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Diagnostic whole transcriptome sequencing in a series of 1233 FFPE solid tumor samples

Ball, Markus ; Beck, Susanne ; Wlochowitz, Darius ; Fuchs, Tina ; Lorenz, Katja ; Zgorzelski, Christiane ; Pallares Robles, Alejandro ; Allgäuer, Michael ; Volckmar, Anna Lena and Goldschmid, Hannah , et al. (2026) In British Journal of Cancer
Abstract

Background: Whole Transcriptome Sequencing (WTS) is a comprehensive alternative to targeted panels for detecting gene fusions and splice variants. To integrate WTS into clinical diagnostics, we compared its performance against established fusion assays (Archer FusionPlex and TSO500 RNA). Methods: WTS was evaluated in an initial cohort of 64 FFPE tumor samples, and quality control (QC) thresholds were defined based on missed fusions correlating with low tumor cell content (TCC < 40%). Key QC metrics included TCC ≥ 40%, RNA input ≥50 ng, ≥50 million reads, and median insert size >100 bp. Results: WTS identified 92% of known fusions in the initial cohort. Validation in 357 samples showed 100% concordance with panel-based results when... (More)

Background: Whole Transcriptome Sequencing (WTS) is a comprehensive alternative to targeted panels for detecting gene fusions and splice variants. To integrate WTS into clinical diagnostics, we compared its performance against established fusion assays (Archer FusionPlex and TSO500 RNA). Methods: WTS was evaluated in an initial cohort of 64 FFPE tumor samples, and quality control (QC) thresholds were defined based on missed fusions correlating with low tumor cell content (TCC < 40%). Key QC metrics included TCC ≥ 40%, RNA input ≥50 ng, ≥50 million reads, and median insert size >100 bp. Results: WTS identified 92% of known fusions in the initial cohort. Validation in 357 samples showed 100% concordance with panel-based results when QC thresholds were met. Subsequent clinical deployment across 812 diverse tumor cases detected 121 fusions, though 423 (34%) required fallback to targeted assays due to low TCC. WTS provided added value by detecting novel fusions, pathogens, and enabling oncogenic pathway analysis. Conclusion: WTS is a reliable and informative method for fusion and splice variant detection in clinical diagnostics, provided rigorous pre-analytical and sequencing QC metrics are strictly applied.

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publishing date
type
Contribution to journal
publication status
in press
subject
in
British Journal of Cancer
publisher
Nature Publishing Group
external identifiers
  • scopus:105027596355
  • pmid:41530577
ISSN
0007-0920
DOI
10.1038/s41416-025-03307-8
language
English
LU publication?
yes
id
82bbdcc5-0e73-41ae-aa8f-329a4b3fdf18
date added to LUP
2026-03-16 10:39:15
date last changed
2026-05-26 23:17:04
@article{82bbdcc5-0e73-41ae-aa8f-329a4b3fdf18,
  abstract     = {{<p>Background: Whole Transcriptome Sequencing (WTS) is a comprehensive alternative to targeted panels for detecting gene fusions and splice variants. To integrate WTS into clinical diagnostics, we compared its performance against established fusion assays (Archer FusionPlex and TSO500 RNA). Methods: WTS was evaluated in an initial cohort of 64 FFPE tumor samples, and quality control (QC) thresholds were defined based on missed fusions correlating with low tumor cell content (TCC &lt; 40%). Key QC metrics included TCC ≥ 40%, RNA input ≥50 ng, ≥50 million reads, and median insert size &gt;100 bp. Results: WTS identified 92% of known fusions in the initial cohort. Validation in 357 samples showed 100% concordance with panel-based results when QC thresholds were met. Subsequent clinical deployment across 812 diverse tumor cases detected 121 fusions, though 423 (34%) required fallback to targeted assays due to low TCC. WTS provided added value by detecting novel fusions, pathogens, and enabling oncogenic pathway analysis. Conclusion: WTS is a reliable and informative method for fusion and splice variant detection in clinical diagnostics, provided rigorous pre-analytical and sequencing QC metrics are strictly applied.</p>}},
  author       = {{Ball, Markus and Beck, Susanne and Wlochowitz, Darius and Fuchs, Tina and Lorenz, Katja and Zgorzelski, Christiane and Pallares Robles, Alejandro and Allgäuer, Michael and Volckmar, Anna Lena and Goldschmid, Hannah and Ourailidis, Iordanis and Brandt, Regine and Christopoulos, Petros and Thomas, Michael and Seker-Cin, Huriye and Fink, Annette and Schnecko, Fabian and Neuman, Olaf and Menzel, Michael and Kirchner, Martina and Fioretos, Thoas and Schirmacher, Peter and Peters, Solange and Budczies, Jan and Stenzinger, Albrecht and Kazdal, Daniel}},
  issn         = {{0007-0920}},
  language     = {{eng}},
  publisher    = {{Nature Publishing Group}},
  series       = {{British Journal of Cancer}},
  title        = {{Diagnostic whole transcriptome sequencing in a series of 1233 FFPE solid tumor samples}},
  url          = {{http://dx.doi.org/10.1038/s41416-025-03307-8}},
  doi          = {{10.1038/s41416-025-03307-8}},
  year         = {{2026}},
}