Determining relative importance of variables in developing and validating predictive models

<p>Abstract</p> <p>Background</p> <p>Multiple regression models are used in a wide range of scientific disciplines and automated model selection procedures are frequently used to identify independent predictors. However, determination of relative importance of potential predictors and validating the fitted models for their stability, predictive accuracy and generalizability are often overlooked or not done thoroughly.</p> <p>Methods</p> <p>Using a case study aimed at predicting children with acute lymphoblastic leukemia (ALL) who are at low risk of Tumor Lysis Syndrome (TLS), we propose and compare two strategies, bootstrapping and random split of data, for ordering potential predictors according to their relative importance with respect to model stability and generalizability. We also propose an approach based on relative increase in percentage of explained variation and area under the Receiver Operating Characteristic (ROC) curve for developing models where variables from our ordered list enter the model according to their importance. An additional data set aimed at identifying predictors of prostate cancer penetration is also used for illustrative purposes.</p> <p>Results</p> <p>Age is chosen to be the most important predictor of TLS. It is selected 100% of the time using the bootstrapping approach. Using the random split method, it is selected 99% of the time in the training data and is significant (at 5% level) 98% of the time in the validation data set. This indicates that age is a stable predictor of TLS with good generalizability. The second most important variable is white blood cell count (WBC). Our methods also identified an important predictor of TLS that was otherwise omitted if relying on any of the automated model selection procedures alone. A group at low risk of TLS consists of children younger than 10 years of age, without T-cell immunophenotype, whose baseline WBC is < 20 × 10⁹/L and palpable spleen is < 2 cm. For the prostate cancer data set, the Gleason score and digital rectal exam are identified to be the most important indicators of whether tumor has penetrated the prostate capsule.</p> <p>Conclusion</p> <p>Our model selection procedures based on bootstrap re-sampling and repeated random split techniques can be used to assess the strength of evidence that a variable is truly an independent and reproducible predictor. Our methods, therefore, can be used for developing stable and reproducible models with good performances. Moreover, our methods can serve as a good tool for validating a predictive model. Previous biological and clinical studies support the findings based on our selection and validation strategies. However, extensive simulations may be required to assess the performance of our methods under different scenarios as well as check their sensitivity to a random fluctuation in the data.</p

Studi Volume Lalu Lintas di Jalan Raya Narogong Cileungsi, Kabupaten Bogor, Periode Agustus 2011

Survey of traffic volume is one of the simplest methods to obtain traffic data in order to better understand optimalisation andefficiency so that it can minimize vehicle traffic congestion problems on the highway. The method used is based on descriptive andanalytical methods, which is done is to classify the vehicles in classes manually by counting the number of vehicles per time unitbased on class - class. The purpose of the volume of traffic surveys carried out in the classified Narogong Cullinan Road, Bogorregency during the period August, 2011, results that can be found is the degree of saturation of the highway is still in an acceptablelevel. Analysis of traffic flow at the study site is still under the limit congestion. It is suggested that to reduce the traffic density, thetype of heavy vehicles such as out of the factory operates around the study site between the hours of 10:00 pm to 3:00 am

Chemical exchange saturation transfer MRI in central nervous system tumours on a 1.5 T MR-Linac

Purpose: To describe the implementation and initial results of using Chemical Exchange Saturation Transfer (CEST) for monitoring patients with central nervous system (CNS) tumours treated using a 1.5 tesla MR-guided radiotherapy system. Methods: CNS patients were treated with up to 30 fractions (total dose up to 60 Gy) using a 1.5 T Elekta Unity MR-Linac. CEST scans were obtained in 54 subjects at one or more time points during treatment. CEST metrics, including the amide magnetization transfer ratio (MTRAmide), nuclear Overhauser effect (NOE) MTR (MTRNOE) and asymmetry, were quantified in phantoms and CNS patients. The signal was investigated between tumour and white matter, across time, and across disease categories including high- and low-grade tumours. Results: The gross tumour volume (GTV) exhibited lower MTRAmide and MTRNOE and higher asymmetry compared to contralateral normal appearing white matter. Signal changes in the GTV during fractionated radiotherapy were observed. There were differences between high- and low-grade tumours, with higher CEST asymmetry associated with higher grade disease. Conclusion: CEST MRI using a 1.5 T MR-Linac was demonstrated to be feasible for in vivo imaging of CNS tumours. CEST images showed tumour/white-matter contrast, temporal CEST signal changes, and associations with tumour grade. These results show promise for the eventual goal of using metabolic imaging to inform the design of adaptive radiotherapy protocols

Glioma consensus contouring recommendations from a MR-Linac International Consortium Research Group and evaluation of a CT-MRI and MRI-only workflow

Introduction: This study proposes contouring recommendations for radiation treatment planning target volumes and organs-at-risk (OARs) for both low grade and high grade gliomas. Methods: Ten cases consisting of 5 glioblastomas and 5 grade II or III gliomas, including their respective gross tumor volume (GTV), clinical target volume (CTV), and OARs were each contoured by 6 experienced neuro-radiation oncologists from 5 international institutions. Each case was first contoured using only MRI sequences (MRI-only), and then re-contoured with the addition of a fused planning CT (CT-MRI). The level of agreement among all contours was assessed using simultaneous truth and performance level estimation (STAPLE) with the kappa statistic and Dice similarity coefficient. Results: A high level of agreement was observed between the GTV and CTV contours in the MRI-only workflow with a mean kappa of 0.88 and 0.89, respectively, with no statistically significant differences compared to the CT-MRI workflow (p = 0.88 and p = 0.82 for GTV and CTV, respectively). Agreement in cochlea contours improved from a mean kappa of 0.39 to 0.41, to 0.69 to 0.71 with the addition of CT information (p < 0.0001 for both cochleae). Substantial to near perfect level of agreement was observed in all other contoured OARs with a mean kappa range of 0.60 to 0.90 in both MRI-only and CT-MRI workflows. Conclusions: Consensus contouring recommendations for low grade and high grade gliomas were established using the results from the consensus STAPLE contours, which will serve as a basis for further study and clinical trials by the MR-Linac Consortium

Heterogeneity of circulating tumour cell-associated genomic gains in breast cancer and its association with the host immune response.

Tumor cells that preferentially enter circulation include the precursors of metastatic cancer. Previously, we characterized circulating tumor cells (CTC) from patients with breast cancer and identified a signature of genomic regions with recurrent copy-number gains. Through FISH, we now show that these CTC-associated regions are detected within the matched untreated primary tumors of these patients (21% to 69%, median 55.5%, n = 19). Furthermore, they are more prevalent in the metastases of patients who died from breast cancer after multiple rounds of treatment (70% to 100%, median 93%, samples n = 41). Diversity indices revealed that higher spatial heterogeneity for these regions within primary tumors is associated with increased dissemination and metastasis. An identified subclone with multiple regions gained (MRG clone) was enriched in a posttreatment primary breast carcinoma as well as multiple metastatic tumors and local breast recurrences obtained at autopsy, indicative of a distinct early subclone with the capability to resist multiple lines of treatment and eventually cause death. In addition, multiplex immunofluorescence revealed that tumor heterogeneity is significantly associated with the degree of infiltration of B lymphocytes in triple-negative breast cancer, a subtype with a large immune component. Collectively, these data reveal the functional potential of genetic subclones that comprise heterogeneous primary breast carcinomas and are selected for in CTCs and posttreatment breast cancer metastases. In addition, they uncover a relationship between tumor heterogeneity and host immune response in the tumor microenvironment. SIGNIFICANCE: As breast cancers progress, they become more heterogeneous for multiple regions amplified in circulating tumor cells, and intratumoral spatial heterogeneity is associated with the immune landscape

Survival Benefit for Individuals With Constitutional Mismatch Repair Deficiency Undergoing Surveillance

PURPOSE: Constitutional mismatch repair deficiency syndrome (CMMRD) is a lethal cancer predisposition syndrome characterized by early-onset synchronous and metachronous multiorgan tumors. We designed a surveillance protocol for early tumor detection in these individuals. PATIENTS AND METHODS: Data were collected from patients with confirmed CMMRD who were registered in the International Replication Repair Deficiency Consortium. Tumor spectrum, efficacy of the surveillance protocol, and malignant transformation of low-grade lesions were examined for the entire cohort. Survival outcomes were analyzed for patients followed prospectively from the time of surveillance implementation. RESULTS: A total of 193 malignant tumors in 110 patients were identified. Median age of first cancer diagnosis was 9.2 years (range: 1.7-39.5 years). For patients undergoing surveillance, all GI and other solid tumors, and 75% of brain cancers were detected asymptomatically. By contrast, only 16% of hematologic malignancies were detected asymptomatically (P \u3c .001). Eighty-nine patients were followed prospectively and used for survival analysis. Five-year overall survival (OS) was 90% (95% CI, 78.6 to 100) and 50% (95% CI, 39.2 to 63.7) when cancer was detected asymptomatically and symptomatically, respectively (P = .001). Patient outcome measured by adherence to the surveillance protocol revealed 4-year OS of 79% (95% CI, 54.8 to 90.9) for patients undergoing full surveillance, 55% (95% CI, 28.5 to 74.5) for partial surveillance, and 15% (95% CI, 5.2 to 28.8) for those not under surveillance (P \u3c .0001). Of the 64 low-grade tumors detected, the cumulative likelihood of transformation from low-to high-grade was 81% for GI cancers within 8 years and 100% for gliomas in 6 years. CONCLUSION: Surveillance and early cancer detection are associated with improved OS for individuals with CMMRD