ArticleNature communications2021
Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 45 citations in OpenAlex.
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- Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies.Cell genomics · 2026Article
- Circulating tumor DNA from blood and cerebrospinal fluid in DLBCL: simultaneous evaluation of mutations, IG rearrangement, and IG clonality.British journal of cancer · 2025Article
- A 3D genome compendium of breast cancer progression.iScience · 2025Article
- Recurrent ETV3::NCOA2 fusions and MAPK pathway mutations in indeterminate dendritic cell histiocytosis.Blood advances · 2025Article
- Integrating genetic subtypes with PET scan monitoring to predict outcome in diffuse large B-cell lymphoma.Nature communications · 2025Article
- Detection of leukemia gene fusions on DNA-level through targeted Next-Generation Sequencing.PloS one · 2025Article
- Antigen-independent, autonomous B cell receptor signaling drives activated B cell DLBCL.The Journal of experimental medicine · 2024Article
- Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients.Cancer cell · 2024Article
- Non-IG::MYC in diffuse large B-cell lymphoma confers variable genomic configurations and MYC transactivation potential.Leukemia · 2024Article
- Comparison of NTRK fusion detection methods in microsatellite-instability-high metastatic colorectal cancer.Virchows Archiv : an international journal of pathology · 2023Article
- Genomic Stratification of Hematological Malignancies.HemaSphere · 2023Article
- Clinicogenomic associations in childhood Langerhans cell histiocytosis: an international cohort study.Blood advances · 2023Article
- Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution.Nature communications · 2023Article
- Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors.Frontiers in oncology · 2023Article
- Article
- Lymphoproliferative disorder involving body fluid: diagnostic approaches and roles of ancillary studies.Journal of pathology and translational medicine · 2022Review
- The path towards consensus genome classification of diffuse large B-cell lymphoma for use in clinical practice.Frontiers in oncology · 2022Review
- Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing.Nature communications · 2021Article
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Authors and funding
29 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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