Compendium of primary head and neck cancer gene expression datasets with accompanying clinical data

We assembled a compendium of 30 primary HNC gene expression datasets with accompanying clinical data, representing the largest such resource for HNC. This resource was specifically built to identify genes associated with two outcome variables: patient survival and lymph node metastasis (LNM) status. Meta-analyses were applied to uniformly preprocessed gene expression data, as in our PRECOG resource (Gentles et al, Nat Med, 2016). Briefly, datasets were quality controlled, normalized, log transformed, and standardized to calculate gene expression profiles. Clinical data were manually curated and included survival and LNM status as well as variables relevant to HNC prognosis, such as tumor grade, tumor subanatomic location, and HPV status. The resulting 30 cleaned studies included 2,134 HNC tumors. 1,666 patients (across 17 cohorts) had survival outcome data and 1,490 patients (21 cohorts) had LNM status. Fully processed datasets are provided here as a resource to enable efficient meta-analyses of gene expression data in head and neck cancer.