Section 4 Molecular subtypes

4.1 Subtypes and prognosis

Collectively considering the information obtained from unsupervised clustering and CNV-based stratification, we were able to categorize PAAD patients into four molecular subtypes:

• repair-deficient (the repair-deficient group with low CNV score)

• proliferation-active (the repair-deficient group with high CNV score)

• repair-proficient (the repair-proficient group with low CNV score)

• repair-enhanced (the repair-proficient group with high CNV score; notably lacking the survival information for prognostic analysis)

Our identified subtypes were informative in prognosis (as shown in the figure): the best for repair-deficient patients, and the worse for repair-proficient and proliferation-active patients.

4.2 Repair-deficient patients

Comparing repair-deficient patients with high or low CNV score, we identified 203 genes with differential CNV (FDR < 0.05 on Wilcoxon rank sum test).

• List of genes with differential CNV comparing repair-deficient patients with high CNV score (CNVscoreH) against repair-deficient patients with low CNV score (CNVscoreL), with the column log(CNVscoreH / CNVscoreL) indicative of log-transformed differential change.