Genome-wide identification of microRNA-related genetic variants associated with overall survival of head and neck squamous cell carcinoma
Owen M. Wilkins, Alexander J. Titus, Lucas A. Salas, Jiang Gui, Melissa Eliot, Rondi A. Butler, Erich M. Sturgis, Guojun Li, Karl T. Kelsey, Brock C. Christensen
Project details
Previous studies have identified microRNA-related single nucleotide polymirphisms (miR-SNPs) associated with head and neck squamous cell carcinoma (HNSCC), in addition to other cancers. These studies are typically candidate-based and are therefore lacking in scale. We adopted a genome-wide approach to identify miR-SNPs associated with overall survival in HNSCC, using a discovery and validation phase approach. We then utilized publicaly available miRNA and mRNA expression data to provide additional support for the observed associations.
Genotyping data details
Genotype data for discovery and validation populations are being submitted to dbGAP. Accession codes linking to these data on dbGAP will be posted here once submission is complete.
R-scripts included in this repository
This repository includes R-scripts used to perform the analyses of predicted miRNA-target sites overlapping HNSCC-associated miR-SNPs, TCGA-miRseq data, and TCGA-RNAseq data.
For questions about the manuscript or data generation please e-mail: owen.m.wilkins.GR@dartmouth.edu