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Systematic review and feasibility study on pre-analytical factors and genomic analyses on archival formalin-fixed paraffin-embedded breast cancer tissue.
Salgkamis, Dimitrios; Sifakis, Emmanouil G; Agartz, Susanne; Wirta, Valtteri; Hartman, Johan; Bergh, Jonas; Foukakis, Theodoros; Matikas, Alexios; Zerdes, Ioannis.
Afiliación
  • Salgkamis D; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden. dimitrios.salgkamis@ki.se.
  • Sifakis EG; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
  • Agartz S; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
  • Wirta V; Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Stockholm, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
  • Hartman J; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
  • Bergh J; Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden.
  • Foukakis T; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
  • Matikas A; Breast Center, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden.
  • Zerdes I; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
Sci Rep ; 14(1): 18275, 2024 08 06.
Article en En | MEDLINE | ID: mdl-39107471
ABSTRACT
Formalin-fixed paraffin-embedded (FFPE) tissue represents a valuable source for translational cancer research. However, the widespread application of various downstream methods remains challenging. Here, we aimed to assess the feasibility of a genomic and gene expression analysis workflow using FFPE breast cancer (BC) tissue. We conducted a systematic literature review for the assessment of concordance between FFPE and fresh-frozen matched tissue samples derived from patients with BC for DNA and RNA downstream applications. The analytical performance of three different nucleic acid extraction kits on FFPE BC clinical samples was compared. We also applied a newly developed targeted DNA Next-Generation Sequencing (NGS) 370-gene panel and the nCounter BC360® platform on simultaneously extracted DNA and RNA, respectively, using FFPE tissue from a phase II clinical trial. Of the 3701 initial search results, 40 articles were included in the systematic review. High degree of concordance was observed in various downstream application platforms. Moreover, the performance of simultaneous DNA/RNA extraction kit was demonstrated with targeted DNA NGS and gene expression profiling. Exclusion of variants below 5% variant allele frequency was essential to overcome FFPE-induced artefacts. Targeted genomic analyses were feasible in simultaneously extracted DNA/RNA from FFPE material, providing insights for their implementation in clinical trials/cohorts.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Neoplasias de la Mama / Estudios de Factibilidad / Fijación del Tejido / Adhesión en Parafina / Genómica / Formaldehído Límite: Female / Humans Idioma: En Revista: Sci Rep Año: 2024 Tipo del documento: Article País de afiliación: Suecia Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Neoplasias de la Mama / Estudios de Factibilidad / Fijación del Tejido / Adhesión en Parafina / Genómica / Formaldehído Límite: Female / Humans Idioma: En Revista: Sci Rep Año: 2024 Tipo del documento: Article País de afiliación: Suecia Pais de publicación: Reino Unido