Dataset Information

A study design for statistical learning technique to predict radiological progression with an application of idiopathic pulmonary fibrosis using chest CT images.

ABSTRACT:

Background

Idiopathic pulmonary fibrosis (IPF) is a fatal interstitial lung disease characterized by an unpredictable decline in lung function. Predicting IPF progression from the early changes in lung function tests have known to be a challenge due to acute exacerbation. Although it is unpredictable, the neighboring regions of fibrotic reticulation increase during IPF's progression. With this clinical information, quantitative characteristics of high-resolution computed tomography (HRCT) and a statistical learning paradigm, the aim is to build a model to predict IPF progression.

Design

A paired set of anonymized 193 HRCT images from IPF subjects with 6-12 month intervals were collected retrospectively. The study was conducted in two parts: (1) Part A collects the ground truth in small regions of interest (ROIs) with labels of "expected to progress" or "expected to be stable" at baseline HRCT and develop a statistical learning model to classify voxels in the ROIs. (2) Part B uses the voxel-level classifier from Part A to produce whole-lung level scores of a single-scan total probability's (STP) baseline.

Methods

Using annotated ROIs from 71 subjects' HRCT scans in Part A, we applied Quantum Particle Swarm Optimization-Random Forest (QPSO-RF) to build the classifier. Then, 122 subjects' HRCT scans were used to test the prediction. Using Spearman rank correlations and survival analyses, we ascertained STP associations with 6-12 month changes in quantitative lung fibrosis and forced vital capacity.

Conclusion

This study can serve as a reference for collecting ground truth, and developing statistical learning techniques to predict progression in medical imaging.

SUBMITTER: Kim GHJ

PROVIDER: S-EPMC8204677 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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Publications

A study design for statistical learning technique to predict radiological progression with an application of idiopathic pulmonary fibrosis using chest CT images.

Kim Grace Hyun J GHJ Shi Yu Y Yu Wenxi W Wong Weng Kee WK

Contemporary clinical trials 20210319

<h4>Background</h4>Idiopathic pulmonary fibrosis (IPF) is a fatal interstitial lung disease characterized by an unpredictable decline in lung function. Predicting IPF progression from the early changes in lung function tests have known to be a challenge due to acute exacerbation. Although it is unpredictable, the neighboring regions of fibrotic reticulation increase during IPF's progression. With this clinical information, quantitative characteristics of high-resolution computed tomography (HRCT ...[more]

PMID: 33753286

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Project description:ObjectivesTo quantify the heterogeneity of fibrosis boundaries in idiopathic pulmonary fibrosis (IPF) using the Gaussian curvature analysis for evaluating disease severity and predicting survival.MethodsWe retrospectively included 104 IPF patients and 52 controls who underwent baseline chest CT scans. Normal lungs below - 500 HU were segmented, and the boundary was three-dimensionally reconstructed using in-house software. Gaussian curvature analysis provided histogram features on the heterogeneity of the fibrosis boundary. We analyzed the correlations between histogram features and the gender-age-physiology (GAP) and CT fibrosis scores. We built a regression model to predict diffusing capacity of carbon monoxide (DLCO) using the histogram features and calculated the modified GAP (mGAP) score by replacing DLCO with the predicted DLCO. The performances of the GAP, CT-GAP, and mGAP scores were compared using 100 repeated random-split sets.ResultsPatients with moderate-to-severe IPF had more numerous Gaussian curvatures at the fibrosis boundary, lower uniformity, and lower 10th to 30th percentiles of Gaussian curvature than controls or patients with mild IPF (all p < 0.0033). The 20th percentile was most significantly correlated with the GAP score (r = - 0.357; p < 0.001) and the CT fibrosis score (r = - 0.343; p = 0.001). More numerous Gaussian curvatures, higher entropy, lower uniformity, and 10th to 30th percentiles (p < 0.001-0.041) were associated with mortality. The mGAP score was comparable to the GAP and CT-GAP scores for survival prediction (mean C-indices, 0.76 vs. 0.79 vs. 0.77, respectively).ConclusionsGaussian curvatures of fibrosis boundaries became more heterogeneous as the disease progressed, and heterogeneity was negatively associated with survival in IPF.Key points• Gaussian curvature of the fibrotic lung boundary was more heterogeneous in patients with moderate-to-severe IPF than those with mild IPF or normal controls. • The 20th percentile of the Gaussian curvature of the fibrosis boundary was linearly correlated with the GAP score and the CT fibrosis score. • A modified GAP score that replaced the diffusing capacity of carbon monoxide with a composite measure using histogram features of the Gaussian curvature of the fibrosis boundary showed a comparable ability to predict survival to both the GAP and the CT-GAP score.

Project description:BackgroundTo clarify whether dynamic quantification of variables derived from chest high-resolution computed tomography (HRCT) can assess the progression of idiopathic pulmonary fibrosis (IPF).MethodsPatients with IPF who underwent serial computed tomography (CT) imaging were retrospectively enrolled. Several structural abnormalities seen on HRCT in IPF were segmented and quantified. Patients were divided into 2 groups according to their pulmonary function test (PFT) results: those with disease stabilization and those with disease progression, and differences between the groups were analyzed.ResultsThere were no statistically significant differences between the 2 patient groups for the following parameters: baseline PFTs, total lesion extent, lesion extent at different sites in the lungs, and pulmonary vessel-related parameters (with P values ranging from 0.057 to 0.894). Median changes in total lung volume, total lesion volume, and total lesion ratio were significantly higher in patients with worsening disease compared with those with stable disease (P<0.001). There was a significant increase in total lesion volume of 214.73 mL [interquartile range (IQR), 68.26 to 501.46 mL] compared with 3.67 mL (IQR, -71.70 to 85.33 mL) in the disease progression group compared with the disease stability group (P=0.001). The decline in pulmonary vessel volume and number of pulmonary vessel branches was more pronounced in the group with functional worsening compared with the group with functional stability. Moreover, changes in lesion volume ratio were negatively correlated with changes in diffusing capacity of the lungs for carbon monoxide (DLco) during follow-up (R=-0.57, P<0.001), and changes in pulmonary vessel-related parameters demonstrated positive correlation with DLco (with R ranging from 0.27 to 0.53, P<0.001) and forced vital capacity (FVC) (with R ranging from 0.44 to 0.61, P<0.001).ConclusionsChanges in CT-related parameters during follow-up may have better predictive performance compared with baseline imaging parameters and PFTs for disease progression in IPF.

Project description:The Rationale: Molecular markers of disease activity that are predictive of forced vital capacity (FVC) progression in idiopathic pulmonary fibrosis are needed. Objectives: Develop a predictor using longitudinal within-patient gene expression differences (ΔGE) in peripheral blood mononuclear cells (PBMC) to predict of FVC progression. Methods: Patients in the training cohort (n=74) experiencing ≥10% relative reduction in FVC% of predicted over 12 months were categorized as progressors in contrast to the remaining stable patients. Baseline to 4-month within-patient ΔGE were correlated with FVC status. FVC-predictor genes were prioritized by two-group comparison with FDR<5%, logistic LASSO regression with p<0.05, and 10-Fold Cross-Validation with ≥50% support. Receiver operating characteristic with area under the curve (AUC) analyses were conducted in training subsets and independent validation cohorts from UChicago (n=27), UPMC (n=35), and Imperial (n=24) where different transcriptome assay platforms and varying transcriptome sampling times were used to derive ΔGE. Results: Intra-subject Compared to cross-sectional analysis of baseline GE, our longitudinal ΔGE variation approach demonstratedlargely reduced within-group sample variation and increased statistic power fin progressor and stable groups for prediction model development. A 25-gene FVC-predictor separated “progressors” from “stable” by Principal Component Analysis in the training and subsets of the training cohort. The resulting FVC-predictor consistently demonstrated high discriminatory performance independent of transcriptome assay platforms and varying sampling times in validation cohorts (AUC= 0.77-0.80). TGF beta was the highest-ranking canonical pathway by Gene Set Enrichment Analysis. Conclusions: Our novel short-term longitudinal within-patient ΔGE approach identified a FVC-predictor which may reflect disease activity and prove to be a reliable biomarker predictive of future FVC decline.

Dataset Information

A study design for statistical learning technique to predict radiological progression with an application of idiopathic pulmonary fibrosis using chest CT images.

Background

Design

Methods

Conclusion

Publications

A study design for statistical learning technique to predict radiological progression with an application of idiopathic pulmonary fibrosis using chest CT images.

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