RT Journal Article SR Electronic T1 Population-level characterization of pathway alterations with SLAPenrich dissects heterogeneity of cancer hallmark acquisition JF bioRxiv FD Cold Spring Harbor Laboratory SP 077701 DO 10.1101/077701 A1 Francesco Iorio A1 Luz Garcia-Alonso A1 Jonathan Brammeld A1 IƱigo Martincorena A1 David R Wille A1 Ultan McDermott A1 Julio Saez-Rodriguez YR 2016 UL http://biorxiv.org/content/early/2016/09/27/077701.abstract AB We present SLAPenrich, a statistical approach implemented in an R package to search for pathways enriched for genomic alterations in large datasets. SLAPenrich mines for sample-population level enrichments, accounting for mutation rates, gene exonic lengths, and mutational mutual exclusivity. We show that SLAPenrich detects in lung adenocarcinoma pathways known to be typically altered, therapeutic targets, and associations with clinicopathological features. Finally, we explore with SLAPenrich the landscape of pathways contributing to the acquisition of the cancer hallmarks in large cohorts of patients across 10 cancer types, highlighting potential novel cancer driver genes and networks.