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

Macagno N., Pissaloux D., de la Fouchardière A., Karanian M., Lantuejoul S., Galateau Salle F., ...Daha Fazla

Genes Chromosomes and Cancer, cilt.61, sa.6, ss.382-393, 2022 (SCI-Expanded) identifier identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 61 Sayı: 6
  • Basım Tarihi: 2022
  • Doi Numarası: 10.1002/gcc.23026
  • Dergi Adı: Genes Chromosomes and Cancer
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, Chemical Abstracts Core, EMBASE, MEDLINE
  • Sayfa Sayıları: ss.382-393
  • Anahtar Kelimeler: clustering, FFPE, fusion transcript, RNAseq, sarcoma, variant analysis, GENE-EXPRESSION, FUSION GENES, TISSUE, CANCER
  • Marmara Üniversitesi Adresli: Hayır

Özet

© 2022 Wiley Periodicals LLC.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.