Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Project description:We sequenced and analyzed the genome of a highly inbred miniature Chinese pig strain, the Banna Minipig Inbred Line (BMI). we conducted whole genome screening using next generation sequencing (NGS) technology and performed SNP calling using Sus Scrofa genome assembly Sscrofa11.1.
Project description:Porcine 60K BeadChip genotyping arrays (Illumina) are increasingly being applied in pig genomics to validate SNPs identified by re-sequencing or assembly-versus-assembly method. Here we report that more than 98% SNPs identified from the porcine 60K BeadChip genotyping array (Illumina) were consistent with the SNPs identified from the assembly-based method. This result demonstrates that whole-genome de novo assembly is a reliable approach to deriving accurate maps of SNPs.
Project description:Juvenile localized scleroderma (LS) and systemic sclerosis (SSc) are rare autoimmune diseases that can cause substantial morbidity and disability in children. However, the cellular and molecular mechanisms underlying juvenile scleroderma remain poorly understood. To investigate disease pathogenesis, we applied Visium CytAssist spatial transcriptomics (ST), which preserves tissue architecture while enabling whole-transcriptome profiling, to skin lesions from pediatric patients with LS and SSc. Spatial domains identified from ST data showed strong concordance with pathologist-defined anatomical structures. Integration of paired ST and single-cell RNA sequencing (scRNA-seq) data from the same patients validated the biological consistency of both platforms and enabled estimation of cell-type composition within spatial domains. Moreover, ST analysis accurately delineated pathologist-annotated immune infiltrates, including perivascular inflammatory regions, highlighting the biological relevance of the spatial transcriptomic findings. To our knowledge, this is the first study to apply spatial transcriptomics to skin lesions from patients with juvenile scleroderma. Integration of ST with scRNA-seq and pathological assessment provided a high-resolution view of tissue organization and immune infiltration, offering new insights into the pathogenesis of juvenile scleroderma.
