Single nucleus DNA sequencing of flow sorted archived frozen and formalin fixed paraffin embedded solid tumors
Our flow sorting based protocol provides intact nuclei suitable for snDNA-seq from archival FF and FFPE tissues. Furthermore, we have developed QC steps that optimize the preparation and selection of samples for deep single cell clonal profiling. Our data processing pipeline captures rare subclones in tumors with highly variable genomes based on variants in genes of interest.
Authors
- Jocelyn Chapman (ORCID: https://orcid.org/0000-0002-4260-3016)
- Yumei Zhou (ORCID: https://orcid.org/0009-0001-6382-6278)
- Michael T. Barrett (ORCID: https://orcid.org/0000-0002-5646-1530)
- Xianfeng Chen (ORCID: https://orcid.org/0000-0002-7531-5862)
Institutions
- University of California, San Francisco (US)
- WinnMed (US)
- Mayo Clinic in Arizona (US)
Publication Details
- Journal
- BMC Genomics
- Published
- 2024-10-08
- DOI
- https://doi.org/10.1186/s12864-024-10850-w
- Citations
- 1
- Primary Topic
- Cancer Genomics and Diagnostics
- Type
- article
- Field-Weighted Citation Impact
- 0.29
Funders
- Emerson Collective
- Center for Individualized Medicine, Mayo Clinic
- National Cancer Institute