10x Genomics and Prognosys Biosciences Allege Illumina Infringed Four Spatial Transcriptomics Patents

On October 21, 10x Genomics, Inc. and Prognosys Biosciences, Inc. filed a complaint for patent infringement against Illumina, Inc. in the United States District Court for the District of Delaware, asserting that Illumina’s spatial technology products infringed on patents covering technology for spatial transcriptomics, which allows researchers to study gene activity within a cell’s tissue.

U.S. Patent Nos. 11,008,607, 11,549,138, 12,234,505, and 12,297,487 are owned by Prognosys Biosciences and have significant applications in cancer research, neuroscience and immunology.

10x, a company that described itself in the filing as a “pioneering innovator of genomics and sequencing technologies,” is the exclusive licensee of the patents.. 10x stated that it has invested approximately $2 billion in research and development to create products that provide “single cell and spatial views of complex biological systems.”

Prognosys’s former CEO and CSO, Dr. Mark S. Chee, a co-founder of Illumina and its former Vice President of Genomics, is a key figure mentioned in the complaint and an inventor on the ‘607, ‘138, ‘505, and ‘487 patents that are part of a patent family titled “Spatially Encoded Biological Assays.”

In February 2025, Illumina announced its own “‘spatial technology program,’ for “whole-transcriptome profiling with cellular resolution and high sensitivity.” Illumina’s subsequent presentations and product descriptions revealed a workflow that infringed on the ‘607, ‘138, ‘505, and ‘487 patents, 10x Genomics and Prognosys Biosciences argued. Specifically, the filing detailed Illumina’s process as including the capture of messenger RNA (mRNA) from tissue, its conversion to complementary DNA (cDNA) tagged with a location barcode, and subsequent sequencing and analysis to create a spatial map of gene expression, with evidence of this workflow presented at the Advances in Genome Biology and Technology (AGBT) General Meeting.

10x’s contributions to genomics were detailed in the complaint, which noted that its “expanding suite of products has fueled a revolution in genomics, winning wide acclaim and commercial success.”

The complaint emphasized the importance of 10x’s Chromium platform, launched in 2016, which enables single-cell genomics by allowing researchers to study gene activity on a cell-by-cell basis. This approach preserves the heterogeneity of cells and their transcriptomes within larger biological samples, a significant advancement over prior techniques that analyzed genetic material in bulk. For example, a cancer tumor can contain varied cell populations, some healthy and some cancerous, with genetically distinct subpopulations, according to the complaint. The Chromium platform, including the Chromium X, launched in July 2021, enabling the expansion of single-cell studies to experiments on the scale of a million cells.

Furthermore, 10x Genomics was identified as a pioneer in spatial transcriptomics, a field that facilitates the study of gene activity in cells within their spatial context, which ultimately allows researchers to map where different cells are found in tissue, providing insights into biological processes and disease.

In 2018, 10x Genomics acquired Spatial Transcriptomics AB, a company that first commercialized a product for capturing the transcriptome of a tissue section. Building on this, 10x Genomics launched its Visium Platform in 2019, which included the Visium Spatial Gene Expression Solution. In 2024, Visium HD Spatial Gene Expression was launched, which represented a “significant advancement in spatial transcriptomics, offering whole transcriptome analysis at single cell-scale resolution.”

Illumina’s alleged infringing activities were detailed, stemming from its February 2025 announcement of a “spatial technology program” and subsequent presentations at the AGBT General Meeting. At this meeting, Illumina employees, including Kareem Ahmad et al., presented a poster describing their work. The complaint specifically referenced Michal Lipinski, a senior research scientist at the Broad Institute, who presented details about the Illumina spatial product and workflow at AGBT.

Lipinski explained that the process includes: “(1) capturing mRNA from a tissue, (2) converting the mRNA to cDNA tagged with a location barcode, (3) releasing the spatially tagged cDNA, and (4) sequencing and analyzing the data, thereby generating a spatial image.” The complaint stated that these steps, as presented, closely align with the methods protected by the ‘607, ‘138, ‘505, and ‘487 patents.

10x Genomics and Prognosys are seeking a judgment that Illumina has directly and indirectly infringed the patents; that the infringement was willful and deliberate; permanent injunctions to stop the infringement, or in the alternative, post-judgment royalty; a declaration of validity for each patent; and attorneys’ fees and damages to compensate for the infringement.

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Author: alexskopje