Tumor and peripheral biomarker analysis from the phase 3 CheckMate 9ER trial of nivolumab plus cabozantinib versus sunitinib for advanced renal cell carcinoma

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Dataset ID	Description	Technology	Samples
EGAD50000002762	Cytokine analyses were performed on peripheral blood samples obtained at baseline (treatment start date) and on treatment. Serum cytokine levels were measured using multiple enzyme-linked immunosorbent assays (Rules Based Medicine).		610
EGAD50000002763	Cytoplasmic and membrane c-MET immunohistochemistry staining was performed using an anti-c-MET antibody (SP44, Ventana Medical Systems). c-MET staining categories were negative (denoting the absence of tumor cell staining), low (denoting 1–49% of tumor cells with 1+, 2+, and/or 3+ staining) and high (denoting ≥ 50% of tumor cells with 2+ and/or 3+ staining).		664
EGAD50000002764	PathAI’s (Boston, MA, USA) artificial intelligence–powered CD8 algorithm was applied to whole-slide images of CD8-stained samples.		453
EGAD50000002765	PD-L1 immunohistochemistry staining was performed using an anti-PD-L1 antibody (Dako PD-L1 IHC 28-8 pharmDx assay, Agilent, Santa Clara, CA, USA). Tumor PD-L1 expression was quantified as the proportion of PD-L1-expressing tumor cells of the total number of viable tumor cells and expressed as a percentage (%TC). Patients were categorized as having tumors with PD-L1 expression <1% and ≥1%.		640
EGAD50000002766	DNA was extracted from tumor samples and blood samples using the Qiagen DNA FFPE and Qiagen DNA Blood Mini Kit, respectively (Qiagen, Germantown, CA). Whole-exome libraries for tumor and blood DNA samples were prepared using the SureSelectXT v5 Kit (Agilent) following validated standard operating procedures for DNA extracted from tumors and germline control samples. Libraries sequenced using the Illumina HiSeq2500 (Illumina, San Diego, CA) following 2 × 100 paired-end sequencing, targeting a depth of coverage of 100×. Sequence alignment and variant calling were performed using a published WES processing pipeline[Chang H, Sasson A, Srinivasan S, et al. Bioinformatic methods and bridging of assay results for reliable tumor mutational burden assessment in non-small cell lung cancer. Mol Diagn Ther 2019;23:507–20] based on Human Build 37 (GRCh37). A maf file is provided.	Illumina HiSeq 2500	152
EGAD50000002767	RNA-sequencing was performed on formalin-fixed, paraffin-embedded tumor samples obtained at baseline (pretreatment). Whole-transcriptome RNA-seq libraries were prepared using TruSeq Stranded Total RNA Kit with Ribo-Zero (Illumina) following a validated standard operating procedure. Libraries were sequenced using NovoSeq (Illumina) following 2 × 100 paired-end sequencing, targeting a depth of 80 million reads. Raw RNA-seq reads were aligned and filtered using STAR v2.6.0c.10 After removing microbial contaminants, sequences were aligned to the human reference genome GRCh38 using the Ensembl 91 gene model, and read counts were quantified using RSEM. Read counts are provided.	Illumina NovaSeq 6000	453
EGAD50000002768	The dataset contains the Clinical Data of 640 patients from the CheckMate-9ER Clinical Trial, including Outcome Survival (OS), Progression-Free Survival (PFSIRC), Treatment Arm, Patient Risk (IMDC), Patient Well-Being (KPSB), Tumor Type, and Demographics.		640