Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity
Abstract
Abstract Recent advancements in probe-based, full-transcriptome technologies for FFPE tissues, such as Visium CytAssist, Chromium Flex, and GeoMx DSP, enable analysis of archival samples, facilitating the generation of data from extensive cohorts. However, these methods can be labor-intensive and costly, requiring informed selection based on research objectives. We compare these methods on FFPE tumor samples in Breast, NSCLC and DLBCL showing 1) good-quality, highly reproducible data from all methods; 2) GeoMx data containing cell mixtures despite marker-based preselection; 3) Visium and Chromium outperform GeoMx in discovering tumor heterogeneity and potential drug targets. We recommend the use of Visium and Chromium for high-throughput and discovery projects, while the manually more challenging GeoMx platform with targeted regions remains valuable for specialized questions.
Article Details
Authors (27)
Yixing Dong
Chiara Saglietti
Quentin Bayard
Almudena Espin Perez
Sabrina Carpentier
Daria Buszta
Stephanie Tissot
Rémy Dubois
Atanas Kamburov
Senbai Kang
Carla Haignere
Rita Sarkis
Sylvie Andre
Marina Alexandre Gaveta
Silvia Lopez Lastra
Nathalie Piazzon
Rita Santos
Katharina von Loga
Caroline Hoffmann
George Coukos
Solange Peters
Vassili Soumelis
Eric Yves Durand
Laurence de Leval
Raphael Gottardo
Krisztian Homicsko
Elo Madissoon