Bronchiectasis Phenotype Identification Model

BPIM: Bronchiectasis Phenotype Identification Model for Supervised Baseline Translation of Latent Class Trajectory Analysis-Derived Phenotypes in Non-Cystic Fibrosis Bronchiectasis

The Bronchiectasis Phenotype Identification Model (BPIM) is a prospective observational development-validation study within the Assiut University bronchiectasis translational research platform.

The study evaluates whether latent class trajectory analysis (LCTA)-derived bronchiectasis phenotype classes can be translated into a supervised baseline classifier for adults with non-cystic fibrosis bronchiectasis (NCFB).

Latent class trajectory analysis (LCTA) will first identify trajectory-derived phenotype classes using prospectively collected longitudinal disease-signature data. The Bronchiectasis Phenotype Identification Model (BPIM) will then be trained to predict the accepted latent class trajectory analysis (LCTA)-derived phenotype class using the locked baseline disease-signature architecture.

This study is observational and non-interventional. No treatment, medication, intervention, exposure, or management strategy is assigned by the protocol. All participants receive routine clinical care according to institutional practice and treating physician judgment.

The locked methodological disclosure, protocol, and deterministic statistical analysis plan are archived in the version-specific Zenodo record: https://doi.org/10.5281/zenodo.20157926.

The Bronchiectasis Phenotype Identification Model (BPIM) is developed within the Assiut University prospective bronchiectasis translational research platform as a supervised baseline phenotype-translation framework for adults with non-cystic fibrosis bronchiectasis (NCFB).

The Bronchiectasis Phenotype Identification Model (BPIM) follows a two-step analytical architecture. First, latent class trajectory analysis (LCTA) identifies trajectory-derived bronchiectasis phenotype classes using prospectively collected longitudinal disease-signature data. Second, the Bronchiectasis Phenotype Identification Model (BPIM) translates the accepted latent class trajectory analysis (LCTA)-derived phenotype structure into a supervised baseline classifier using the locked baseline disease-signature architecture.

The Bronchiectasis Phenotype Identification Model (BPIM) is methodologically separated from the Bronchiectasis Assessment of Severity and Exacerbations (BASE) framework while remaining scientifically linked to it. The Bronchiectasis Assessment of Severity and Exacerbations Severity model (BASE-S) classifies current bronchiectasis severity at baseline. The Bronchiectasis Assessment of Severity and Exacerbations Prognostic model (BASE-P) predicts 12-month bronchiectasis exacerbation risk. The Bronchiectasis Phenotype Identification Model (BPIM) predicts the accepted latent class trajectory analysis (LCTA)-derived phenotype class.

The study uses a prospective observational development-validation design. The development cohort will be used to execute the prespecified latent class trajectory analysis (LCTA) hierarchy, identify the accepted trajectory-derived phenotype structure, assign phenotype labels according to the locked convention, and train the supervised Bronchiectasis Phenotype Identification Model (BPIM) classifier. The validation cohort will be used only to evaluate the locked Bronchiectasis Phenotype Identification Model (BPIM) classifier without refitting, recalibration, predictor substitution, phenotype relabeling, threshold retuning, or post hoc classifier rescue.

The latent class trajectory analysis (LCTA) component will use a prespecified top-down variable-combination hierarchy based on longitudinal functional, oxygenation, and inflammatory disease-signature domains. Three-domain latent class trajectory analysis (LCTA) options will be attempted first. If no acceptable three-domain solution is identified, two-domain options will be attempted. If all three-domain and two-domain options fail, one-domain options will be attempted as the final fallback level. Class-number selection, acceptability criteria, failure criteria, and phenotype-labeling rules are prespecified in the locked protocol and statistical analysis plan.

Following acceptance of the latent class trajectory analysis (LCTA) solution, phenotype classes will be ordered according to increasing composite inflammatory and functional disease burden. Depending on the accepted class number, phenotype labels may include Stable phenotype, Progressive/Frequent Exacerbator phenotype, Frequent Exacerbator/Inflammatory phenotype, Advanced Multidomain phenotype, and End-stage/Terminal-risk phenotype according to the locked labeling convention.

The Bronchiectasis Phenotype Identification Model (BPIM) classifier will be trained as a supervised baseline classifier. Binary logistic regression will be used if the accepted latent class trajectory analysis (LCTA) solution contains two classes. Multinomial logistic regression will be used if the accepted latent class trajectory analysis (LCTA) solution contains three or four classes. Classification performance will be evaluated using confusion matrix, overall accuracy, class-specific sensitivity, class-specific specificity, positive predictive value, negative predictive value, macro-average F1 score where applicable, and agreement between predicted Bronchiectasis Phenotype Identification Model (BPIM) class and accepted latent class trajectory analysis (LCTA)-derived class. Where predicted class probabilities are generated, probability calibration will be assessed using calibration plots, observed-versus-predicted class probability summaries, and calibration metrics where appropriate.

The Bronchiectasis Phenotype Identification Model (BPIM) study is observational and non-interventional. No treatment, medication, intervention, exposure, or management strategy is assigned by this protocol. All clinical care follows routine institutional practice and treating physician judgment. The study is not designed to estimate causal treatment effects.

The locked methodological disclosure, protocol, deterministic statistical analysis plan, latent class trajectory analysis (LCTA) variable ledger, phenotype-labeling convention, supervised classifier structure, and validation governance are archived in the version-specific Zenodo record: https://doi.org/10.5281/zenodo.20157926.

The related Bronchiectasis Assessment of Severity and Exacerbations (BASE) structural lock is archived separately at: https://doi.org/10.5281/zenodo.20143505.

Inclusion Criteria:

• Adult patients aged 18 years or older.
• Diagnosis of non-cystic fibrosis bronchiectasis (NCFB) based on clinical assessment and high-resolution computed tomography (HRCT).
• Patients attending outpatient clinics, inpatient wards, or respiratory follow-up services at Assiut University Hospitals during the study enrollment period.
• Patients suitable for baseline disease-signature assessment within the Bronchiectasis Phenotype Identification Model (BPIM) framework.
• Ability to undergo routine clinical, functional, radiological, oxygenation, and inflammatory assessment according to the study protocol.
• Ability to complete planned longitudinal follow-up required for latent class trajectory analysis (LCTA) and Bronchiectasis Phenotype Identification Model (BPIM) validation.
• Written informed consent obtained from the patient or legal representative.

Exclusion Criteria:

• Cystic fibrosis-related bronchiectasis.
• Traction bronchiectasis due to advanced fibrotic interstitial lung disease as the dominant respiratory diagnosis.
• Active pulmonary tuberculosis at enrollment.
• Active nontuberculous mycobacterial pulmonary disease requiring specific treatment at enrollment.
• Active malignancy or terminal non-respiratory illness expected to prevent planned follow-up.
• Acute life-threatening illness preventing safe enrollment or reliable baseline assessment.
• Recent major thoracic surgery or acute thoracic trauma interfering with baseline respiratory assessment.
• Inability to complete required baseline disease-signature assessment according to the Bronchiectasis Phenotype Identification Model (BPIM) protocol.
• Inability or unwillingness to complete planned longitudinal follow-up.
• Refusal to participate.