Amin Allahyar 1 , Mark Pieterse 1 , Joost Swennenhuis 2 , G. Tjitske Los-de Vries 3 , Mehmet Yilmaz 2 , Roos Leguit 4 , Ruud W. J. Meijers 4 , Robert van der Geize 5 , Joost Vermaat 6 , Arjen Cleven 7 , Tom van Wezel 7 , Arjan Diepstra 8 , Léon C. van Kempen 8 , Nathalie J. Hijmering 3 , Phylicia Stathi 3 , Milan Sharma 1 , Adrien S. J. Melquiond 1 , Paula J. P. de Vree 1 , Marjon J. A. M. Verstegen 1 , Peter H. L. Krijger 1 , Karima Hajo 2 , Marieke Simonis 2 , Agata Rakszewska 2 , Max van Min 2 , Daphne de Jong 3 , Bauke Ylstra 3 , Harma Feitsma 2 , Erik Splinter , 2 , Wouter de Laat , 1
7 June 2021
In routine diagnostic pathology, cancer biopsies are preserved by formalin-fixed, paraffin-embedding (FFPE) procedures for examination of (intra-) cellular morphology. Such procedures inadvertently induce DNA fragmentation, which compromises sequencing-based analyses of chromosomal rearrangements. Yet, rearrangements drive many types of hematolymphoid malignancies and solid tumors, and their manifestation is instructive for diagnosis, prognosis, and treatment. Here, we present FFPE-targeted locus capture (FFPE-TLC) for targeted sequencing of proximity-ligation products formed in FFPE tissue blocks, and PLIER, a computational framework that allows automated identification and characterization of rearrangements involving selected, clinically relevant, loci. FFPE-TLC, blindly applied to 149 lymphoma and control FFPE samples, identifies the known and previously uncharacterized rearrangement partners. It outperforms fluorescence in situ hybridization (FISH) in sensitivity and specificity, and shows clear advantages over standard capture-NGS methods, finding rearrangements involving repetitive sequences which they typically miss. FFPE-TLC is therefore a powerful clinical diagnostics tool for accurate targeted rearrangement detection in FFPE specimens.
Preservation of cancer biopsies by FFPE introduces DNA fragmentation, hindering analysis of rearrangements. Here the authors introduce FFPE Targeted Locus Capture for identification of translocations in preserved samples.