This study investigated the genomic mechanisms underlying acquired resistance (AR) to immune checkpoint inhibitors (ICIs) across tumor types, specifically examining how copy number variant (CNV)-driven subclonal evolution contributes to clinical relapses in melanoma patients. We analyzed longitudinal clinical melanoma samples from patients who experienced relapses on ICI therapy, complemented by isogenic human melanoma cell line models (M486) and murine melanoma tumor systems. Single-cell whole-genome sequencing (scWGS) was employed to resolve subclonal CNV patterns in AR tumors. scWGS datasets from isogenic human melanoma cell lines, patient-matched tumor samples, and murine melanoma models will be made available through dbGaP, enabling researchers to access high-resolution subclonal CNV profiles that define the genomic landscape of acquired ICI resistance evolution.: Sample M486-P
M486/AR cultured sublines were dissociated with trypsin-EDTA and stained with Hoechst 33342 (ThermoFisher) and propidium iodide (BD). Cells were diluted and dispensed into ICELL8 chips. Single live cells were selected using the ICELL8 CellSelect software. scWGS libraries were prepared by lysing selected cells, followed by tagmentation using the Illumina Tagment DNA kit. Samples were barcoded with 72×72 indexed primers and PCR-amplified. Libraries were collected (Takara Collection Kit), purified with 1.8× Ampure XP beads (Beckman), QC'ed by Qubit and TapeStation, and sequenced on Illumina NovaSeq X Plus (~1 million reads per cell/nucleus).