess the risk of bias and synthesize multiple validation studies in order to infer model generalizability. We describe the methodological challenges faced when using multiple big datasets to perform the first retrospective external validation study of the Prospective Comparison of Methods for thromboembolic risk assessment with clinical Perceptions and AwareneSS in real life patients-Cancer Associated Thrombosis (COMPASS-CAT) Risk Assessment Model for predicting venous thromboembolism in patients with cancer. The challenges included choosing the starting point, defining time sensitive variables that serve both as risk factors and outcome variables and using non-research oriented databases to form validated definitions from administrative codes. We also present the structured plan we used so as to overcome those obstacles and reduce bias with the target of producing an external validation study that successfully complies with prediction model reporting guidelines.

External Validation of a Venous Thromboembolic Risk Score for Cancer Outpatients with Solid Tumors: The COMPASS-CAT Venous Thromboembolism Risk Assessment Model.

BACKGROUND: Current risk assessment models (RAMs) for prediction of venous thromboembolism (VTE) risk in the outpatient cancer population have shown poor predictive value in many of the most common cancers. The Comparison of Methods for Thromboembolic Risk Assessment with Clinical Perceptions and AwareneSS in Real Life Patients-Cancer Associated Thrombosis (COMPASS-CAT) RAM was derived in this patient population and predicted patients at high risk for VTE even after initiation of chemotherapy. We sought to externally validate this RAM. MATERIALS AND METHODS: Patients aged ≥18 years who presented to a tertiary care center between January 1, 2014, and December 31, 2016, with invasive breast, ovarian, lung, or colorectal cancers were included. The COMPASS-CAT RAM was applied using our health system's tumor registry and variables that were identified by International Statistical Classification of Diseases and Related Health Problems-9 and -10 codes of the electronic health record and independent chart review. The primary endpoint at 6-month study follow-up was documented VTE. RESULTS: A total of 3,814 patients were included. Documented VTE at 6-month follow-up occurred in 5.85% of patients. Patients stratified into low/intermediate- and high-risk groups had VTE rates of 2.27% and 6.31%, respectively. The sensitivity, specificity, and negative and positive predictive value of the RAM were 95%, 12%, 97.73%, and 6.31%, respectively. Diagnostic accuracy via receiver operating characteristic curve was calculated at 0.62 of the area under the curve. CONCLUSION: In this large retrospective external validation study of the COMPASS-CAT RAM for VTE in patients with cancer undergoing active treatment, model discrimination was moderate and calibration was poor. The model had good negative predictive value. Further prospective validation studies-especially within 6 months of cancer diagnosis-are needed before the model can be implemented into routine clinical practice for primary thromboprophylaxis of high-VTE-risk patients with cancer with solid tumors. IMPLICATIONS FOR PRACTICE: This study provides further guidance for researchers and clinicians in determining clinical and laboratory risk factors associated with development of venous thromboembolism among the ambulatory population of patients being treated for lung, breast, colorectal, or ovarian cancer. It validates the COMPASS-CAT risk model that was developed in this cancer population and suggests that further prospective validation of the model, with more focus on patients within 6 months of their index cancer diagnosis, would likely enhance the accuracy and usefulness of this model as a clinical prediction tool.

Development of new microsatellite markers from Mango (Mangifera indica) and cross-species amplification.

PREMISE OF THE STUDY: Microsatellite markers were developed and characterized to assess the genetic diversity among mango (Mangifera indica) cultivars and to test their amplification in closely related species. METHODS AND RESULTS: Thirty-six microsatellite (simple sequence repeats; SSR) loci were isolated by a microsatellite-enriched partial genomic library method. Primers designed for these loci were characterized using 30 diverse mango cultivars. The number of alleles ranged from 3 to 19 with an average of 9.2 alleles per locus. Polymorphic information content values ranged from 0.185 to 0.920 with a mean of 0.687. The total value for the probability of identity was 2.42 × 10(-31). CONCLUSIONS: The newly identified SSRs would be useful in genetic diversity studies, finger-printing, and mapping. Loci from five related species, M. odorata, M. anadamanica, M. zeylanica, M. camptosperma, and M. griffithii, were successfully amplified using these SSR primers, showing their potential utility across species.

Serendipitous Finding of Asymptomatic Babesiosis in a Patient With Symptomatic Thrombocytopenia.

We report a case of isolated immune thrombocytopenic purpura (ITP) as a result of babesiosis infection. The patient initially presented with a history, physical exam and laboratory findings consistent with idiopathic thrombocytopenic purpura. She was treated with standard of care therapy without clinical response. Daily evaluation of the peripheral smear ultimately revealed a red blood cell inclusion, identified and confirmed as a low-titer babesiosis infection indicative of past exposure. As described below, isolated thrombocytopenia related to babesiosis infection has not been reported prior to the patient's presentation. There are a few cases reported to show a relationship between babesiosis and autoimmune hemolytic anemia without an understood pathophysiologic mechanism. We review the literature, propose a possible pathophysiologic mechanism of disease and consider the implications of swift identification to prevent clinical deterioration.

Cloning and characterization of differentially expressed genes of internal breakdown in mango fruit (Mangifera indica).

Internal breakdown in mango fruits has become a major concern in recent years. This disorder renders the fruits unfit for human consumption. The overall loss due to this disorder is about 35-55%. Environmental and physiological factors like high temperature, humidity, respiration and low transpiration rates have been attributed to cause spongy tissue due to reduced loss of heat from fruits. Biochemical studies have shown that there is a reduction in pH, total soluble solids, ascorbic acid, total sugars and carotenoids, low reducing and non-reducing sugar contents, lower amylase and invertase activities and high acid and starch content in spongy tissue affected pulp. There are no reports on molecular studies to determine changes in gene expression in these tissues. The present study was conducted using PCR based subtractive hybridization and RNA gel blot analysis of a few selected genes. The latter showed a higher expression of catalase, ubiquitin, alcohol dehydrogenase, coproporphyrinogen oxidase and keratin associated protein. A lower expression of ribosomal gene, fructose bisphosphate aldolase and cysthathionine gamma synthase was also noticed in spongy tissue. Biochemical studies indicated a lower amylase activity and a lower content of the total and reducing sugars in spongy tissue as compared to healthy tissue. Analyses of results indicate that oxidative stress may be one of the causes for formation of spongy tissue, which affects the expression of many genes. The role of these genes in spongy tissue formation is discussed.