A novel tree-based procedure for deciphering the genomic spectrum of clinical disease entities.

Background: Dissecting the genomic spectrum of clinical disease entities is a challenging task. Recursive partitioning (or classification trees) methods provide powerful tools for exploring complex interplay among genomic factors, with respect to a main factor, that can reveal hidden genomic patterns. To take confounding variables into account, the partially linear tree-based regression (PLTR) model has been recently published. It combines regression models and tree-based methodology. It is however computationally burdensome and not well suited for situations for which a large number of exploratory variables is expected.

Methods: We developed a novel procedure that represents an alternative to the original PLTR procedure, and considered different selection criteria. A simulation study with different scenarios has been performed to compare the performances of the proposed procedure to the original PLTR strategy.

Results: The proposed procedure with a Bayesian Information Criterion (BIC) achieved good performances to detect the hidden structure as compared to the original procedure. The novel procedure was used for analyzing patterns of copy-number alterations in lung adenocarcinomas, with respect to Kirsten Rat Sarcoma Viral Oncogene Homolog gene (KRAS) mutation status, while controlling for a cohort effect. Results highlight two subgroups of pure or nearly pure wild-type KRAS tumors with particular copy-number alteration patterns.

Conclusions: The proposed procedure with a BIC criterion represents a powerful and practical alternative to the original procedure. Our procedure performs well in a general framework and is simple to implement.