213 Concordance assessment study of Xenium and Visium spatial transcriptomics assays using multiple carcinoma samples

Background

The Xenium In Situ platform from 10X Genomics offers sub-cellular resolution for precise spatial transcriptomics study of cellular mechanisms and interactions, while the Visium CytAssist Spatial Gene Expression v2 is a whole transcriptome assay offering 55um resolution. This study assessed the quality of Xenium and the Post-Xenium Visium assay on the same section and was compared with its serial section using Visium assay additionally. BioChain is conducting precision and concordance studies to validate these assays for clinical research use.

Methods

The previously constructed tissue array for Xenium assay was used in this study. Briefly, FFPE tissues from BioChain's biorepository were screened for at least 30% tumor content and four carcinoma tissues from human breast, colon, lung, and kidney with high DV200 scores were selected. An array was constructed with these tissues to place within the Xenium slide's imageable area. Two serial sections were used in Xenium assay, which were performed according to the10x Genomics' protocol by different operators independently. The pre-designed Human Multi-Tissue and Cancer Panel was used for targeting 377 genes. The post-Xenium tissue sections were designed to perform H&E staining for breast and kidney tissues as well as whole transcriptome Visium assay. Another consecutive breast tissue section was selected to perform Visium assay for comparison. BioChain's pathologist annotated the regions of stroma, carcinoma and immune cells within the tissue images for further computational analysis and image integration by Aspect Analytics.

Results

Xenium reproducibility results show no observed batch effects across the serial Xenium samples. The Post-Xenium H&E staining and Visium assay performed on the same section was successful and data from the two assays is in concordance. The kidney sample failed to show satisfactory results with the Xenium platform. Visium results from this kidney sample were in concordance with the xenium results, showing low fraction of gene expression per spot.

Conclusions

The non-destructive nature of Xenium assay enables further downstream applications such as H&E staining and Visium CytAssist Spatial Gene Expression following Xenium measurements of the tissues. This study showed reliability and validity as a measure of the performance of these assays, and our results imply the future development of spatial transcriptomics assays for the clinical research applications.