Combined BIOMED-2 Clonality Assays for IGH and IGK and Assessment of t(14;18) on Formalin-Fixed, Paraffin Embedded Tissues Effectively Separates Primary Cutaneous B Cell Lymphomas from Reactive Cutaneous Lymphoid Hyperplasia.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2623-2623
Author(s):  
Anjali V. Morales ◽  
Katie Seo ◽  
Daniel A. Arber ◽  
Sabine Kohler ◽  
Youn H. Kim ◽  
...  

Abstract Primary cutaneous B-cell lymphomas (PCBCL) are a diverse group of lymphomas that are limited to the skin at the time of diagnosis. Clonally rearranged immunoglobulin (Ig) genes are a key feature of B-cell malignancies. While PCR for Ig rearrangement is well-established and characterized in nodal malignancies, PCR investigations of Ig clonality in PCBCL have been unstandardized and extremely inconsistent. In this study, we analyzed 27 cases of PCBCL (22 cases of PCBCL diagnosed at initial presentation and 5 cases of atypical lymphoid infiltrates (ALI)) for Ig clonality using standardized BIOMED-2 PCR protocols (InVivoScribe Technologies, San Diego, CA). We defined lesions of ALI as those that were clinically suspicious for lymphoma, but could not be confirmed as lymphoma by morphologic and/or immunohistochemical methods. These patients were followed clinically where an eventual diagnosis of lymphoma was made by morphologic and/or immunohistochemical methods. Our primary objective was to evaluate the sensitivity and specificity of the BIOMED-2 method for detecting clonality in PCBCL, including cases initially diagnosed as ALI. Our secondary objective was to assess the role of clonality in the diagnosis of PCBCL. 47 biopsies from 27 cases of PCBCL (7 T1aN0M0, 4 T2aN0M0, 3 T2bN0M0, 3 T3aN0M0, and 10 T3bN0M0) were tested for IGH and IGK gene rearrangements and the (14;18) translocation using BIOMED-2 primers. Select cases from patients with multiple biopsies were further analyzed by sequencing to identify identical clones. We found a clone in 24/27 (89%) cases overall (10/11, 91% marginal zone lymphoma (MZL); 10/11, 91% follicle center lymphoma (FCL); and 4/5 ALI)). Among the 47 biopsies, a clone was detected in 35/47 (75%) cases (13/19, 68% MZL; 15/19, 79% FCL; and 7/9, 78% ALI). We found that clonal detection was improved in cases with multiple biopsies. The t(14;18) translocation was present in 3/11 FCL cases and 1/5 ALI cases, but not detected in any biopsy from MZL cases. Addition of IGK analysis to IGH analysis alone increased sensitivity of clonal detection from 57% to 75%. No clonality was detected in 9 cases of reactive cutaneous lymphoid hyperplasia. While our study is small, the initial results demonstrate that the BIOMED-2 protocol shows high sensitivity and specificity in clonality detection in PCBCL the (14;18) translocation is rare in PCBCL in general, but can be detected in a minority of cases of FCL adding IGK primers to the analysis for clonality may increase its sensitivity over detection of IGH rearrangements alone clonality detection may lead to earlier diagnosis of PCBCL in cases otherwise thought to be ALI multiple biopsies can lead to a more definitive diagnosis of PCBCL with increased likelihood of clonal detection and formalin-fixed paraffin embedded tissues can be used very effectively to establish clonality in PCBCL. To our knowledge, this is the first report of a standardized approach for the detection of clonality in PCBCL. We propose a new algorithm in the diagnosis of PCBCL, where clonality assays are implemented when a definitive diagnosis cannot be made on clinical, morphologic, and/or immunophenotypic grounds. This novel characterization of PCBCL using archival tissue and the BIOMED-2 assay is a powerful strategy for clonality assessment and validation of the diagnosis of PCBCL.

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Pauline Gilson ◽  
Julien Levy ◽  
Marie Rouyer ◽  
Jessica Demange ◽  
Marie Husson ◽  
...  

Abstract Microsatellite instability (MSI) status is routinely assessed in patients with colorectal and endometrial cancers as it contributes to Lynch syndrome initial screening, tumour prognosis and selecting patients for immunotherapy. Currently, standard reference methods recommended for MSI/dMMR (deficient MisMatch Repair) testing consist of immunohistochemistry and pentaplex PCR-based assays, however, novel molecular-based techniques are emerging. Here, we aimed to evaluate the performance of a custom capture-based NGS method and the Bio-Rad ddPCR and Idylla approaches for the determination of MSI status for theranostic purposes in 30 formalin-fixed paraffin embedded (FFPE) tissue samples from patients with endometrial (n = 15) and colorectal (n = 15) cancers. All samples were previously characterised using IHC and Promega MSI Analysis System and these assays set as golden standard. Overall agreement, sensitivity and specificity of our custom-built NGS panel were 93.30%, 93.75% and 92.86% respectively. Overall agreement, sensitivity and specificity were 100% with the Idylla MSI system. The Bio-Rad ddPCR MSI assay showed a 100% concordance, sensitivity and specificity. The custom capture-based NGS, Bio-Rad ddPCR and Idylla approaches represent viable and complementary options to IHC and Promega MSI Analysis System for the detection of MSI. Bio-Rad ddPCR and Idylla MSI assays accounts for easy and fast screening assays while the NGS approach offers the advantages to simultaneously detect MSI and clinically relevant genomic alterations.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 620-620
Author(s):  
Lisa M. Rimsza ◽  
George Wright ◽  
Mark Schwartz ◽  
Wing C. Chan ◽  
Elaine S Jaffe ◽  
...  

Abstract Abstract 620 Classification of DLBCL into cell-of-origin (COO) subtypes based on gene expression profiles has well-established prognostic value. These subtypes, termed Germinal Center B cell (GCB) and Activated B cell (ABC) also have different genetic alterations and over-expression of different pathways that may serve as therapeutic targets. Thus, accurate classification is essential for analysis of clinical trial results and planning new trials using targeted agents. The gold standard for COO classification uses gene expression profiling (GEP) of snap frozen tissues, and a Bayesian predictor algorithm utilizing the expression levels of 14 key genes (G. Wright et al PNAS 2003). An immunohistochemistry (IHC) classification scheme by C. Hans et al (Blood 2004), based on 3 antibodies, is widely used as a substitute for GEP classification, however does not completely correlate with GEP. We recently described a qNPA assay (ArrayPlateR, High ThroughPut Genomics, Tucson, AZ) with excellent correlation between frozen and formalin fixed paraffin embedded (FFPE) tissues (R. Roberts et al, Lab Invest 2007). In this study, we investigated whether this technique could be used for accurate classification of COO using FFPE tissues. We expanded the previous gene probe repertoire of the DLBCL-ArrayPlateR assay to include the 14 genes (represented by 17 probe sets) most pertinent to COO classification. 52 cases of R-CHOP treated DLBCL that had undergone GEP using the Affymetrix U133 Plus 2.0 microarray and had matching FFPE blocks were analyzed with qNPA in duplicate. The genes included CD10, LRMP, CCND2, ITPKB, PIM1, IL16, IRF4, FUT8, BCL6, PTPN1, LM02, CD39, MYBL1, IGHM. Results were evaluated using the previously published algorithm with a leave-one-out cross validation scheme to classify cases into GCB or ABC subtypes. These results were compared to COO classification based on frozen tissue GEP profiles. All 14 genes in all 52 cases were successfully analyzed with no missing data points. For each case, a probability statistic was generated indicating the likelihood that the classification using qNPA was accurate. Of the 54 cases, 25 were GCB, 27 were ABC and 4 were unclassifiable by GEP. Of the GCB cases, 23/25 (92%) were classified correctly by qNPA with a confidence cut-off of >0.9 and 25/25 (100%) classified correctly with a confidence cut-off of >0.8. Of the ABC cases, 25/27 (93%) were correctly classified as ABC using qNPA with a confidence cut-off of >0.9 and 27/27 (100%) classified correctly with a confidence cut-off of >0.8. In summary, the qNPA technique accurately categorized DLBCL into GCB and ABC subtypes, as defined by GEP. There were no technical difficulties with any of the pathological materials although they were collected retrospectively from a variety of institutions and countries with different fixation methods. This approach represents a substantial improvement over previously published IHC methods and is applicable to FFPE tissues, therefore overcoming the need for snap frozen materials. This technically robust classification method has potential to have a significant impact on future DLBCL research and clinical trial development. Disclosures: Rimsza: High Throughput Genomics: HTG provided the assays at no charge to Dr. Rimsza's lab. Schwartz:High Throughput Genomics: Employment. Gascoyne:Roche Canada: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3111-3111 ◽  
Author(s):  
Betty J. Glinsmann-Gibson ◽  
Dennis E McMillan ◽  
Sarah Wilkinson ◽  
Julie Teruya-Feldstein ◽  
Lisa M. Rimsza

Abstract Abstract 3111 Diffuse Large B cell lymphoma (DLBCL) is the most common form of non-Hodgkin's lymphoma. The Leukemia Lymphoma Molecular Profiling Project (LLMPP) collaboration has done extensive work regarding this disease including gene expression profiling to show that the cell of origin impacts the prognosis of the patient. Those cases which arise from an activated B cell (ABC) have a worse prognosis than those cases which arise from a germinal center B cell (GCB). We have used a subset of cases from our institution which have had gene expression profiling performed on frozen material and assigned ABC (n=18) or GCB (n=24) status (Rosenwald et al NEJM 2002, 346:1937). We have used matched formalin fixed paraffin embedded (FFPE) tissue block from these cases to obtain a microRNA profile utilizing the qNPA technology (High ThroughPut Genomics) as previously published (Roberts et al Lab Invest 2007, 87:979). This novel FFPE based RNAase protection assay measured 688 human microRNAs. Each microRNA was represented twice on the array and the values averaged for a signal value. The data were normalized to the total signal of the microarray. We were able to define a signature of increased microRNA for each DLBCL subtype as shown in Table 1. ABC subtype GCB subtype hsa-miR-155 hsa-miR-28-5p hsa-miR-196a hsa-miR-138 hsa-miR-501-3p hsa-miR-151-3p hsa-miR-656 hsa-miR-151-5p hsa-miR-1247 hsa-miR-182 hsa-miR-210 hsa-miR-613 The hsa-miR-155 is of importance in lymphoma as it regulates the generation of immunoglobulin class-switch in plasma cells (Turner et al Immunity 2007, 27:847) and was previously identified as a characteristic of ABC cell lines (Lossos et al Blood 2009,113:3754). The hsa-miR-210 has been shown to modulate the MYC antagonist MNT which allows for MYC expression (Grandori et all Cell Cycle 2009, 8:2756). This microRNA profile provides an opportunity to further explore the role microRNA plays in lymphoma biology and in particular, in DLBCL subtype determination. The success of the technique in FFPE tissue holds promise for further microRNA studies on archival material. Disclosures: No relevant conflicts of interest to declare.


2014 ◽  
Vol 167 (2) ◽  
pp. 281-285 ◽  
Author(s):  
Angela M. B. Collie ◽  
Jörk Nölling ◽  
Kiran M. Divakar ◽  
Jeffrey J. Lin ◽  
Paula Carver ◽  
...  

1987 ◽  
Vol 24 (3) ◽  
pp. 211-215 ◽  
Author(s):  
C. B. Andreasen ◽  
E. A. Mahaffey

Sections of formalin-fixed, paraffin-embedded canine leiomyomas, leiomyosarcomas, or fibrosarcomas were examined by immunohistochemical methods for the presence of desmin. Twenty-two leiomyomas and leiomyosarcomas were stained using the avidin-biotin complex technique, and 14 samples demonstrated positive staining for desmin. The eight negative results obtained may reflect differences in fixation or the affinity of the primary antibody for the tissues examined. Desmin was specific for myogenic tissues. Five canine fibrosarcomas examined immunohistochemically were all negative for desmin staining. The results indicate that desmin is a useful marker for immunohistochemical identification of canine leiomyomas and leiomyosarcomas.


Blood ◽  
2018 ◽  
Vol 132 (22) ◽  
pp. 2319-2320 ◽  
Author(s):  
Megan S. Lim

In this issue of Blood, Mottok et al1 demonstrate the utility of a molecular assay that assesses the expression of 58 genes to distinguish primary mediastinal B-cell lymphoma (PMBCL) from diffuse large B-cell lymphoma (DLBCL) by using routinely available formalin-fixed paraffin-embedded tissue (FFPET) biopsies. The results could improve diagnostic accuracy for patients with PMBCL and may have important implications for clinical trial selection and interpretation of clinical outcomes for patients with this rare form of lymphoma.


2015 ◽  
Vol 8 (8) ◽  
pp. 108
Author(s):  
Manoush Tohidirad ◽  
Mehrdad Asghari Estiar ◽  
Azim Rezamand ◽  
Saeid Ghorbian ◽  
Sasan Andalib ◽  
...  

<p>In the present study, our aim was to assess the incidence of BCL-1 gene rearrangements in formalin-fixed paraffin embedded (FFPE) tissue in patients with non-Hodgkin lymphomas (NHL). The BIOMED-2 protocol was applied to assess the BCL-1 gene rearrangements in NHL patients. PCR amplification was carried out on FFPE in 100 patients with B-cell lymphoma including 89 cases with diffused large B-cell lymphoma (DLBCL) (15 cases under 18 years old) and 11 cases with mantle cell lymphoma (MCL). Out of the 100 patients, 19 cases (19%) were identified to have concurrent translocation involving BCL-1. The significant association was seen between BCL-1 gene rearrangements and the lymphomas in patients older than 55 years (P&lt;0.05). Out of 100 cases, 80 cases were positive and 20 cases were negative regarding CD20. No significant association was found between DLBCL lymphoma in patients under 18 years old and BCL-1 gene rearrangements (P&gt;0.05). In addition, the positive and negative expressions of LCA/CD45 marker were 76% (76/100) and 26% (26/100), respectively. Our findings revealed that BCL-1 gene rearrangement assays using BIOMED-2 protocol can be considered as a valuable approach in detection of the lymphomas.</p>


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