93 research outputs found
Preoperative MRI-radiomics features improve prediction of survival in glioblastoma patients over MGMT methylation status alone
Background:
Glioblastoma (GBM) is the most common malignant central nervous system tumor, and MGMT promoter hypermethylation in this tumor has been shown to be associated with better prognosis. We evaluated the capacity of radiomics features to add complementary information to MGMT status, to improve the ability to predict prognosis.
Methods:
159 patients with untreated GBM were included in this study and divided into training and independent test sets. 286 radiomics features were extracted from the magnetic resonance images acquired prior to any treatments. A least absolute shrinkage selection operator (LASSO) selection followed by Kaplan-Meier analysis was used to determine the prognostic value of radiomics features to predict overall survival (OS). The combination of MGMT status with radiomics was also investigated and all results were validated on the independent test set.
Results:
LASSO analysis identified 8 out of the 286 radiomic features to be relevant which were then used for determining association to OS. One feature (edge descriptor) remained significant on the external validation cohort after multiple testing (p=0.04) and the combination with MGMT identified a group of patients with the best prognosis with a survival probability of 0.61 after 43 months (p=0.0005).
Conclusion:
Our results suggest that combining radiomics with MGMT is more accurate in stratifying patients into groups of different survival risks when compared to with using these predictors in isolation. We identified two subgroups within patients who have methylated MGMT: one with a similar survival to unmethylated MGMT patients and the other with a significantly longer OS
An automatic deep learning-based workflow for glioblastoma survival prediction using pre-operative multimodal MR images
We proposed a fully automatic workflow for glioblastoma (GBM) survival
prediction using deep learning (DL) methods. 285 glioma (210 GBM, 75 low-grade
glioma) patients were included. 163 of the GBM patients had overall survival
(OS) data. Every patient had four pre-operative MR scans and manually drawn
tumor contours. For automatic tumor segmentation, a 3D convolutional neural
network (CNN) was trained and validated using 122 glioma patients. The trained
model was applied to the remaining 163 GBM patients to generate tumor contours.
The handcrafted and DL-based radiomic features were extracted from
auto-contours using explicitly designed algorithms and a pre-trained CNN
respectively. 163 GBM patients were randomly split into training (n=122) and
testing (n=41) sets for survival analysis. Cox regression models with
regularization techniques were trained to construct the handcrafted and
DL-based signatures. The prognostic power of the two signatures was evaluated
and compared. The 3D CNN achieved an average Dice coefficient of 0.85 across
163 GBM patients for tumor segmentation. The handcrafted signature achieved a
C-index of 0.64 (95% CI: 0.55-0.73), while the DL-based signature achieved a
C-index of 0.67 (95% CI: 0.57-0.77). Unlike the handcrafted signature, the
DL-based signature successfully stratified testing patients into two
prognostically distinct groups (p-value<0.01, HR=2.80, 95% CI: 1.26-6.24). The
proposed 3D CNN generated accurate GBM tumor contours from four MR images. The
DL-based signature resulted in better GBM survival prediction, in terms of
higher C-index and significant patient stratification, than the handcrafted
signature. The proposed automatic radiomic workflow demonstrated the potential
of improving patient stratification and survival prediction in GBM patients
Precise enhancement quantification in post-operative MRI as an indicator of residual tumor impact is associated with survival in patients with glioblastoma
MatemĂ tiques i informĂ tica; Neurologia; OncologiaMatemĂĄticas e informĂĄtica; NeurologĂa; OncologĂaMathematics and computing; Neurology; OncologyGlioblastoma is the most common primary brain tumor. Standard therapy consists of maximum safe resection combined with adjuvant radiochemotherapy followed by chemotherapy with temozolomide, however prognosis is extremely poor. Assessment of the residual tumor after surgery and patient stratification into prognostic groups (i.e., by tumor volume) is currently hindered by the subjective evaluation of residual enhancement in medical images (magnetic resonance imaging [MRI]). Furthermore, objective evidence defining the optimal time to acquire the images is lacking. We analyzed 144 patients with glioblastoma, objectively quantified the enhancing residual tumor through computational image analysis and assessed the correlation with survival. Pathological enhancement thickness on post-surgical MRI correlated with survival (hazard ratio: 1.98, pâ<â0.001). The prognostic value of several imaging and clinical variables was analyzed individually and combined (radiomics AUC 0.71, pâ=â0.07; combined AUC 0.72, pâ<â0.001). Residual enhancement thickness and radiomics complemented clinical data for prognosis stratification in patients with glioblastoma. Significant results were only obtained for scans performed between 24 and 72 h after surgery, raising the possibility of confounding non-tumor enhancement in very early post-surgery MRI. Regarding the extent of resection, and in agreement with recent studies, the association between the measured tumor remnant and survival supports maximal safe resection whenever possible.This work was supported by the Fundacio La Caixa. R.P.L is supported by a Prostate Cancer Foundation Young Investigator Award, CRIS Foundation Talent Award (TALENT-05), Fero Foundation, and the Spanish Ministry of Health FIS Program (Instituto de Salud Carlos III-InvestigaciĂłn en Salud PI18/01395). Mr Guillermo Villacampa Javierre kindly provided statistical advice for this manuscript
Precise enhancement quantification in post-operative MRI as an indicator of residual tumor impact is associated with survival in patients with glioblastoma
Glioblastoma is the most common primary brain tumor. Standard therapy consists of maximum safe resection combined with adjuvant radiochemotherapy followed by chemotherapy with temozolomide, however prognosis is extremely poor. Assessment of the residual tumor after surgery and patient stratification into prognostic groups (i.e., by tumor volume) is currently hindered by the subjective evaluation of residual enhancement in medical images (magnetic resonance imaging [MRI]). Furthermore, objective evidence defining the optimal time to acquire the images is lacking. We analyzed 144 patients with glioblastoma, objectively quantified the enhancing residual tumor through computational image analysis and assessed the correlation with survival. Pathological enhancement thickness on post-surgical MRI correlated with survival (hazard ratio: 1.98, p < 0.001). The prognostic value of several imaging and clinical variables was analyzed individually and combined (radiomics AUC 0.71, p = 0.07; combined AUC 0.72, p < 0.001). Residual enhancement thickness and radiomics complemented clinical data for prognosis stratification in patients with glioblastoma. Significant results were only obtained for scans performed between 24 and 72 h after surgery, raising the possibility of confounding non-tumor enhancement in very early post-surgery MRI. Regarding the extent of resection, and in agreement with recent studies, the association between the measured tumor remnant and survival supports maximal safe resection whenever possible
The University of Pennsylvania Glioblastoma (UPenn-GBM) cohort: Advanced MRI, clinical, genomics, & radiomics
Glioblastoma is the most common aggressive adult brain tumor. Numerous studies have reported results from either private institutional data or publicly available datasets. However, current public datasets are limited in terms of: a) number of subjects, b) lack of consistent acquisition protocol, c) data quality, or d) accompanying clinical, demographic, and molecular information. Toward alleviating these limitations, we contribute the University of Pennsylvania Glioblastoma Imaging, Genomics, and Radiomics (UPenn-GBM) dataset, which describes the currently largest publicly available comprehensive collection of 630 patients diagnosed with de novo glioblastoma. The UPenn-GBM dataset includes (a) advanced multi-parametric magnetic resonance imaging scans acquired during routine clinical practice, at the University of Pennsylvania Health System, (b) accompanying clinical, demographic, and molecular information, (d) perfusion and diffusion derivative volumes, (e) computationally-derived and manually-revised expert annotations of tumor sub-regions, as well as (f) quantitative imaging (also known as radiomic) features corresponding to each of these regions. This collection describes our contribution towards repeatable, reproducible, and comparative quantitative studies leading to new predictive, prognostic, and diagnostic assessments
Towards personalized diagnosis of Glioblastoma in Fluid-attenuated inversion recovery (FLAIR) by topological interpretable machine learning
Glioblastoma multiforme (GBM) is a fast-growing and highly invasive brain
tumour, it tends to occur in adults between the ages of 45 and 70 and it
accounts for 52 percent of all primary brain tumours. Usually, GBMs are
detected by magnetic resonance images (MRI). Among MRI, Fluid-attenuated
inversion recovery (FLAIR) sequence produces high quality digital tumour
representation. Fast detection and segmentation techniques are needed for
overcoming subjective medical doctors (MDs) judgment. In the present
investigation, we intend to demonstrate by means of numerical experiments that
topological features combined with textural features can be enrolled for GBM
analysis and morphological characterization on FLAIR. To this extent, we have
performed three numerical experiments. In the first experiment, Topological
Data Analysis (TDA) of a simplified 2D tumour growth mathematical model had
allowed to understand the bio-chemical conditions that facilitate tumour
growth: the higher the concentration of chemical nutrients the more virulent
the process. In the second experiment topological data analysis was used for
evaluating GBM temporal progression on FLAIR recorded within 90 days following
treatment (e.g., chemo-radiation therapy - CRT) completion and at progression.
The experiment had confirmed that persistent entropy is a viable statistics for
monitoring GBM evolution during the follow-up period. In the third experiment
we had developed a novel methodology based on topological and textural features
and automatic interpretable machine learning for automatic GBM classification
on FLAIR. The algorithm reached a classification accuracy up to the 97%.Comment: 22 pages; 16 figure
The relationship between radiomics and pathomics in Glioblastoma patients: Preliminary results from a cross-scale association study
: Glioblastoma multiforme (GBM) typically exhibits substantial intratumoral heterogeneity at both microscopic and radiological resolution scales. Diffusion Weighted Imaging (DWI) and dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) are two functional MRI techniques that are commonly employed in clinic for the assessment of GBM tumor characteristics. This work presents initial results aiming at determining if radiomics features extracted from preoperative ADC maps and post-contrast T1 (T1C) images are associated with pathomic features arising from H&E digitized pathology images. 48 patients from the public available CPTAC-GBM database, for which both radiology and pathology images were available, were involved in the study. 91 radiomics features were extracted from ADC maps and post-contrast T1 images using PyRadiomics. 65 pathomic features were extracted from cell detection measurements from H&E images. Moreover, 91 features were extracted from cell density maps of H&E images at four different resolutions. Radiopathomic associations were evaluated by means of Spearman's correlation (Ï) and factor analysis. p values were adjusted for multiple correlations by using a false discovery rate adjustment. Significant cross-scale associations were identified between pathomics and ADC, both considering features (n = 186, 0.45 < Ï < 0.74 in absolute value) and factors (n = 5, 0.48 < Ï < 0.54 in absolute value). Significant but fewer Ï values were found concerning the association between pathomics and radiomics features (n = 53, 0.5 < Ï < 0.65 in absolute value) and factors (n = 2, Ï = 0.63 and Ï = 0.53 in absolute value). The results of this study suggest that cross-scale associations may exist between digital pathology and ADC and T1C imaging. This can be useful not only to improve the knowledge concerning GBM intratumoral heterogeneity, but also to strengthen the role of radiomics approach and its validation in clinical practice as "virtual biopsy", introducing new insights for omics integration toward a personalized medicine approach
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Machine Learning Decision Tree Models for Differentiation of Posterior Fossa Tumors Using Diffusion Histogram Analysis and Structural MRI Findings.
We applied machine learning algorithms for differentiation of posterior fossa tumors using apparent diffusion coefficient (ADC) histogram analysis and structural MRI findings. A total of 256 patients with intra-axial posterior fossa tumors were identified, of whom 248 were included in machine learning analysis, with at least 6 representative subjects per each tumor pathology. The ADC histograms of solid components of tumors, structural MRI findings, and patients' age were applied to construct decision models using Classification and Regression Tree analysis. We also compared different machine learning classification algorithms (i.e., naĂŻve Bayes, random forest, neural networks, support vector machine with linear and polynomial kernel) for dichotomized differentiation of the 5 most common tumors in our cohort: metastasis (n = 65), hemangioblastoma (n = 44), pilocytic astrocytoma (n = 43), ependymoma (n = 27), and medulloblastoma (n = 26). The decision tree model could differentiate seven tumor histopathologies with terminal nodes yielding up to 90% accurate classification rates. In receiver operating characteristics (ROC) analysis, the decision tree model achieved greater area under the curve (AUC) for differentiation of pilocytic astrocytoma (p = 0.020); and atypical teratoid/rhabdoid tumor ATRT (p = 0.001) from other types of neoplasms compared to the official clinical report. However, neuroradiologists' interpretations had greater accuracy in differentiating metastases (p = 0.001). Among different machine learning algorithms, random forest models yielded the highest accuracy in dichotomized classification of the 5 most common tumor types; and in multiclass differentiation of all tumor types random forest yielded an averaged AUC of 0.961 in training datasets, and 0.873 in validation samples. Our study demonstrates the potential application of machine learning algorithms and decision trees for accurate differentiation of brain tumors based on pretreatment MRI. Using easy to apply and understandable imaging metrics, the proposed decision tree model can help radiologists with differentiation of posterior fossa tumors, especially in tumors with similar qualitative imaging characteristics. In particular, our decision tree model provided more accurate differentiation of pilocytic astrocytomas from ATRT than by neuroradiologists in clinical reads
Forecasting Molecular Features in IDH-Wildtype Gliomas: The State of the Art of Radiomics Applied to Neurosurgery
Simple Summary The prognostic expectancies of patients affected by glioblastoma have remained almost unchanged during the last thirty years. Along with specific oncological research and surgical technical alternatives, corollary disciplines are requested to provide their contributions to improve patient management and outcomes. Technological improvements in radiology have led to the development of radiomics, a new discipline able to detect tumoral phenotypical features through the extraction and analysis of a large amount of data. Intuitively, the early foreseeing of glioma features may constitute a tremendous contribution to the management of patients. The present manuscript analyzes the pertinent literature regarding the current role of radiomics and its potentialities. Background: The fifth edition of the WHO Classification of Tumors of the Central Nervous System (CNS), published in 2021, marks a step forward the future diagnostic approach to these neoplasms. Alongside this, radiomics has experienced rapid evolution over the last several years, allowing us to correlate tumor imaging heterogeneity with a wide range of tumor molecular and subcellular features. Radiomics is a translational field focused on decoding conventional imaging data to extrapolate the molecular and prognostic features of tumors such as gliomas. We herein analyze the state-of-the-art of radiomics applied to glioblastoma, with the goal to estimate its current clinical impact and potential perspectives in relation to well-rounded patient management, including the end-of-life stage. Methods: A literature review was performed on the PubMed, MEDLINE and Scopus databases using the following search items: "radiomics and glioma", "radiomics and glioblastoma", "radiomics and glioma and IDH", "radiomics and glioma and TERT promoter", "radiomics and glioma and EGFR", "radiomics and glioma and chromosome". Results: A total of 719 articles were screened. Further quantitative and qualitative analysis allowed us to finally include 11 papers. This analysis shows that radiomics is rapidly evolving towards a reliable tool. Conclusions: Further studies are necessary to adjust radiomics' potential to the newest molecular requirements pointed out by the 2021 WHO classification of CNS tumors. At a glance, its application in the clinical routine could be beneficial to achieve a timely diagnosis, especially for those patients not eligible for surgery and/or adjuvant therapies but still deserving palliative and supportive care
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