| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological samples | ||
| Cohort A | This paper | See STAR methods: Cohort description and analysis overview |
| Cohort B | This paper and Strandgaard et al.11 | See STAR methods: Cohort description and analysis overview |
| Chemicals, peptides, and recombinant proteins | ||
| PD-L1 monoclonal antibody (Rabbit) | Ventana | Clone: Sp263 |
| PD-1 monoclonal antibody (Mouse) | Ventana | Clone: NAT105 |
| Pan-cytokeratin monoclonal antibody (Mouse) | Dako | Clone: AE1/AE3 |
| CD3 monoclonal antibody (Rabbit) | Ventana | Clone: 2GV6 |
| CD8 monoclonal antibody (Mouse) | Dako | Clone: C8/144B |
| FOXP3 monoclonal antibody (Mouse) | Thermo Fisher | Clone: SP97 |
| CD68 monoclonal antibody (Mouse) | Dako | Clone: PG-M1 |
| CD163 monoclonal antibody (Mouse) | Ventana | Clone: MRQ-26 |
| CD20 monoclonal antibody (Mouse) | Ventana | Clone: L26 |
| Critical commercial assays | ||
| GeneRead FFPE Kit | Qiagen | Cat# 180134 |
| Twist Library Preparation | Twist Bioscience | Cat# 101058 |
| Twist Human Core Exome capture kit | Twist Bioscience | Cat# 100795 |
| Twist Human RefSeq Panel | Twist Bioscience | Cat# 101023 |
| Gentra Puregene Tissue Kit (Proteinase K, RNase A Solution, Cell Lysis Solution, Protein Precipitation Solution, ATE buffer) | Qiagen | Cat# 19131, 158922, 158906, 1045701, 1067929, respectively |
| Qiasymphony DSP DNA midi kit | Qiagen | Cat# 937255 |
| Deposited data | ||
| RNAseq data | This paper | Table S1 |
| Whole Exome Sequencing Data | This paper and a subset from Strandgaard et al.11 | Processed and non-sensitive data provided upon request |
| Immune contexture | This paper | Processed and non-sensitive data provided upon request |
| Software and algorithms | ||
| STAR (2.7.1a) | Dobin et al.28 | https://github.com/alexdobin/STAR |
| RSEM (v 1.3.1) | Li and Dewey29 | https://github.com/deweylab/RSEM |
| WebGestalt | Liao et al.30 | http://www.webgestalt.org |
| MSigDB | Subramanian, Tamayo et al.31 | https://www.gsea-msigdb.org/gsea/msigdb |
| R v4.1.2 | R Core Team 2020 | https://www.r-project.org |
| Visiopharm (Version 2018.9.5.59.52) | Visiopharm A/S, Hørsolm, Denmark | |
| PurBayes | Plummer et al.32 | https://cran.r-project.org/web/packages/PurBayes/index.html |
| bwa mem v.0.7.17. | Li33 (https://arxiv.org/abs/1303.3997) | https://github.com/lh3/bwa |
| MuTect2 | Benjamin et al.34 (doi: https://doi.org/10.1101/861054) | https://github.com/broadinstitute/gatk |
| SnpEffv4.3i | Cingolani et al.35 | http://pcingola.github.io/SnpEff/ |
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