Collaboration Explores Clinical Use of Single-Cell and Spatial Technologies

Clinical teams need multimodal evidence that links tumor biology to outcomes and supports molecular tumor board decisions. A new research collaboration now aims to generate such evidence by applying single-cell and spatial platforms at scale to discover biomarkers predictive of treatment response.

10x Genomics and Lausanne University Hospital (CHUV) announced a multi-year collaboration to advance research into diagnostic applications of single-cell and spatial technologies for cancer care. The study will use 10x’s Flex Apex and Xenium platforms, with a goal of expanding to the Atera platform, to examine tumor samples from patients with advanced cancer under clinical molecular tumor board review. The program is designed to identify clinically relevant biomarkers that may predict treatment response and prognosis while supporting diagnostic development.

The effort is expected to include hundreds of patients across multiple solid tumor types, including non-small cell lung cancer (NSCLC), breast cancer, bladder cancer, and melanoma. Researchers plan to integrate single-cell and spatial readouts with clinical outcomes to characterize mechanisms of response and resistance across therapeutic classes, including antibody-drug conjugates (ADCs), bispecific antibodies, and immune checkpoint inhibitors (ICIs). The collaboration also intends to evaluate how single-cell and spatial technologies could be deployed clinically alongside current standard-of-care assays.

Expected outputs include a comprehensive, multimodal resource that integrates single-cell and spatial data to support discovery of clinically actionable biomarkers of treatment response and resistance. The partners also plan to assess how emergent biomarkers could be incorporated into future clinical reporting frameworks to inform personalized treatment planning and support molecular tumor board decisions. The work aligns with broader initiatives to generate evidence for potential diagnostic applications of single-cell and spatial approaches.

“This collaboration brings together complementary expertise in spatial biology, pathology, computational AI and clinical precision oncology to address one of the biggest challenges in cancer care: predicting which patients will benefit from treatment. Together, we aim to discover clinically actionable biomarkers that improve patient selection and bring more precise treatment decisions closer to routine clinical care,” said Raphael Gottardo, Professor and Director of the Biomedical Data Science Center, CHUV.

“The promise of precision oncology depends on understanding the biology that helps determine which therapies are most likely to benefit a given patient. We believe single cell and spatial technologies provide a fundamentally richer view of the biology within tumors and their microenvironment, creating opportunities to discover biomarkers that can help guide treatment decisions and enable future diagnostic approaches in cancer care,” said Serge Saxonov, Co-founder and CEO of 10x Genomics.

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