Automated dissection protocol for tumor enrichment in low tumor content tissues

Charles A. Havnar, Oliver Zill, Jeff Eastham, Jeffrey Hung, Manana Javey, Emmanuel Naouri, Jennifer Giltnane, Justin M. Balko, Andrew Wallace, Nicolas Lounsbury, Daniel Oreper, Sarajane Saturnio, G. Y. Yang, Amy A. Lo*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Tumor enrichment in low tumor content tissues, those below 20% tumor content depending on the method, is required to generate quality data reproducibly with many downstream assays such as next generation sequencing. Automated tissue dissection is a new methodology that automates and improves tumor enrichment in these common, low tumor content tissues by decreasing the user-dependent imprecision of traditional macro-dissection and time, cost, and expertise limitations of laser capture microdissection by using digital image annotation overlay onto unstained slides. Here, digital hematoxylin and eosin (H&E) annotations are used to target small tumor areas using a blade that is 250 µm2 in diameter in unstained formalin fixed paraffin embedded (FFPE) or fresh frozen sections up to 20 µm in thickness for automated tumor enrichment prior to nucleic acid extraction and whole exome sequencing (WES). Automated dissection can harvest annotated regions in low tumor content tissues from single or multiple sections for nucleic acid extraction. It also allows for capture of extensive pre-and post-harvest collection metrics while improving accuracy, reproducibility, and increasing throughput with utilization of fewer slides. The described protocol enables digital annotation with automated dissection on animal and/or human FFPE or fresh frozen tissues with low tumor content and could also be used for any region of interest enrichment to boost adequacy for downstream sequencing applications in clinical or research workflows.

Original languageEnglish (US)
Article numbere62394
JournalJournal of Visualized Experiments
Issue number169
StatePublished - Mar 2021

ASJC Scopus subject areas

  • Neuroscience(all)
  • Chemical Engineering(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)


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