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Spatially Resolved Single-Cell DNA Sequencing: A General Spatial Genomics Platform with Application to HIV Reservoir Mapping

Award Number: R44AI197850
ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/01/2026
PERIOD OF PERFORMANCE END DATE: 08/31/2027

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Spatially Resolved Single-Cell DNA Sequencing: A General Spatial Genomics Platform with Application to HIV Reservoir Mapping - ABSTRACT Spatial genomics has emerged as a transformative approach over the past five years, with numerous platforms now enabling high-resolution mapping of cellular transcripts and proteins. However, these instruments all share a critical limitation: The inability to sequence genomic DNA in situ. Genomic DNA is inherently challenging to assay because it is embedded in chromatin and bound by nuclear proteins, rendering it less accessible to probes. Moreover, being present as a single copy per cell, its detection requires extremely sensitive methods. This gap is significant given that genomic DNA is fundamental to understanding basic biology and has broad applications in areas such as cancer, infectious diseases, and neurodegeneration, where somatic mutations play a pivotal role. This proposal will develop the first commercially viable spatial genomics platform that integrates hydrogel-based spatial barcoding, advanced droplet microfluidics, and innovative Bayesian reconstruction algorithms to simultaneously capture DNA, RNA, and protein from individual cells while preserving their native spatial context. The system is designed to analyze tissue sections containing from hundreds of thousands to up to one million cells per run at a cost comparable to existing spatial genomic technologies, making it feasible for large-scale tissue mapping. Building on extensive academic research, published protocols, and collaborations with world-class institutions, our approach will be demonstrated through a focused application in HIV reservoir mapping. In Phase 1, we will adapt and integrate these proven methods into a robust commercial prototype and rigorously validate its performance using HIV-positive spike-ins and primary specimens. In Phase 2, we will optimize hardware and software integration for enhanced reproducibility and scalability, expand validation to additional specimen types, and develop a comprehensive target product profile through beta testing with academic and industry partners.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = $299,991 )
2026	2026	VIVID BIOINNOVATIONS, PBC	953 INDIANA ST	SAN FRANCISCO	CA	94107	SAN FRANCISCO	USA	Allergy and Infectious Diseases Research	000	1	8/19/2026	NEW	$299,991
														Subtotal = $299,991

Grand Total All Awards = $299,991

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Spatially Resolved Single-Cell DNA Sequencing: A General Spatial Genomics Platform with Application to HIV Reservoir Mapping

Award Number: R44AI197850

ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 09/01/2026

PERIOD OF PERFORMANCE END DATE: 08/31/2027

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