HNSCCtargetGenes

Genomic analysis of HPV-induced oropharyngeal cancer (paired tumor/normal samples).

Raw data are available from NCBI SRA #SRP081299

Associated publication: Kannan, A., Hertweck, K.L., Philley, J.V., Wells, R.B. and Dasgupta, S., 2017. Genetic Mutation and Exosome Signature of Human Papilloma Virus Associated Oropharyngeal Cancer. Scientific Reports, 7.

Workflow:

• sequencing, SNP calling and annotation performed by Otogenetics (http://www.otogenetics.com)
• raw sequence data can be found at NCBI SRA SRP081299
• data/ contains:
  • Ot6699_Ot6700_Santanu.Dasgupta_300-923_hEx-AV4_30x_01132013_Cancer_Nucleotide_Variation: somatic variation, includes somatic variants and loss of heterozygotes (
  • variantTypes.txt: all possible variants (comparing normal and cancer)
  • all_somatic.csv: original file strictly filtered for only somatic variants (LOH removed)
  • HNSCC_*.csv: all somatic variants, filtered by CDS, nonsynonymous, then unique (not in dbSNP)
  • target_*.csv: somatic variants from target genes, filtered by CDS, nonsynonymous, then unique (not in dbSNP)
• candidateGenes.lst is a list of target genes
• table.sh is the script used to derive the .csv files in data/
• HNSCC.R is the R script used to obtain figures from parsed gene data
• figures/ contains figures produced from HNSCC.R