Conceptual Modeling Applied to Genomics: Challenges Faced in Data Loading

Todays genomic domain evolves around insecurity: too many imprecise concepts, too much information to be properly managed. Considering that conceptualization is the most exclusive human characteristic, it makes full sense to try to conceptualize the principles that guide the essence of why humans are as we are. This question can of course be generalized to any species, but we are especially interested in this work in showing how conceptual modeling is strictly required to understand the ''execution model'' that human beings ''implement''. The main issue is to defend the idea that only by having an in-depth knowledge of the Conceptual Model that is associated to the Human Genome, can this Human Genome properly be understood. This kind of Model-Driven perspective of the Human Genome opens challenging possibilities, by looking at the individuals as implementation of that Conceptual Model, where different values associated to different modeling primitives will explain the diversity among individuals and the potential, unexpected variations together with their unwanted effects in terms of illnesses. This work focuses on the challenges faced in loading data from conventional resources into Information Systems created according to the above mentioned conceptual modeling approach. The work reports on various loading efforts, problems encountered and the solutions to these problems. Also, a strong argument is made about why conventional methods to solve the so called `data chaos¿ problems associated to the genomics domain so often fail to meet the demands.Van Der Kroon ., M. (2011). Conceptual Modeling Applied to Genomics: Challenges Faced in Data Loading. http://hdl.handle.net/10251/16993Archivo delegad

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Coronary calcium scoring (CCS) adds to the diagnostic performance of myocardial perfusion single-photon emission computed tomography (SPECT) to assess the presence of significant coronary artery disease (CAD). Patients with a high pre-test likelihood are expected to have a high CCS which potentially could enhance the diagnostic performance of myocardial perfusion SPECT in this specific patient group. We evaluated the added value of CCS to SPECT in the diagnosis of significant CAD in patients with an intermediate to high pre-test likelihood. In total, 129 patients (mean age 62.7 ± 9.7 years, 65 % male) with stable anginal complaints and intermediate to high pre-test likelihood of CAD (median 87 %, range 22-95) were prospectively included in this study. All patients received SPECT and CCS imaging preceding invasive coronary angiography (CA). Fractional flow reserve (FFR) measurements were acquired from patients with angiographically estimated 50-95 % obstructive CAD. For SPECT a SSS > 3 was defined significant CAD. For CCS the optimal cut-off value for significant CAD was determined by ROC curve analysis. The reference standard for significant CAD was a FFR of 182.5. ROC curve analysis for prediction of the presence of significant CAD for SPECT, CCS and the combination of CCS and SPECT resulted in an area under the curve (AUC) of 0.88 (95 % CI 81-94), 0.75 (95 % CI 66-83 %) and 0.92 (95 % CI 87-97 %) respectively. The difference of the AUC between SPECT and the combination of CCS and SPECT was 0.05 (P = 0.12). The addition of CCS did not significantly improve the diagnostic performance of SPECT in the evaluation of patients with a predominantly high pre-test likelihood of CA

Incremental diagnostic accuracy of hybrid SPECT/CT coronary angiography in a population with an intermediate to high pre-test likelihood of coronary artery disease

Hybrid myocardial perfusion imaging with single photon emission computed tomography (SPECT) and CT coronary angiography (CCTA) has the potential to play a major role in patients with non-conclusive SPECT or CCTA results. We evaluated the performance of hybrid SPECT/CCTA vs. standalone SPECT and CCTA for the diagnosis of significant coronary artery disease (CAD) in patients with an intermediate to high pre-test likelihood of CAD. In total, 98 patients (mean age 62.5 ± 10.1 years, 68.4% male) with stable anginal complaints and a median pre-test likelihood of 87% (range 22-95%) were prospectively included in this study. Hybrid SPECT/CCTA was performed prior to conventional coronary angiography (CA) including fractional flow reserve (FFR) measurements. Hybrid analysis was performed by combined interpretation of SPECT and CCTA images. The sensitivity, specificity, positive (PPV), and negative (NPV) predictive values were calculated for standalone SPECT, CCTA, and hybrid SPECT/CCTA on per patient level, using an FFR 40% of the patients with a high pre-test likelihood no significant CAD was demonstrated, emphasizing the value of accurate pre-treatment cardiovascular imaging. Hybrid SPECT/CCTA was able to accurately diagnose and exclude significant CAD surpassing standalone myocardial SPECT and CCTA, vs. a reference standard of FFR measurement

Hybrid myocardial perfusion SPECT/CT coronary angiography and invasive coronary angiography in patients with stable angina pectoris lead to similar treatment decisions

Objectives: To evaluate to what extent treatment decisions for patients with stable angina pectoris can be made based on hybrid myocardial perfusion single-photon emission CT (SPECT) and CT coronary angiography (CCTA). It has been shown that hybrid SPECT/CCTA has good performance in the diagnosis of significant coronary artery disease (CAD). The question remains whether these imaging results lead to similar treatment decisions as compared to standalone SPECT and invasive coronary angiography (CA). Methods: We prospectively included 107 patients (mean age 62.8±10.0 years, 69% male) with stable anginal complaints and an intermediate to high pre-test likelihood for CAD. Hybrid SPECT/CCTA was performed prior to CA in all patients. The study outcome was the treatment decision categorised as: no revascularisation, percutaneous coronary intervention (PCI) or coronary artery bypass grafting (CABG). Treatment decisions were made by two interventional cardiologists and one cardiothoracic surgeon in two steps: first, based on the results of hybrid SPECT/CCTA; second, based on SPECT and CA. Results: Revascularisation (PCI or CABG) was indicated in 54 (50%) patients based on SPECT and CA. Percentage agreement of treatment decisions in all patients based on hybrid SPECT/CCTA versus SPECT and CA on the necessity of revascularisation was 92%. Percentage agreement of treatment decisions in patients with matched, unmatched and normal hybrid SPECT/CCTA findings was 95%, 84% and 100%, respectively. Conclusions: Panel evaluation shows that patients could be accurately indicated for and deferred from revascularisation based on hybrid SPECT/CCTA

Added value of hybrid myocardial perfusion SPECT and CT coronary angiography in the diagnosis of coronary artery disease

Hybrid single photon emission computed tomography (SPECT)/coronary computed tomography angiography (CCTA) has only been evaluated for its diagnostic accuracy as a single test in patients suspected of significant coronary artery disease (CAD). Added value of hybrid SPECT/CCTA beyond usual clinical work-up, or use of each of these tests separately, remains unclear. We evaluated the added value of hybrid myocardial perfusion SPECT (SPECT) and CCTA, beyond pre-test likelihood and exercise stress ECG (X-ECG), in the diagnosis of CAD. Two hundred and five patients with stable angina pectoris and intermediate-to-high pre-test likelihood were prospectively included. All patients underwent clinical history and examination, X-ECG, stress and rest SPECT, coronary calcium scoring (CCS) and CCTA. Fractional flow reserve measurement 50% on coronary angiography (CA) served as reference standard for significant CAD. Multiple imputation was used to correct for missing test results (17-20%). Added value of hybrid SPECT/CCTA to the basic model of pre-test likelihood plus X-ECG was quantified using logistic regression analysis. Model differences were then assessed using differences in C-index and in net reclassification improvement (NRI). The basic model had a C-index of 0.73 (95%CI 0.66-0.80). This significantly increased to 0.85 (95%CI 0.80-0.91) by addition of only SPECT, to 0.90 (95%CI 0.85-0.94) when adding only CCTA, and to 0.96 (95%CI 0.92-0.99) when adding hybrid SPECT/CCTA. The accompanying NRIs were 0.82 (95%CI 0.62-1.02), 0.86 (95%CI 0.66-1.06) and 1.57 (95%CI 1.11-1.59) respectively. Current analysis resembles clinical routine of layered testing and shows that hybrid SPECT/CCTA imaging has a substantially higher yield than standalone SPECT or CCTA in the diagnostic workup of patients suspected of significant CA