Next generation in situ sequencing

Important results from the project

In-situ sequencing (ISS) is an advanced technology for analysis of biological tissue samples that can assist researchers in understanding different human diseases. In this project we planed to develop the Next Generations ISS (NGISS) towards an integrated package with hardware/instruments, software and reagents that would simplify ISS in laboratories, core facilities, and Pharma companies. As an effect of the global interest in ISS, Cartana was acquired by 10x Genomics Inc in August 2020 which led to cancellation of the project.

Expected long term effects

The project resulted in improved versions of the assays comprised of tissue preparation and sequencing. The new method allowed more tissue types and higher sensitivity, and also FFPE samples, which the previous method was less successful with. The sequencing step was simplified by eliminating the enzymatic steps, a benefit for the subsequent automation of this procedure. The assay worked well in the new hard- and software version developed by Lunaphore.

Approach and implementation

The first step in the assay was changed to target RNA molecules inside the tissue (compared to cDNA previously). It showed, after considerable optimizations, improved sensitivity and that several new tissue types including FFPE could be analyzed. The sequencing step was redesigned to be hybridization based (compared to ligation based as previously), a format much more suited for automation and production of reagents. The new methods were evaluated on different tissue types with several gene panels to demonstrate both sensitivity and specificity.