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1 | Publication status | Data status | Tissue info | Additional | ||||||||||||||||||||||||||||
2 | Dataset Name | Trial (NCT) ID | Publication Date | Usage status in meta-analysis | Pubmed link | Bait source (initial) | Data source link | Raw Data Accession | Data availability | Availability of Raw Data | Processed data availability | Link to ORCESTRA | Curation Status | Cancer type | Metastasis status | Sample size | Tissues included | Tissue timepoint | Multi-omics | RNA profiling | DNA profiling | Drug targets | Treatment regimen | Criteria for R | Criteria for NR | Number of R | Number of NR | Time-to-event Outcome | Additional Notes | Comments | Summary of Datasets | |
3 | ICB_Braun | NCT01358721|NCT01354431|NCT01668784 | 2020 | Bereche et al. | PMID: 32472114 | PredictIO | PMID: 32472114 | EGA, Supplementary materials | Public | No | Yes | Yes | ORCESTRA (PredictIO) | Clear cell renal cell carcinoma (ccRCC) | Yes | 315 | tumor and blood | mostly pre (check the Stable1 for more details - the table inform the number of days between tissue collection and start of trial therapy) | RNAseq|SNV | WTS | SNP | PD-1 | Nivolumab | CR|PR | SD|PD | 69 | 182 | PFS/OS | Curated from https://predictio.ca/datasets and SELECT. Log2-transformed TPM data is available. | Conducted whole-exome, RNA sequencing, and immunofluorescence analyses on 592 tumors from patients with advanced clear cell renal cell cancer (ccRCC) undergoing treatment with anti-PD-1 immune checkpoint blockade. Identified numerous chromosomal alterations and correlated them with responses to, or resistance against, PD-1 blockade. | ||
4 | ICB_Nathanson | 2019 | Bereche et al. | PMID: 27956380 | PredictIO | http://www.hammerlab.org/melanoma-reanalysis/ https://github.com/hammerlab/melanoma-reanalysis | GitHub | Public | No | Yes | Yes | ORCESTRA (PredictIO) | Skin Cutaneous Melanoma | No | 64 | tumor | pre-treatment or post-treatment | RNAseq|SNV | WTS | SNP | CTLA4 | Ipilimumab|Tremelimumab | CR|PR | SD|PD | 37 | 27 | OS | Curated from https://predictio.ca/datasets and SELECT Sample numbers are for pretreatment samples | This study analyzed cancer exome data from 64 melanoma patients treated with CTLA-4 blockade and RNA-seq data from 24 of these patients. The association between somatic mutation burden in pretreatment samples and the response to immune checkpoint blockade was examined. | |||
5 | ICB_Gide | 2019 | Bereche et al. | PMID: 30753825 | PredictIO | https://www.ebi.ac.uk/ena/browser/view/PRJEB23709?show=reads | ENA/BioProject, Supplementary materials | Public | Yes | Yes | Yes | ORCESTRA (PredictIO) | Skin Cutaneous Melanoma | Yes | 41 | tumor | pre-treatment or post-treatment | RNAseq | WTS | PD-1|CTLA4 | anti-PD-1, anti-PD-1+anti-CTLA4 | CR|PR | SD|PD | 19 | 15 | PFS/OS | Curated from https://predictio.ca/datasets and SELECT | Analyzed transcriptomic and immune profiling in 158 tumor biopsies from melanoma patients treated with either anti-PD-1 monotherapy or combined anti-PD-1 and anti-CTLA-4. The study identified activated T cell signatures and T cell populations in responders to both treatments. The gene expression profile of this population was associated with longer progression-free survival (PFS) in patients treated with a single agent and greater tumor shrinkage in both treatments. | ||||
6 | ICB_Miao1 | NCT01358721 | 2018 | Bereche et al. | PMID: 29301960 | PredictIO | PMID: 29301960 | EGA, Supplementary materials | Public | Yes | Yes | Yes | ORCESTRA (PredictIO) | Clear cell renal cell carcinoma (ccRCC) | Yes | 52 | tumor | pre-treatment | RNAseq|SNV | WTS | SNP | PD-1 or PD-1|CTLA4 | Nivolumab or atezolizumab or nivolumab+ipilimumab | CR|PR | SD|PD | 16 | 25 | PFS/OS | Data in supplementary. Curated from https://predictio.ca/datasets and SELECT. Log2-transformed TPM data is available. | There are two cohorts in this study. The BMS-936558, as described in the column "Trial ID", and another validation cohort. The treatment regimen is diferent: four arms with different doses of anti-PD-1 (nivolumab in cohort 1) and anti-PD-L1 (cohort 2). | Conducted whole-exome sequencing on 98 patients with metastatic clear cell renal cell cancer (ccRCC) treated with PD-1 or PD-L1 blockade therapy alone or in combination with anti-CTLA-4 therapies. This study identified an association between loss-of-function mutations in the PBRM1 gene and increased clinical benefit from immune checkpoint therapy. | |
7 | ICB_Kim | NCT02589496 | 2018 | Bereche et al. | PMID: 30013197 | PredictIO | PRJEB25780 | ENA/BioProject | Public | Yes | Yes | Yes | ORCESTRA (PredictIO) | Stomach adenocarcinoma | Yes | 45 | tumor | pre-treatment | RNAseq | WTS | PD-1 | Pembrolizumab | R | NR | 13 | 18 | NA | Curated from https://predictio.ca/datasets and SELECT | Thirty-two (52.5%) patients received pembrolizumab as second-line therapy, and 29 (47.5%) received pembrolizumab as third-line treatment for metastatic dis- ease. | Analyzed molecular characterization of tissues and circulating tumor DNA (ctDNA) from 61 patients with metastatic gastric cancer (mGC) treated with PD-1 targeted therapy. This study identified that changes in ctDNA levels at six weeks post-treatment predicted response and progression-free survival (PFS), with decreased ctDNA associated with improved outcomes. | ||
8 | ICB_Hwang | 2020 | Bereche et al. | PMID: 31959763 | PredictIO | GSE136961 | GEO | Public | No | Yes | Yes | ORCESTRA (PredictIO) | Non-small cell lung cancer (NSCLC) | Yes | 21 | tumor | pre-treatment | RNAseq | WTS | PD-1 | Nivolumab|Pembrolizumab | no recurrence | recurrence | 3 | 13 | PFS/OS | Curated from https://predictio.ca/datasets and SELECT. Raw data were processed to obtain log2-transformed TPM data with Salmon (v1.4.0), using the grch38 GENCODE transcriptome of reference, then TPM values were obtained using tximport R package. | Analyzing 21 patients with non-small-cell lung cancer (NSCLC) treated with anti-PD1 antibody, this study identified two major gene signatures: M1 (including genes like CBLB, CCR7, CD27, CD48, FOXO1, FYB, HLA-B, HLA-G, IFIH1, IKZF4, LAMP3, NFKBIA, SAMHD1) and the peripheral T cell signature (HLA-DOA, GPR18, STAT1). These signatures were predictive of improved responses to anti-PD1 treatment. | ||||
9 | ICB_Van_Allen | 2015 | Litchfield et al. | PMID: 26359337 | PredictIO | https://github.com/vanallenlab/VanAllen_CTLA4_Science_RNASeq_TPM | dbGaP, GitHub, Supplementary materials | Public | No | Yes | Yes | ORCESTRA (PredictIO) | Skin Cutaneous Melanoma | Yes | 112 | tumor | pre-treatment | RNAseq|SNV|CNA | WTS | SNP | CTLA4 | Ipilimumab | CR|PR | SD|PD | 20 | 84 | PFS/OS | Curated from https://predictio.ca/datasets and SELECT. Log2-transformed TPM data is available. | TPM downloaded from the github repo; raw data available in dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001493.v2.p1 | Analyzed whole exomes from pretreatment melanoma tumor biopsies and matching germline tissue samples from 110 patients treated with CTLA-4. Additionally, for 40 of these patients, we obtained and analyzed transcriptome data from the pretreatment tumor samples. Overall mutational load, neoantigen load, and expression of cytolytic markers in the immune microenvironment were significantly associated with clinical benefit. | ||
10 | ICB_Snyder | NCT02108652 | 2017 | Litchfield et al. | PMID: 28552987 | PredictIO | https://zenodo.org/record/546110#.YeXtqFjMJUM | EGA, Supplementary materials | Public | No | Yes | Yes | ORCESTRA (PredictIO) | Bladder Urothelial Carcinoma | Yes | 25 | tumor | pre-treatment | RNAseq | WTS | PDL-1 | Atezolizumab | CR|PR | SD|PD | 8 | 14 | PFS/OS | Curated from https://predictio.ca/datasets and SELECT. Log2-transformed TPM data is available. | Studied whole-exome sequencing, RNA sequencing, and T cell receptor sequencing of pretreatment urothelial tumor and blood samples. The presence of a higher proportion of tumor-infiltrating T lymphocytes was associated with improved responsiveness to anti-PD-L1. Pretreatment peripheral blood TCR clonality below the median was associated with improved PFS to anti-PD-L1, and substantial expansion of tumor-associated T cell receptor (TCR) clones in the peripheral blood 3 weeks after starting anti-PD-L1 treatment was associated with improved responses. The combination of high pretreatment peripheral blood TCR clonality with elevated PD-L1 immune cell staining in tumor tissue was associated with poor clinical outcomes to anti-PD-L1. | |||
11 | ICB_Riaz | NCT01621490 | 2017 | Litchfield et al. | PMID: 29033130 | PredictIO | https://github.com/riazn/bms038_analysis and https://www.ebi.ac.uk/ena/browser/view/PRJNA356761 | ENA/BioProject, GitHub, Supplementary materials | Public | Yes | Yes | Yes | ORCESTRA (PredictIO) | Skin Cutaneous Melanoma | No | 73 | tumor | pre-treatment and post-treatment (43 patients have pre and post RNAseq data) | RNAseq|SNV | WTS | SNP | PD-1 | Nivolumab | CR|PR | SD|PD | 15 | 31 | OS | Curated from https://predictio.ca/datasets and SELECT. Raw data were processed to obtain log2-transformed TPM data with Salmon (v1.4.0), using the grch38 GENCODE transcriptome of reference, then TPM values were obtained using tximport R package. | Conducted whole-exome, transcriptome, and/or T cell receptor (TCR) sequencing on 68 patients who received anti-PD1. A decrease in detectable mutations and expansion of T-cell clones were associated with a response to anti-PD1. Pre-therapy expression analysis identified pre-existing immune programs in responders and expression footprints of 'hot' versus 'cold' tumors based on prior immunotherapy exposure. | ||
12 | ICB_Liu | 2019 | Bereche et al. | PMID: 31792460 | PredictIO | PMID: 31792460 | Supplementary materials | Public | No | Yes | Yes | ORCESTRA (PredictIO) | Skin Cutaneous Melanoma | Yes | 144 | tumor | pre-treatment | RNAseq|SNV|CNA | WTS | SNP | PD-1 | Nivolumab|Pembrolizumab | CR|PR | SD|PD | 62 | 71 | PFS/OS | Data in supplementary. Curated from https://predictio.ca/datasets and SELECT. Log2-transformed TPM data is available. A few patients had previous exposure to ipilimumab | some patients received anti-CTLA4 before anti-PD1. Info available in Stable. They inform about priorMAPKTx, priorCTLA4, postCTLA4, postMAPKTx, postCombinedCTLA_PD1, numPriorTherapies | Conducted whole-exome and whole-transcriptome sequencing of 144 melanoma patients treated with anti-PD1. This study identified genomic and transcriptomic features, including those associated with MHC-I and MHC-II antigen presentation, that predicted the response to immunotherapy. | ||
13 | ICB_Hugo | 2016 | Litchfield et al. | PMID: 26997480 | PredictIO | GSE78220|SRP067938|SRP090294 | ENA/BioProject, GEO, Supplementary materials | Public | Yes | Yes | Yes | ORCESTRA (PredictIO) | Skin Cutaneous Melanoma | Yes | 38 | tumor | pre-treatment | RNAseq | WTS | PD-1 | Nivolumab|Pembrolizumab | CR|PR | SD|PD | 21 | 17 | OS | Curated from https://predictio.ca/datasets and SELECT | This study analyzed the somatic mutanomes and transcriptomes of pretreatment melanoma biopsies. It found that high mutational loads and tumors enriched for mutations in the DNA repair gene BRCA2 are associated with improved survival. Tumors from responding patients were also found to be enriched for mutations in the DNA repair gene BRCA2. The study proposed a transcriptional signature (IPRES, or innate anti-PD-1 resistance) that is associated with resistance to anti-PD1 therapy. | ||||
14 | ICB_Mariathasan | IMvigor210 | 2018 | Litchfield et al. | PMID: 29443960 | PredictIO | http://research-pub.gene.com/IMvigor210CoreBiologies/ | EGA, Supplementary materials | Public | No | Yes | Yes | ORCESTRA (PredictIO) | Bladder Urothelial Carcinoma | Yes | 347 | tumor | pre-treatment | RNAseq|SNV|CNA | WTS | SNP | PDL-1 | Atezolizumab | CR|PR | SD|PD | 68 | 167 | OS | Curated from https://predictio.ca/datasets and SELECT. Log2-transformed TPM data is available. | Analyzed patients with metastatic urothelial cancer treated with an anti-PD-L1 agent. The presence of a CD8+ T-effector cell phenotype and high neoantigen or tumor mutation burden was associated with a response to anti-PD-L1. Conversely, the presence of a signature of transforming growth factor beta (TGF-beta) signaling in fibroblasts was associated with a lack of response to anti-PD-L1. | ||
15 | ICB_Jerby_Arnon | 2018 | Bereche et al. | PMID: 30388455 | PredictIO | PMID: 30388455 | Supplementary materials | Public | No | Yes | Yes | ORCESTRA (PredictIO) | Skin Cutaneous Melanoma | Yes | 112 | tumor | pre-treatment (cohort2) and several timepoint (cohort1) | RNAseq | WTS | PD-1 | Pembrolizumab | CR|PR | SD|PD | 43 | 53 | PFS | Data in supplementary. Curated from https://predictio.ca/datasets. Log2-transformed TPM data is available. | Derived a transcriptional program associated with T cell exclusion and immunotherapy failure from single-cell RNA-seq profiles of cancer cells in 33 human melanoma tumors treated with anti-PD-1. Among the tumors in the single-cell cohort, 15 are post-immune checkpoint inhibitor-resistant tumors. | ||||
16 | ICB_Jung | 2019 | Bereche et al. | PMID: 31537801 | PredictIO | GSE135222, https://zenodo.org/record/6968389, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753140/ | GEO, Supplementary materials | Public | Yes | Yes | Yes | ORCESTRA (PredictIO) | non-small cell lung carcinoma | Yes | 60 | tumor | pre-treatment | RNAseq|SNV | WTS | SNP | PD-1|CTLA4 | Ipilimumab|Pembrolizumab | R | NR | 14 | 44 | PFS | Curated from https://predictio.ca/datasets. Raw data were processed to obtain log2-transformed TPM data with Salmon (v1.4.0), using the grch38 GENCODE transcriptome of reference, then TPM values were obtained using tximport R package. | SMC cohort (Samsung Medical Center) | Methylome analysis of lung cancer patients and melanoma patients found that genomic methylation alterations are associated with an increased resistance to immune checkpoint blockade. | ||
17 | ICB_Puch | 2021 | Bereche et al. | PMID: 33542239 | PredictIO | https://github.com/xmuyulab/ims_gene_signature | GitHub, Supplementary materials | Public | No | Yes | Yes | ORCESTRA (PredictIO) | Melanoma | Yes | 55 | tumor | pre-treatment | RNAseq | WTS | PD-1 | anti-PD-1 | CR|PR | SD|PD | 14 | 35 | NA | Data in supplementary. Curated from https://predictio.ca/datasets The Puch data comes from the Cui et al. publication. Dataset is named Puch because in the paper they call the cohort Puch. | This study generated an RNA-seq dataset from 55 tumor tissues of melanoma patients treated with anti-PD-1 monotherapy at Peking University Cancer Hospital (PUCH), Beijing, China. The study identified the potential value of the Interferonâgamma (IFNG) and immunosuppression signature (IMS) ratio as a combinatorial biomarker for anti-PD-1 treatment in metastatic melanoma. | ||||
18 | ICB_Roh | 2017 | Bereche et al. | PMID: 28251903 | PredictIO | PMID: 28251903 https://ngdc.cncb.ac.cn/bioproject/browse/insdc/PRJNA369259 | ENA/BioProject, Supplementary materials | Public | No | Yes | Yes | ORCESTRA (PredictIO) | Melanoma | Yes | 19 | tumor | pre-treatment | RNAseq|SNV | WTS | SNP | PD-1|CTLA4 | anti-PD-1|anti-CTLA4 | CR|PR | SD|PD | 2 | 17 | OS | Data in supplementary. Curated from https://predictio.ca/datasets | Molecular profiling, including T cell receptor sequencing and whole-exome sequencing, was performed on melanoma patients treated with sequential anti-CTLA-4 followed by anti-PD1. The study found that a more clonal T cell repertoire was predictive of response to PD-1, and nonresponders to immune checkpoint blockade exhibited a higher burden of copy number loss. | |||
19 | ICB_Shiuan | 2021 | Bereche et al. | PMID: 33806963 | PredictIO | PMID: 33806963 | Supplementary materials | Public | No | Yes | Yes | ORCESTRA (PredictIO) | Renal Cell Carcinoma | Yes | 15 | tumor | pre-treatment | RNAseq | WTS | PD-1|PDL-1 | Nivolumab|Atezolizumab | PR | mixed|PD | 6 | 7 | NA | Data in supplementary. Curated from https://predictio.ca/datasets | Analyzed multiplexed immunofluorescence, whole-exome sequencing, T cell receptor (TCR) sequencing, and RNA sequencing of advanced renal cell carcinoma (RCC) patients receiving anti-PD-1/PD-L1 monotherapy. High PD-L1 expression, as well as low TCR diversity, were associated with improved progression-free survival (PFS). Additionally, gene expression signatures, including angiogenesis, myeloid inflammation, T effector presence, and clear cell, also correlated with response. | ||||
20 | ICB_VanDenEnde | PERFECT | 2021 | Bereche et al. | PMID: 33504550 | PredictIO | GSE165252 | GEO | Public | No | Yes | Yes | ORCESTRA (PredictIO) | resectable esophageal adenocarcinoma (rEAC) | No | 35 | tumor | pre-treatment | RNAseq | WTS | PDL-1 | Atezolizumab | R | NR | 12 | 20 | NA | Curated from https://predictio.ca/datasets | Analyzed patients with resectable esophageal adenocarcinoma (rEAC) who received neoadjuvant chemoradiotherapy (nCRT). The study identified that baseline expression of an established interferon gamma (IFNG) signature was higher in responders compared to nonresponders. | |||
21 | ICB_Padron | PRINCE | 2022 | Bereche et al. | PMID: 35662283 | PredictIO | PMID: 35662283 https://github.com/ParkerICI/prince-trial-data | GitHub, Supplementary materials | Public | No | Yes | Yes | ORCESTRA (PredictIO) | Pancreatic ductal adenocarcinoma (PDAC) | Yes | 45 | tumor and blood | pre-treatment or post-treatment | RNAseq | WTS | PD-1 | Nivolumab|Sotigalima+gemcitabine/nab-paclitaxel | R | NR | 3 | 20 | PFS/OS | Analyzed multi-omic circulating and immune signature biomarkers of pancreatic ductal adenocarcinoma (PDAC) patients treated with anti-PD-1 and/or chemotherapy. The study identified potential treatment-specific correlates of efficacy and may enable the selection of biomarker-defined patient populations in subsequent PDAC chemoimmunotherapy trials. | ||||
22 | ICB_Limagne1 | 2022 | Bereche et al. | PMID: 35051357 | PredictIO | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190266 | GEO | Public | No | Yes | Yes | ORCESTRA (PredictIO) | Lung | Yes | 70 | tumor | pre-treatment | RNAseq | PD-1|PDL-1 | Nivolumab|Atezolizumab | R | NR | 17 | 52 | PFS | Analyzed patients with metastatic non-small cell lung cancer (mNSCLC) treated with chemotherapy and anti PD-1/PD-L1 antibodies. The study identified that the MEK inhibitor (MEKi) with pemetrexed and cisplatin (PEM/CDDP) triggers CXCL10 secretion by cancer cells and CD8+ T cell recruitment, sensitizing it to immune checkpoint inhibitors. The combination of MEK inhibitor and chemotherapy synergizes with PD-L1 blockade. | ||||||
23 | ICB_Limagne2 | 2022 | Bereche et al. | PMID: 35051357 | PredictIO | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190265 | GEO | Public | No | Yes | Yes | ORCESTRA (PredictIO) | Lung | Yes | 26 | tumor | pre-treatment | RNAseq | PD-1|PDL-1 | Nivolumab|Atezolizumab | R | NR | 6 | 16 | PFS | Analyzed patients with metastatic non-small cell lung cancer (mNSCLC) treated with chemotherapy and anti PD-1/PD-L1 antibodies. The study identified that the MEK inhibitor (MEKi) with pemetrexed and cisplatin (PEM/CDDP) triggers CXCL10 secretion by cancer cells and CD8+ T cell recruitment, sensitizing it to immune checkpoint inhibitors. The combination of MEK inhibitor and chemotherapy synergizes with PD-L1 blockade. | ||||||
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