True spatial multi-omic sequencing is an emerging field with tremendous potential to advance life sciences research, drug development, and clinical diagnostics.

True multi-omic sequencing utilizes the massive multiplexity of next generation sequencing (NGS) and high resolution imaging to simultaneously detect tens to thousands of RNA, DNA, proteins, and therapeutic molecules in situ. However, the adoption of this technology is currently burdened by technical challenges including the need for specialized imaging hardware, laborious and finicky protocols, and unsupported analysis software. To enable the adoption of these exciting methods, we developed a vertically integrated turn-key system, extending from sample preparation through automated sequencing and software analytics.

The underlying technology of our true spatial sequencing platform is powered by proprietary FISSEQ (fluorescent in situ sequencing) technology which combines the massive multiplexity of next generation sequencing (NGS) and high resolution imaging. FISSEQ technology simplifies the preparation of in situ sequencing libraries in cell and tissue samples, providing standardized workflows that require minimal optimization and overcome nuisances such as sample mounting and autofluorescence.

  • RNA FISSEQ enables flexible targeted sequencing for measuring single-cell gene
    expression, splice variation, and expressed sequence variants.
  • DNA FISSEQ detects single-cell chromosomal conformation and structural variation,
    such as CNV.
  • Protein FISSEQ provides rich morphological context around RNA & DNA localizations.

Together these assays enable spatial multi-omic measurements within a single sample.

Spatial Multi-Omics Workflow










Bioinformatics Tools for True Spatial Sequencing

“Discovering an HIV cure requires high-resolution in situ sequencing of cellular immune neighborhoods and inflammatory landscapes to elucidate immune pathways driving viral persistence.”

Jacob D. Estes, PhD, Oregon Health State University

The ability to generate data with RNA, DNA, protein, and morphology within a single 3D volume is unprecedented, and it requires new and novel tools to visualize and analyze. We developed our cloudware to view the data as a volume, with the ability to turn off and on molecules and morphology features, pan and zoom, and select-regions of interest.

In this sample from Dr. Jacob Estes, explore virus transcripts and host response in the lymph tissue, choose genes of interest, and compare frequencies.


Featured Applications

Our technology has been developed to advance research, drug development and clinical diagnosis. As part of our initial product offering, we have validated applications in Oncology, Neuroscience and Infectious Disease. We will also offer a custom application.

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Spatial multi-omic profiling to understand a patient’s tumor and therapeutic response is essential to improve the success of immunotherapies. Our oncology application combines molecular and histological diagnostics into a single assay.

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Infectious Disease

Our initial infectious disease application is designed to advance our understanding of HIV biology. This approach has the potential to provide insights into many aspects of HIV’s lifecycle and ultimately inform better treatment options towards eradicating this disease.

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Creation of a comprehensive brain cell atlas will have enormous benefit to both basic neuroscience research and biomedical applications such understanding and treating traumatic brain injury and neurodegenerative diseases.

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