We use cookies to understand how you use our site and to improve your experience. This includes personalizing content and advertising. To learn more, click here. By continuing to use our site, you accept our use of cookies. Cookie Policy.

Features Partner Sites Information LinkXpress
Sign In
Advertise with Us
Technopath Clinical Diagnostics

Download Mobile App


ATTENTION: Due to the COVID-19 PANDEMIC, many events are being rescheduled for a later date, converted into virtual venues, or altogether cancelled. Please check with the event organizer or website prior to planning for any forthcoming event.
20 Oct 2021 - 22 Oct 2021
21 Oct 2021 - 24 Oct 2021
Virtual Venue

Targeted Locus Amplification Validated for Lymphoma

By LabMedica International staff writers
Posted on 15 Jul 2021
Print article
Image: Bone marrow aspirate from a patient with diffuse large B-cell lymphoma (Photo courtesy of Dr. Peter G. Maslak, MD)
Image: Bone marrow aspirate from a patient with diffuse large B-cell lymphoma (Photo courtesy of Dr. Peter G. Maslak, MD)
Structural variation (SV) in the genome is a recurring hallmark of cancer. Translocations (genomic rearrangements between chromosomes) in particular are found as recurrent drivers in many types of hematolymphoid malignancies.

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.

Medical Scientists at the University Medical Center Utrecht (Utrecht, the Netherlands) and colleagues carried out a retrospective study using a set of 129 archival B-cell Non-Hodgkin lymphoma tissue samples, which were selected by the respective sites. The patients had been mostly diagnosed as Diffuse Large B-Cell Lymphoma (DLBCL), but also Burkitt, follicular and marginal zone lymphomas and some other diagnoses were included. Non-lymphoma control samples were also analyzed, mostly reactive lymph node samples and tonsillectomy specimens. FFPE tissue samples were obtained using standard diagnostic procedures.

The team developed FFPE-targeted locus capture (FFPE-TLC) method 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. This method 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. The team included core needle biopsy samples in this study, which showed that even very small samples yielded good quality FFPE-TLC results.

The authors concluded that FFPE-TLC combined with PLIER for objective rearrangement calling offers clear advantages over regular NGS-capture approaches and over FISH for the molecular diagnosis of lymphoma FFPE specimens. The study was published on June 7, 2021, in the journal Nature Communications.

Related Links:
University Medical Center Utrecht

Gold Supplier
SARS-CoV-2 Multiplex Real-Time RT-PCR Assay
GSD NovaPrime Plus SARS-CoV-2
Real Time PCR Platform
Laboratory Automation System
COVID-19 Severity Algorithm
Atellica COVID-19 Severity Algorithm

Print article


Molecular Diagnostics

view channel
Image: The QuikRead go iFOBT is an immunochemical fecal immunochemical test for detection and quantification of human hemoglobin in feces in case of suspected bleeding from the lower gastrointestinal tract (Photo courtesy of Aidian)

Fecal Immunochemical Tubes Sourced to Analyze Gut Microbiome for CRC

Colorectal cancer (CRC) is a challenging public health problem which successful treatment depends on the stage at diagnosis. Recently, CRC-specific microbiome signatures have been proposed as a marker... Read more


view channel
Image: GastroPanel Quick Test (Photo courtesy of Biohit Healthcare)

Biohit’s Innovative GastroPanel Quick Test Receives CE Mark

Biohit Healthcare’s (Helsinki, Finland) GastroPanel Quick Test, the latest innovation in its unique GastroPanel product family, is now CE marked. The GastroPanel Quick Test is intended for diagnosing... Read more
Copyright © 2000-2021 Globetech Media. All rights reserved.