Wholistic approach: Transcriptomic analysis and beyond using archival material for molecular diagnosis

Nicolas Macagno (1, 2, 3) , Daniel Pissaloux (4, 3) , Arnaud de La Fouchardiere (4, 3) , Marie Karanian (4, 3) , Sylvie Lantuejoul (4, 3) , Francoise Galateau Salle (3) , Alexandra Meurgey (3) , Catherine Chassagne-Clement (3) , Isabelle Treilleux (3) , Caroline Renard (3) , Juliette Roussel (3) , Julie Gervasoni (3) , Vincent Cockenpot (3) , Carole Crozes (3) , Aline Baltres (3) , Aurelie Houlier (3) , Sandrine Paindavoine (3) , Laurent Alberti (4) , Adeline Duc (4) , Francois Le Loarer (5) , Armelle Dufresne (4, 3) , Mehdi Brahmi (4, 3) , Nadege Corradini (4, 3, 6) , Jean‐yves Blay (3, 7) , Franck TIRODE (4, 3)

1 MMG - Marseille medical genetics - Centre de génétique médicale de Marseille
2 MarMaRa - Institut Marseille Maladies Rares
3 Centre Léon Bérard [Lyon]
4 UNICANCER/CRCL - Centre de Recherche en Cancérologie de Lyon
5 Institut Bergonié [Bordeaux]
6 IHOPe - Institut d'hématologie et d'oncologie pédiatrique [CHU - HCL]
7 UNICANCER [Paris]

Many neoplasms remain unclassified after histopathological examination, which requires further molecular analysis. To this regard, mesenchymal neoplasms are particularly challenging due to the combination of their rarity and the large number of subtypes, and many entities still lack robust diagnostic hallmarks. RNA transcriptomic profiles have proven to be a reliable basis for the classification of previously unclassified tumors and notably for mesenchymal neoplasms. Using exome-based RNA capture sequencing on more than 5000 samples of archival material (formalin-fixed, paraffin-embedded), the combination of expression profiles analyzes (including several clustering methods), fusion genes, and small nucleotide variations has been developed at the Centre Léon Bérard (CLB) in Lyon for the molecular diagnosis of challenging neoplasms and the discovery of new entities. The molecular basis of the technique, the protocol, and the bioinformatics algorithms used are described herein, as well as its advantages and limitations.

Keywords: FFPE; RNAseq; clustering; fusion transcript; sarcoma; variant analysis

Domains: Life Sciences [q-bio]; Genetics

Nicolas Macagno, Daniel Pissaloux, Arnaud de La Fouchardiere, Marie Karanian, Sylvie Lantuejoul, et al.. Wholistic approach: Transcriptomic analysis and beyond using archival material for molecular diagnosis. GENES CHROMOSOMES & CANCER, 2022, 61 (6, SI), pp.382-393. ⟨10.1002/gcc.23026⟩. ⟨hal-03780373⟩