Nature communications, 2021-06, Vol.12 (1), p.3361-15, Article 3361
- Allahyar, Amin
- Pieterse, Mark
- Swennenhuis, Joost
- Los-de Vries, G Tjitske
- Yilmaz, Mehmet
- Leguit, Roos
- Meijers, Ruud W J
- van der Geize, Robert
- Vermaat, Joost
- Cleven, Arjen
- van Wezel, Tom
- Diepstra, Arjan
- van Kempen, Léon C
- Hijmering, Nathalie J
- Stathi, Phylicia
- Sharma, Milan
- Melquiond, Adrien S J
- de Vree, Paula J P
- Verstegen, Marjon J A M
- Krijger, Peter H L
- Hajo, Karima
- Simonis, Marieke
- Rakszewska, Agata
- van Min, Max
- de Jong, Daphne
- Ylstra, Bauke
- Feitsma, Harma
- Splinter, Erik
- de Laat, Wouter
2021
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- Autor(en) / Beteiligte
- Allahyar, Amin
- Pieterse, Mark
- Swennenhuis, Joost
- Los-de Vries, G Tjitske
- Yilmaz, Mehmet
- Leguit, Roos
- Meijers, Ruud W J
- van der Geize, Robert
- Vermaat, Joost
- Cleven, Arjen
- van Wezel, Tom
- Diepstra, Arjan
- van Kempen, Léon C
- Hijmering, Nathalie J
- Stathi, Phylicia
- Sharma, Milan
- Melquiond, Adrien S J
- de Vree, Paula J P
- Verstegen, Marjon J A M
- Krijger, Peter H L
- Hajo, Karima
- Simonis, Marieke
- Rakszewska, Agata
- van Min, Max
- de Jong, Daphne
- Ylstra, Bauke
- Feitsma, Harma
- Splinter, Erik
- de Laat, Wouter
- Titel
- Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing
- Ist Teil von
- Nature communications, 2021-06, Vol.12 (1), p.3361-15, Article 3361
- Ort / Verlag
- England: Nature Publishing Group
- Erscheinungsjahr
- 2021
- Quelle
- MEDLINE
- Beschreibungen/Notizen
- 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.
- Sprache
- Englisch
- Identifikatoren
- ISSN: 2041-1723eISSN: 2041-1723DOI: 10.1038/s41467-021-23695-8Titel-ID: cdi_doaj_primary_oai_doaj_org_article_15e52e7d12f34aa7b62f485085760e59
- Format
- –
- Schlagworte
- Biopsy, Cancer, Chromosome rearrangements, Chromosome translocations, Computational Biology - methods, Computer applications, Deoxyribonucleic acid, DNA, DNA fragmentation, DNA sequencing, Embedding, Fluorescence, Fluorescence in situ hybridization, Fragmentation, Gene Rearrangement, Genes, bcl-2 - genetics, Genes, myc - genetics, Hand tools, High-Throughput Nucleotide Sequencing - methods, Humans, In Situ Hybridization, Fluorescence - methods, Loci, Lymphoma, Lymphoma, B-Cell - diagnosis, Lymphoma, B-Cell - genetics, Lymphoma, Non-Hodgkin - diagnosis, Lymphoma, Non-Hodgkin - genetics, Morphology, Paraffin, Paraffin Embedding - methods, Paraffins, Proto-Oncogene Proteins c-bcl-6 - genetics, Reproducibility of Results, Retrospective Studies, Sensitivity and Specificity, Solid tumors, Tissue Fixation - methods, Translocation, Genetic, Tumors