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Cell type inference in cell-free nucleic acid liquid biopsy.
Sevahn K Vorperian1, Lucas M Dennis2, Anna Hupalowska3
1Genentech Research and Early Development, Genentech Inc., South San Francisco, CA, USA. vorperian.sevahn@gene.com.
Nature Biotechnology
|November 26, 2025
Summary
Cell-free nucleic acid (cfNA) liquid biopsies offer noninvasive disease diagnosis. Integrating single-cell data with cfNA analysis allows for cell type inference, enhancing diagnostic resolution for various conditions.
Area of Science:
- Biomolecular analysis
- Genomics
- Translational medicine
Background:
- Cell-free nucleic acid (cfNA) liquid biopsy is a noninvasive diagnostic tool.
- cfNA lacks the cellular resolution of traditional needle biopsies.
- Cell type-specific changes are crucial in disease pathology and cfNA profiles.
Purpose of the Study:
- To review the strengths of cell-free DNA and cell-free RNA for diagnostics.
- To describe computational methods for inferring cell type contributions in cfNA.
- To highlight the role of single-cell transcriptomic data in cfNA analysis.
Main Methods:
- Review of current literature on cfNA detection and single-cell transcriptomics.
- Description of computational frameworks for cell type inference from cfNA data.
- Analysis of diagnostic applications and future directions.
Main Results:
- cfNA liquid biopsy provides a versatile, noninvasive diagnostic alternative.
- Single-cell transcriptomic data enables cell type inference from cfNA.
- Computational advances are key to unlocking cellular resolution in cfNA.
Conclusions:
- Cell type inference from cfNA liquid biopsies enhances diagnostic capabilities.
- The integration of single-cell data with cfNA analysis presents a significant opportunity.
- Further research is needed to address outstanding questions in the field.
