| Antibodies |
|
| Anti-CD3 |
Ventana |
Clone 2GV6; RRID:AB_2335978
|
| Anti-CD4 |
Ventana |
Clone SP35; RRID:AB_2335982
|
| Anti-CD8 |
Ventana |
Clone SP57; RRID:AB_2335985
|
| Anti-PD-L1 |
Ventana |
Clone SP263; RRID:AB_2819099
|
|
| Biological samples |
|
| Primary, p16(+) OPSCC tumor tissue and derived DNA and RNA |
Institutional Tissue Acquisition |
|
| Primary, p16(+) OPSCC tumor RNA – normalized transcript reads |
HNSC-TCGA (Lawrence et al., 2015) |
|
|
| Deposited data |
|
| Whole exome sequencing data |
This paper |
NIH dbGaP Accession:phs002768.v1.p1
|
| NanoString mRNA hybridization data |
This paper |
NIH GEO Accession:GSE199029
|
|
| Software and algorithms |
|
| R |
R Core Team |
https://www.r-project.org/ |
| Survival |
R package |
https://github.com/therneau/survival |
| Survminer |
R package |
https://github.com/kassambara/survminer |
| somatic_exome |
McDonnell Genome Institute |
https://github.com/genome/analysis-workflows |
| GATK |
Auwera et al.(Auwera et al., 2013) |
https://gatk.broadinstitute.org/hc/en-us |
| Strelka |
Saunders et al.(Saunders et al., 2012) |
https://github.com/Illumina/strelka |
| MuTect |
Cibulskis et al.(Cibulskis et al., 2013) |
https://software.broadinstitute.org/cancer/cga/mutect |
| VarScan |
Koboldt et al.(Koboldt et al., 2013) |
http://dkoboldt.github.io/varscan/ |
| Pindel |
Ye et al.(Ye et al., 2009) |
http://gmt.genome.wustl.edu/packages/pindel/ |
| Ensembl Variant Effect Predictor |
McLaren et al.(McLaren et al., 2016) |
https://github.com/Ensembl/ensembl-vep |
| DeepSVR |
Ainscough et al.(Ainscough et al., 2018) |
https://github.com/griffithlab/DeepSVR |
| gnomAD |
Karczewski et al.(Karczewski et al., 2020) |
https://gnomad.broadinstitute.org/ |
| MuSiC |
Dees et al.(Dees et al., 2012) |
https://github.com/ding-lab/MuSiC2 |
| MUFFINN |
Cho et al.(Cho et al., 2016) |
https://www.inetbio.org/muffinn/ |
| deconstructSigs |
Rosenthal et al.(Rosenthal et al., 2016) |
https://github.com/raerose01/deconstructSigs |
| CNVkit |
Talevich et al.(Talevich et al., 2016) |
https://github.com/etal/cnvkit |
| GenVisR |
Skidmore et al.(Skidmore et al., 2016) |
https://github.com/griffithlab/GenVisR |
| GISTIC2.0 |
Mermel et al.(Mermel et al., 2011) |
https://github.com/broadinstitute/gistic2 |
| WebGestalt |
Liao et al.(Liao et al., 2019) |
http://www.webgestalt.org/ |
| Visiopharm |
|
https://visiopharm.com/ |
| nSolver |
NanoString |
https://www.nanostring.com/ |
| GraphPad Prism |
|
https://www.graphpad.com/ |
