Search for a command to run...
Background The 10x Genomics Visium and Xenium platform and assays are now providing sub cellular resolution and mapping transcripts to the tissue morphology to study complex biology from whole transcriptomics to precisely targeted gene panels.These assays are of great significance to clinical research in precision medicine and biomarker discovery.However, third party validations on reproducibility, orthogonal concordance, specificity and sensitivity raise questions that are critical to their use.At BioChain Institute Inc. (BioChain), we are running a series of tests on Xenium v1 as well as Visium Cytassist v2 chemistry, using multiple human carcinoma FFPE tissues to address the specificity and sensitivity questions of these platforms.Methods FFPE tissues from BioChain's repository were screened for quality assessment by our pathologist and molecular scientists for tumor content above 30% as well as the RNA quality.Human carcinoma tissues from Breast, Colon, and Lung with high DV200 scores were selected.An array was constructed with these tissues to fit the Xenium slide's imageable area.Two serial sections were used for the Xenium v1 run per 10x Genomics' protocol.The Off-the shelf Human Multi-Tissue and Cancer Panel was used for targeting 377 genes.After the completion of the Xenium assay, these slides were used for H&E staining and imaging followed by Visium v2 assay on the same section.The H&E images were annotated by the pathologist and integrated with Xenium images using Xenium Explorer.The data was sub-sampled for the different regions per pathologist's annotations of stroma, tumor and immune cell regions.Data from these regions were compared between the serial sections processed using Xenium and Visium platforms to evaluate specificity of selected markers and per gene sensitivity.Sensitivity of Xenium data versus the Visium data was also compared for these specific regions. ResultsWe have previously demonstrated reproducibility of Xenium data between serial sections prepared by different operators as well as concordance between the two assays performed on the same section.In this study, we focus on assessing specificity of gene expression and per gene detection sensitivity through the integration of pathologist annotations of the morphology and spatial gene expression data across multiple types of carcinomas.Conclusions Our findings show the sensitivity and specificity of Xenium and Visium assays to delve further into the heterogeneity of tumor microenvironment and patient stratification for precision medicine and biomarker discovery studies.