{
  "abstract": "Background Spatial transcriptomics (ST) provides unparalleled resolution to interrogate tumor-immune interactions directly within tissue contexts. However, clinical adoption of ST relies heavily on demonstrable biological insight and robust technical reproducibility. Here, we present a comparative analysis of two breast cancer tissues processed using the 10x Genomics Xenium in Situ platform. This comparison investigates consensus cell annotation, sensitivity and the standardized reproducibility of spatial profiling enabled by BioChain’s validated workflow.Methods Two human formalin-fixed paraffin-embedded (FFPE) breast ductal carcinoma tissue samples were analyzed to profile transcriptional differences between immune and tumor regions. Cell annotations were independently generated using three bioinformatics tools: TACCO, SingleR, and RCTD.ScTriangulate was used to reach a consensus cell type labeling (TACCO, SingleR, RCTD), and marker genes identified by each method were assessed for biological relevance. The serial breast tumor slides run across multiple batches, with segmentation, cell typing, clustering and quality scores were used to assess reproducibility.Results Immune and tumor regions revealed distinct gene expression profiles, including enrichment of checkpoint signaling in immune zones and Epithelial- Mesenchymal Transition (EMT) markers in tumor areas. Consensus cell labels demonstrated strong concordance, and Gene Ontology (GO) analysis supported the strong biological significance of the marker genes.Cell type distributions and UMAP clustering across multiple sections of the same tissue showed high consistency despite being processed independently by two technicians at different time points. The consistency in cell type labeling across these runs further validated BioChain’s ability to generate reproducible high-quality data.Conclusions Our comparative analysis of discovery- and validation-focused breast cancer spatial datasets demonstrates both the biological insight and technical reproducibility provided by BioChain’s spatial transcriptomics platform. These findings establish BioChain as a premier CRO partner for oncology programs seeking scalable, high-quality spatial data to accelerate biomarker discovery and immunotherapy development.",
  "authors": [
    {
      "affiliations": [
        "BiChain Institute Inc"
      ],
      "name": "Jinghao Tian"
    },
    {
      "affiliations": [
        "BiChain Institute Inc",
        ", Newark, CA, USA"
      ],
      "name": "Elim Cheung"
    },
    {
      "affiliations": [
        "BiChain Institute Inc",
        ", Newark, CA, USA"
      ],
      "name": "Tommy Tran"
    },
    {
      "affiliations": [
        "BiChain Institute Inc",
        ", Newark, CA, USA"
      ],
      "name": "Vidyodhaya Sundaram"
    },
    {
      "affiliations": [
        "BiChain Institute Inc",
        ", Newark, CA, USA"
      ],
      "name": "Rikita Gakhar"
    }
  ],
  "title": "179 Spatial transcriptomic reproducibility and biological resolution in breast cancer FFPE tissues using multiple bioinformatics tools",
  "uid": "8e767f8e-db80-5713-987f-573c68cbe68b"
}