دورية أكاديمية
أعرض في EDS

Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing.

التفاصيل البيبلوغرافية
العنوان: Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing.
المؤلفون: Allahyar A; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Pieterse M; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Swennenhuis J; Cergentis BV, Utrecht, the Netherlands., Los-de Vries GT; Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands., Yilmaz M; Cergentis BV, Utrecht, the Netherlands., Leguit R; University Medical Centre Utrecht, Department of Pathology, Utrecht, the Netherlands., Meijers RWJ; University Medical Centre Utrecht, Department of Pathology, Utrecht, the Netherlands., van der Geize R; Laboratorium Pathologie Oost-Nederland, Hengelo, the Netherlands., Vermaat J; Leiden University Medical Centre, Department of Hematology, Leiden, the Netherlands., Cleven A; Leiden University Medical Center, Department of Pathology, Leiden, the Netherlands., van Wezel T; Leiden University Medical Center, Department of Pathology, Leiden, the Netherlands., Diepstra A; University of Groningen, University Medical Centre Groningen, Department of Pathology & Medical Biology, Groningen, the Netherlands., van Kempen LC; University of Groningen, University Medical Centre Groningen, Department of Pathology & Medical Biology, Groningen, the Netherlands., Hijmering NJ; Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands., Stathi P; Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands., Sharma M; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Melquiond ASJ; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., de Vree PJP; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Verstegen MJAM; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Krijger PHL; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Hajo K; Cergentis BV, Utrecht, the Netherlands., Simonis M; Cergentis BV, Utrecht, the Netherlands., Rakszewska A; Cergentis BV, Utrecht, the Netherlands., van Min M; Cergentis BV, Utrecht, the Netherlands., de Jong D; Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands., Ylstra B; Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands., Feitsma H; Cergentis BV, Utrecht, the Netherlands., Splinter E; Cergentis BV, Utrecht, the Netherlands. erik.splinter@cergentis.com., de Laat W; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands. w.laat@hubrecht.eu.
المصدر: Nature communications [Nat Commun] 2021 Jun 07; Vol. 12 (1), pp. 3361. Date of Electronic Publication: 2021 Jun 07.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Pub. Group
مواضيع طبية MeSH: Translocation, Genetic*, High-Throughput Nucleotide Sequencing/*methods , Lymphoma, B-Cell/*genetics , Lymphoma, Non-Hodgkin/*genetics , Paraffin Embedding/*methods , Tissue Fixation/*methods, Computational Biology/methods ; Gene Rearrangement ; Genes, bcl-2/genetics ; Genes, myc/genetics ; Humans ; In Situ Hybridization, Fluorescence/methods ; Lymphoma, B-Cell/diagnosis ; Lymphoma, Non-Hodgkin/diagnosis ; Proto-Oncogene Proteins c-bcl-6/genetics ; Reproducibility of Results ; Retrospective Studies ; Sensitivity and Specificity
مستخلص: 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.
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المشرفين على المادة: 0 (BCL6 protein, human)
0 (Proto-Oncogene Proteins c-bcl-6)
تواريخ الأحداث: Date Created: 20210608 Date Completed: 20210628 Latest Revision: 20240402
رمز التحديث: 20240402
مُعرف محوري في PubMed: PMC8184748
DOI: 10.1038/s41467-021-23695-8
PMID: 34099699
قاعدة البيانات: MEDLINE
الوصف
تدمد:2041-1723
DOI:10.1038/s41467-021-23695-8