| Biological samples |
|
|
| Tumor biopsies and peripheral blood collected from melanoma patients (CheckMate 064) |
Weber, et al. (PMID: 27269740) |
https://clinicaltrials.gov/ct2/show/NCT01783938
|
| Tumor biopsies and peripheral blood collected from melanoma patients (CheckMate 067) |
Wolchok, et al. (PMID: 28889792) |
https://clinicaltrials.gov/ct2/show/NCT01844505
|
| Critical commercial assays |
| Agilent SureSelect All Exome V2 |
Agilent |
https://www.agilent.com/en/product/next-generation-sequencing/hybridization-based-next-generation-sequencing-ngs/exome-probes/sureselect-clinical-research-exome-v2-232867#productdetails
|
| Agilent SureSelect All Exome V5 |
Agilent |
https://www.agilent.com/en/product/next-generation-sequencing/hybridization-based-next-generation-sequencing-ngs/exome-probes/sureselect-human-all-exon-232866
|
| Illumina Stranded mRNA |
Illumina |
https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/stranded-mrna-prep.html
|
| Illumina TruSeq RNA Exome |
Illumina |
https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-rna-access.html
|
| Deposited data |
| Processed data |
This paper |
https://github.com/ParkerICI/MORRISON-1-public
|
| CheckMate 064 and 067 WES data |
This paper |
BioProject: PRJNA923698 |
| CheckMate 064 and 067 RNAseq data |
This paper |
BioProject: PRJNA923698 |
| CheckMate 038 WES and RNAseq data |
Riaz, et al. (PMID: 29033130) |
SRA: SRP094781; SRA: SRP095809 |
| Gide, et al. RNAseq dataa |
Gide, et al. (PMID: 30753825) |
ENA: PRJEB23709 |
| Hugo, et al. WES and RNAseq |
Hugo, et al. (PMID: 26997480) |
SRA: SRP067938; GEO: GSE78220
|
| Liu, et al. WES and RNAseq |
Liu, et al. (PMID: 31792460) |
dbGaP: phs000452.v3.p1 |
| Van Allen, et al. RNAseq |
Van Allen, et al. (PMID: 26359337) |
dbGaP: phs000452.v2.p1 |
| Software and algorithms |
| GATK4 |
Van der Auwera, et al. |
https://github.com/broadinstitute/gatk/releases
|
| BWA-MEM v0.7.15 |
Li (PMID: 19451168) |
https://bio-bwa.sourceforge.net/bwa.shtml
|
| Mutect2 |
Benjamin, et al. (https://doi.org/10.1101/861054) |
https://gatk.broadinstitute.org/hc/en-us/articles/360036713131-Mutect2
|
| Varscan2 |
Koboldt, et al. (PMID: 22300766) |
https://varscan.sourceforge.net/
|
| Strelka |
Saunders, et al. (PMID: 22581179) |
https://github.com/Illumina/strelka
|
| SomaticSniper |
Larson, et al. (PMID: 22155872) |
https://gmt.genome.wustl.edu/packages/somatic-sniper/
|
| DeepSVR |
Ainscough, et al. (PMID: 30397337) |
https://github.com/griffithlab/DeepSVR
|
| MNVdetect |
This paper |
https://github.com/kcampbel/public/scripts/mnvDetection.py
|
| Ensembl-VEP |
McLaren, et al. (PMID: 27268795) |
https://uswest.ensembl.org/info/docs/tools/vep/index.html
|
| Sequenza |
Favero, et al. (PMID: 25319062) |
https://cran.r-project.org/web/packages/sequenza/vignettes/sequenza.html
|
| HISAT2 |
Kim, et al. (PMID: 31375807) |
https://daehwankimlab.github.io/hisat2/
|
| HTseq-counts |
Anders, et al. (PMID: 25260700) |
https://htseq.readthedocs.io/en/release_0.11.1/count.html
|
| Stringtie |
Pertea, et al. (PMID: 25690850) |
https://ccb.jhu.edu/software/stringtie/
|
| edgeR |
Robinson, et al. (PMID: 19910308) |
https://bioconductor.org/packages/release/bioc/html/edgeR.html
|
| MSigDB |
Liberzon, et al (PMID: 26771021) |
https://www.gsea-msigdb.org/gsea/msigdb/
|
| clusterProfiler |
Yu, et al. (PMID: 22455463) |
https://github.com/YuLab-SMU/clusterProfiler
|
| XGR |
Fang, et al. (PMID: 27964755) |
https://xgr.r-forge.r-project.org/
|
| ComBat-seq) |
Zhang, et al. (PMID: 33015620) |
https://github.com/zhangyuqing/ComBat-seq
|
| TIDE |
Jiang, et al. (PMID: 30127393) |
http://tide.dfci.harvard.edu
|
| Glmnet |
Friedman, et al. (PMID: 20808728) |
https://glmnet.stanford.edu/articles/glmnet.html
|
