Clinical and Translational Study of Ivosidenib Plus Nivolumab in Advanced Solid Tumors Harboring IDH1 Mutations

This record describes the Visium HD dataset from Nguyen et al. manuscript, entitled "Clinical and translational study of ivosidenib plus nivolumab in advanced solid tumors harboring IDH1 mutations". Visium HD library preparation and sequencing of tumor FFPE tissues. Spatial transcriptomics by Visium HD was performed on pre/on-treatment tumor biopsies from one patient, and sufficient viable tumor tissues were identified by a pathologist. The pre-treatment tumor biopsy was obtained prior to C1D1 and within 28 days of treatment start. The on-treatment tumor biopsy was obtained at C2D1. All samples were processed at the same time and assayed on the same Visium HD slide to minimize batch effect. Samples were assessed for RNA quality, and all FFPE samples had a DV200 score above the minimum threshold ≥30%. Spatial transcriptomic libraries were generated with Visium HD Human Transcriptome gene expression kit (10x Genomics: 1000675). 5 micron FFPE sections were placed on Schott Nexterion H-3D Hydrogel Coated Slides (Schott North America: 1800434) to minimize the risk of tissue detachment and processed through the 10x Visium HD for FFPE protocol according to the manufacturer’s instructions (CG000685 Rev B). H&E images were taken at 40x magnification using a Leica Aperio CS2 slide scanner (Leica Biosystems). Library QC was completed with an Agilent TapeStation 4150. Libraries were normalized and pooled to 2nM prior to loading on an Illumina NextSeq 2000, using a P4 100 flow cell with a target of a minimum of 275 million reads per sample for transcriptomic libraries. Visium HD reads were aligned to human transcriptome GRCh38-2020-A with 10x Genomics Space Ranger (v3.1.3), and analyzed using Seurat (v5.3.0).