Comparison Between Integrated Genomic DNA/RNA Profiling and Fluorescence In Situ Hybridization in the Detection of MYC, BCL-2, and BCL-6 Gene Rearrangements in Large B-Cell Lymphomas

Cassidy, Daniel P.; Chapman, Jennifer R.; López, Rafael; White, Kyle; Fan, Yao Shan; Casas, Carmen; Severson, Eric Allan; Vega, Francisco

doi:10.1093/ajcp/aqz172

Cited by 6 publications

(3 citation statements)

References 16 publications

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“…MYC break-apart FISH was performed on the cell block of this FNAB specimen and is depicted. Morphology and even immunohistochemistry are poor predictors of high-grade B-cell lymphoma- MYC/BCL2 , and FISH or other comparable fusion detection assay such as targeted or whole genome next generation sequencing ( 12 , 29 , 30 ), RNA based sequencing ( 31 ), or integrated DNA/RNA sequencing ( 32 ) must be performed to identify this important subset of large B-cell lymphoma ( 28 ).…”

Section: Discussionmentioning

confidence: 99%

Performance of MYC, BCL2, and BCL6 break-apart FISH in small biopsies with large B-cell lymphoma: a retrospective Cytopathology Hematopathology Interinstitutional Consortium study

Menke,

Aypar,

Bangs

et al. 2024

Front. Oncol.

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IntroductionFluorescence in situ hybridization (FISH) is an essential ancillary study used to identify clinically aggressive subsets of large B-cell lymphomas that have MYC, BCL2, or BCL6 rearrangements. Small-volume biopsies such as fine needle aspiration biopsy (FNAB) and core needle biopsy (CNB) are increasingly used to diagnose lymphoma and obtain material for ancillary studies such as FISH. However, the performance of FISH in small biopsies has not been thoroughly evaluated or compared to surgical biopsies.MethodsWe describe the results of MYC, BCL2, and BCL6 FISH in a series of 222 biopsy specimens, including FNAB with cell blocks, CNBs, and surgical excisional or incisional biopsies from 208 unique patients aggregated from 6 academic medical centers. A subset of patients had FNAB followed by a surgical biopsy (either CNB or excisional biopsy) obtained from the same or contiguous anatomic site as part of the same clinical workup; FISH results were compared for these paired specimens.ResultsFISH had a low hybridization failure rate of around 1% across all specimen types. FISH identified concurrent MYC and BCL2 rearrangements in 20 of 197 (10%) specimens and concurrent MYC and BCL6 rearrangements in 3 of 182 (1.6%) specimens. The paired FNAB and surgical biopsy specimens did not show any discrepancies for MYC or BCL2 FISH; of the 17 patients with 34 paired cytology and surgical specimens, only 2 of the 49 FISH probes compared (4% of all comparisons) showed any discrepancy and both were at the BCL6 locus. One discrepancy was due to necrosis of the CNB specimen causing a false negative BCL6 FISH result when compared to the FNAB cell block that demonstrated a BCL6 rearrangement.DiscussionFISH showed a similar hybridization failure rate in all biopsy types. Ultimately, MYC, BCL2, or BCL6 FISH showed 96% concordance when compared across paired cytology and surgical specimens, suggesting FNAB with cell block is equivalent to other biopsy alternatives for evaluation of DLBCL or HGBCL FISH testing.

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Section: Discussionmentioning

confidence: 99%

Performance of MYC, BCL2, and BCL6 break-apart FISH in small biopsies with large B-cell lymphoma: a retrospective Cytopathology Hematopathology Interinstitutional Consortium study

Menke,

Aypar,

Bangs

et al. 2024

Front. Oncol.

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“…More recently, next-generation sequencing (NGS) DNA capture methods have been introduced for rearrangement detection in selected gene panels in FFPE samples, which makes it possible to detect breakpoints at base-pair resolution and identify translocation partner genes 7 – 10 . However, such methods rely on capturing unambiguous fusion-reads, which can be challenging when non-unique sequences flank the breakpoint 11 .…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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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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“…6,7 In recent years, targeted NGS has been increasingly used in clinical diagnosis and therapeutic guidance. Targeted NGS has the ability to detect precise break point locations and identify translocation partner genes, [8][9][10] while also providing additional mutation data with prognostic and therapeutic implications. In addition, large multigene panels could make targeted NGS a cost-effective option than FISH in the detection of DLBCL-associated rearrangements in terms of per-gene cost.…”

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confidence: 99%

Characteristics and Clinical Value of MYC, BCL2, and BCL6 Rearrangement Detected by Next-generation Sequencing in DLBCL

Zeng,

Wei,

Bao

et al. 2024

American Journal of Surgical Pathology

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MYC, BCL2, and BCL6 rearrangements are clinically important events of diffuse large B-cell lymphoma (DLBCL). The ability and clinical value of targeted next-generation sequencing (NGS) in the detection of these rearrangements in DLBCL have not been fully determined. We performed targeted NGS (481-gene-panel) and break-apart FISH of MYC, BCL2, and BCL6 gene regions in 233 DLBCL cases. We identified 88 rearrangements (16 MYC; 20 BCL2; 52 BCL6 ) using NGS and 96 rearrangements (28 MYC; 20 BCL2; 65 BCL6) using FISH. The consistency rates between FISH and targeted NGS for the detection of MYC, BCL2, and BCL6 rearrangements were 93%, 97%, and 89%, respectively. FISH-cryptic rearrangements (NGS+/FISH−) were detected in 7 cases (1 MYC; 3 BCL2; 2 BCL6; 1 MYC::BCL6), mainly caused by small chromosomal insertions and inversions. NGS−/FISH+ were detected in 38 cases (14 MYC; 4 BCL2; 20 BCL6).To clarify the cause of the inconsistencies, we selected 17 from the NGS−/FISH+ rearrangements for further whole genome sequencing (WGS), and all 17 rearrangements were detected with break points by WGS. These break points were all located outside the region covered by the probe of targeted NGS, and most (16/17) were located in the intergenic region. These results indicated that targeted NGS is a powerful clinical diagnostics tool for comprehensive MYC, BCL2, and BCL6 rearrangement detection. Compared to FISH, it has advantages in describing the break point distribution, identifying uncharacterized partners, and detecting FISH-cryptic rearrangements. However, the lack of high-sensitivity caused by insufficient probe coverage is the main limitation of the current technology.

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Comparison Between Integrated Genomic DNA/RNA Profiling and Fluorescence In Situ Hybridization in the Detection of MYC, BCL-2, and BCL-6 Gene Rearrangements in Large B-Cell Lymphomas

Cited by 6 publications

References 16 publications

Performance of MYC, BCL2, and BCL6 break-apart FISH in small biopsies with large B-cell lymphoma: a retrospective Cytopathology Hematopathology Interinstitutional Consortium study

Performance of MYC, BCL2, and BCL6 break-apart FISH in small biopsies with large B-cell lymphoma: a retrospective Cytopathology Hematopathology Interinstitutional Consortium study

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

Characteristics and Clinical Value of MYC, BCL2, and BCL6 Rearrangement Detected by Next-generation Sequencing in DLBCL

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