Targeted next generation sequencing reveals high mutation frequency of CREBBP, BCL2 and KMT2D in high-grade B cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements

Morphologie ◽  
2019 ◽  
Vol 103 (342) ◽  
pp. 80-81
Author(s):  
Solène Evrard ◽  
Sarah Péricart ◽  
David Grand ◽  
Nadia Amara ◽  
Frédérice Escudié ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
B Cell ◽  
Mutation Frequency ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
High Grade ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
High Mutation Frequency ◽  
Generation Sequencing

scholarly journals A capture-sequencing strategy identifies IRF8, EBF1, and APRIL as novel IGH fusion partners in B-cell lymphoma

Blood ◽  
2013 ◽  
Vol 122 (5) ◽  
pp. 726-733 ◽  
Author(s):  
Hakim Bouamar ◽  
Saman Abbas ◽  
An-Ping Lin ◽  
Long Wang ◽  
Daifeng Jiang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
B Cell ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Next Generation ◽  
Key Points ◽  
Sequencing Strategy ◽  
Targeted Capture ◽  
Generation Sequencing ◽  
Capture Sequencing

Key Points Targeted capture/next-generation sequencing is a powerful tool for the diagnosis of known and discovery of new IGH fusions in DLBCL. IGH-mediated deregulation of IRF8 and EBF1 in DLBCL is characterized by induction of AID and BCL6, suppression of PRDM1, and antiapoptosis.

scholarly journals Next-Generation Sequencing in Diffuse Large B-Cell Lymphoma Highlights Molecular Divergence and Therapeutic Opportunities: a LYSA Study

2016 ◽  
Vol 22 (12) ◽  
pp. 2919-2928 ◽  
Author(s):  
Sydney Dubois ◽  
Pierre-Julien Viailly ◽  
Sylvain Mareschal ◽  
Elodie Bohers ◽  
Philippe Bertrand ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
B Cell ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Next Generation ◽  
Large B Cell Lymphoma ◽  
Molecular Divergence ◽  
Generation Sequencing ◽  
Large B Cell

scholarly journals Targeted Next Generation Sequencing Reveals Molecular Heterogeneity in Non-CLL Clonal B-Cell Lymphocytosis

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1502-1502
Author(s):  
Irene Defrancesco ◽  
Silvia Zibellini ◽  
Emanuela Boveri ◽  
Marco Frigeni ◽  
Virginia Valeria Ferretti ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
B Cell ◽  
Somatic Mutations ◽  
B Cell Lymphoma ◽  
Absolute Number ◽  
Chromatin Organization ◽  
Next Generation ◽  
Wild Type ◽  
Targeted Next Generation Sequencing ◽  
Generation Sequencing

Background. Non-chronic lymphocytic leukemia (non-CLL) clonal B-cell lymphocytosis (CBL) encompasses a heterogeneous group of hematologic disorders that are still poorly understood. The main purpose of this study was to explore the genomic landscape of non-CLL CBL, correlating the results with clinical, histological and immunogenetic features. Methods. We retrospectively analysed the disease characteristics in a highly selected series of 28 patients, who had a clonal lymphocytosis in peripheral blood (PB) and clonal lymphoid populations in the bone marrow (BM), without evidence of lymphadenopathy, splenomegaly, peripheral cytopenia or constitutional symptoms.In all patients the BM evaluation, comprising flow cytometry, histology and immunohistochemistry, was not able to classify the lymphoproliferative disorder in any of the WHO-defined entities. A diagnosis of CLL or a leukemic phase of mantle cell or follicular lymphoma was ruled out in each subject. Targeted next generation sequencing (NGS) was performed on DNA extracted from CD19+ BM or PB cells using a core panel of 138 genes frequently reported in mature B cell neoplasms.On the basis of the information retrieved from the KEGG and REACTOME databases, each mutated gene was assigned to a specific lymphoma-enriched pathway. Results: Clinical, flow cytometric and histological data are presented in Table 1.The median BM infiltration was 30% (range: 5-80%); the pattern of infiltration was interstitial or mixed (nodular and interstitial) in the majority of the cases; sinusoidal localization was noticed in 54% of cases. There was a borderline correlation between the extent of BM infiltration and the absolute number of PB clonal B cells count (Spearman's Rho: 0.38, p=0.05), that ranged from 851/mmc to 14508/mmc (median: 3604/mmc). With a median follow-up of 35.2 months (range: 6-125), only 1 patient developed disease progression to a B-cell lymphoma not otherwise specified (5-yrs CI of progression: 11.9%; 95%CI: 0.6%-40.7%). The sequence analysis of 138 genes revealed a total number of 74 somatic mutations in 51 genes. All the 28 cases displayed at least 1 mutation, with the number of mutations ranging from 1 to 7 (median 2). The most frequently mutated genes were MYD88 (14%), PDE4DIP (14%), BIRC3 (11%), CCND3 (11%), NOTCH1 (11%) and TNFAIP3 (11%) (fig.1).Notably, 3 out of 4 MYD88 variants were different from the classical p.L265P (p.M232T, p.V217F and p.L204F not previously described). Data on IGHV were available for 22 patients (79%) (Fig.2): VH gene repertoire was similar to that reported in non-CLL malignancies and no distinct stereotyped subset was found. Truly unmutated IGHV genes with 100% of germline identity were present in 3 cases (11%). The analysis of disease features according to mutated genes showed that MCwas more frequent in patients harbouring mutations in MYD88 (p=0.08) or TNFAIP3 (p=0.02); these patients had also a higher number of mast cells on BM histology than the wild type ones (p=0.02 and p=0.05, respectively). NOTCH1 mutated patients showed an absolute number of B-cell peripheral clonal lymphocytes higher than wild type cases (p=0.037). The most frequently involved pathways were NF-kB signalling (32%) and cell communication pathways (32%), followed by cell cycle (29%), chromatin organization (25%), transcriptional misregulation (21%), Toll-like receptor (TLR) signalling (18%) and NOTCH signalling pathways (14%) (Fig. 3).Patients with mutated chromatin organization pathway more often showed normal LDH levels compared with wild type cases (100% vs 40% p=0.01). Conclusions. We characterised non-CLL CBL, integrating BM histological features and IGHV data with an extended NGS panel. The mutational landscape was extremely heterogeneous, pointing out a wide spectrum of somatic mutations. Most of them have been already described in Waldenström's Macroglobulinemia and splenic B-cell lymphomas; of note, we found a new variant of MYD88 associated with an IgM MC and recurrent mutations of PDE4DIP, which have not been previously reported in indolent B-cell malignancies. Disclosures Varettoni: Janssen: Consultancy; Roche: Consultancy; ABBVIE: Other: travel expenses; Gilead: Other: travel expenses. Arcaini:Bayer, Celgene, Gilead Sciences, Roche, Sandoz, Janssen-Cilag, VERASTEM: Consultancy; Celgene: Speakers Bureau; Celgene, Roche, Janssen-Cilag, Gilead: Other: Travel expenses; Gilead Sciences: Research Funding.

scholarly journals Biological and Clinical Relevance of Associated Genomic Alterations in MYD88 L265P and Non-L265P Mutated Diffuse Large B-Cell Lymphoma: Analysis of 361 Cases

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4097-4097
Author(s):  
Sydney Dubois ◽  
Pierre-Julien Viailly ◽  
Elodie Bohers ◽  
Philippe Bertrand ◽  
Philippe Ruminy ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
B Cell ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Next Generation ◽  
Large B Cell Lymphoma ◽  
Pathway Activation ◽  
Generation Sequencing ◽  
Myd88 L265p ◽  
Large B Cell

Abstract Introduction: MYD88 mutations, notably the recurrent gain-of-function L265P variant, are a distinguishing feature of Activated B-Cell like (ABC) Diffuse Large B Cell Lymphoma (DLBCL), leading to constitutive NFkB pathway activation. The frequency of MYD88 mutations in DLBCL and other hematologic malignancies is well described; however, there has not yet been a large-scale study of a MYD88 mutated patient cohort with additional Next Generation Sequencing (NGS), copy number variation (CNV), and gene expression data, in order to thoroughly characterize the associated genomic profiles of these patients. The aims of our study were to compare the L265P and non-L265P mutations in terms of pathological and genetic features, to better detail the genomic background associated with MYD88 mutations in order to delineate patients potentially sensitive to targeted therapies, and to define the prognostic value of MYD88 mutations according to different genomic contexts. Methods: A cohort of 361 DLBCL patients (94 MYD88 mutant and 267 MYD88 wild-type) was selected among the prospective, multicenter and randomized LNH-03B and LNH09-7B (NCT01195714) LYSA trials, as well as among patients sequenced at our institution as part of routine procedure. Cell of origin (COO) classification was obtained with HGU133+2.0 Affymetrix GeneChip arrays for 214 patients, with RT-MLPA for 77 patients1 and with Hans immunohistochemistry (IHC) method for 49 patients. All cases were submitted to next generation sequencing (NGS) focusing on 34 genes (Lymphopanel2) in order to analyze associated mutations and copy number variations (CNVs), as well as IHC, FISH, and clinical and prognostic analyses. Results: Importantly, we highlighted different genomic profiles for MYD88 L265P and MYD88 non-L265P mutant DLBCL, shedding light on their divergent backgrounds. Clustering analysis segregated subgroups according to associated genetic alterations among patients with either MYD88 L265P or non-L265P mutations. As such, clustering separated MYD88 L265P mutated DLBCL with associated PIM1 (52%), CD79B (52%), KMT2D (42%), and PRDM1 (32%) mutations, as well as MYD88 L265P mutated DLBCL with CDKN2A/B (67%/50%), PRDM1 (57%) and TNFAIP3 (52%) CNVs. We showed that associated CD79B and MYD88 L265P mutations act synergistically to increase NFkB pathway activation, although the majority of ABC MYD88 L265P mutant cases harbor downstream NFkB alterations, which can potentially predict BTK inhibitor resistance. Of note, although the MYD88 L265P variant was not an independent prognostic factor in ABC DLBCL, associated CD79B mutations significantly improved the survival of MYD88 L265P mutant ABC DLBCL in our cohort both in OS (p=0.02) and PFS (p=0.01), whereas the association of CARD11 or TNFAIP3 alterations did not impact survival. Interestingly, MYD88 mutant DLBCL cases were significantly more likely to experience central nervous system (CNS) relapse than MYD88 WT cases (p=0.02), as were MYD88 L265P mutant cases specifically (p=0.03). This result still tended toward statistical significance when considering only ABC patients (7 of 11 ABC CNS-relapsing cases were MYD88 mutant, p=0.1) but would have to be confirmed in a larger cohort. Conclusions: This study highlights the relative heterogeneity of MYD88 mutant DLBCBL, adding to the field's knowledge of the distinct genetic backgrounds of these subgroups. Our data highlights the theranostic and prognostic relevance of examining MYD88 and associated genomic alterations, emphasizing the usefulness of genomic profiling to best stratify patients for targeted therapy. 1. Mareschal S, Ruminy P, Bagacean C, et al. Accurate Classification of Germinal Center B-Cell-Like/Activated B-Cell-Like Diffuse Large B-Cell Lymphoma Using a Simple and Rapid Reverse Transcriptase-Multiplex Ligation-Dependent Probe Amplification Assay: A CALYM Study. The Journal of molecular diagnostics : JMD. 2015;17(3):273-283. 2. Dubois S, Viailly P-J, Mareschal S, et al. Next Generation Sequencing in Diffuse Large B Cell Lymphoma Highlights Molecular Divergence and Therapeutic Opportunities: a LYSA Study. Clinical cancer research : an official journal of the American Association for Cancer Research. 2016;22(12):2919-2928. Disclosures Salles: Novartis: Consultancy, Honoraria; Mundipharma: Honoraria; Amgen: Consultancy, Honoraria; Celgene: Consultancy, Honoraria; Gilead: Honoraria, Research Funding; Janssen: Consultancy, Honoraria; Roche/Genentech: Consultancy, Honoraria, Research Funding.

scholarly journals Molecular Fingerprinting of Anatomically and Temporally Distinct B-Cell Lymphoma Samples by Next-Generation Sequencing to Establish Clonal Relatedness

2018 ◽  
Vol 143 (1) ◽  
pp. 105-111
Author(s):  
Anna P. Matynia ◽  
K. David Li ◽  
Philippe Szankasi ◽  
Jonathan Schumacher ◽  
Michael Liew ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
B Cell ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Translocation Breakpoint ◽  
Derivative Chromosome ◽  
Next Generation ◽  
Molecular Fingerprint ◽  
Clonal Relatedness ◽  
Generation Sequencing

Context.— B-cell lymphomas exhibit balanced translocations that involve immunoglobulin loci and result from aberrant V(D)J recombination, class switch recombination, or somatic hypermutation. Although most of the breakpoints in the immunoglobulin loci occur in defined regions, those in the partner genes vary; therefore, it is unlikely that 2 independent clones would share identical breakpoints in both partners. Establishing whether a new lesion in a patient with history of lymphoma represents recurrence or a new process can be relevant. Polymerase chain reaction (PCR)–based clonality assays used in this setting rely only on evaluating the length of a given rearrangement. In contrast, next-generation sequencing (NGS) provides the exact translocation breakpoint at single-base resolution. Objective.— To determine if translocation breakpoint coordinates can serve as a molecular fingerprint unique to a distinct clonal population. Design.— Thirty-eight follicular lymphoma/diffuse large B-cell lymphoma samples collected from different anatomic sites and/or at different time points from 18 patients were analyzed by NGS. For comparison, PCR-based B-cell clonality and fluorescence in situ hybridization studies were performed on a subset of cases. Results.— IGH-BCL2 rearrangements were detected in all samples. The breakpoint coordinates on derivative chromosome(s) were identical in all samples from a given patient, but distinct between samples derived from different patients. Additionally, 5 patients carried a second rearrangement also with conserved breakpoint coordinates in the follow-up sample(s). Conclusions.— Breakpoint coordinates in the immunoglobulin and partner genes can be used to establish clonal relatedness of anatomically/temporally distinct lesions. Additionally, an NGS-based approach has the potential to detect secondary translocations that may have prognostic and therapeutic significance.

scholarly journals Targeted next generation sequencing identifies a genetic spectrum of DNA variants in patients with hemiplegic migraine

2019 ◽  
Vol 2 ◽  
pp. 251581631988163 ◽  
Author(s):  
Neven Maksemous ◽  
Robert A Smith ◽  
Heidi G Sutherland ◽  
Bridget H Maher ◽  
Omar Ibrahim ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Diagnostic Yield ◽  
Next Generation ◽  
Hemiplegic Migraine ◽  
Targeted Next Generation Sequencing ◽  
Variants Of Unknown Significance ◽  
High Mutation Frequency ◽  
Unknown Significance ◽  
Atp1a2 Gene ◽  
Generation Sequencing

Objective: Hemiplegic migraine in both familial (FHM) and sporadic (SHM) forms is a rare subtype of migraine with aura that can be traced to mutations in the CACNA1A, ATP1A2 and SCN1A genes. It is characterised by severe attacks of typical migraine accompanied by hemiparesis, as well as episodes of complex aura that vary significantly between individuals. Methods: Using a targeted next generation sequencing (NGS) multigene panel, we have sequenced the genomic DNA of 172 suspected hemiplegic migraine cases, in whom no mutation had previously been found by Sanger sequencing (SS) of a limited number of exons with high mutation frequency in FHM genes. Results: Genetic screening identified 29 variants, 10 of which were novel, in 35 cases in the three FHM genes ( CACNA1A, ATP1A2 and SCN1A). Interestingly, in this suspected HM cohort, the ATP1A2 gene harboured the highest number of variants with 24/35 cases (68.6%), while CACNA1A ranked the second gene, with 5 variants identified in 7/35 cases (20%). All detected variants were confirmed by SS and were absent in 100 non-migraine healthy control individuals. Assessment of variants with the American College of Medical Genetics and Genomics guidelines classified 8 variants as pathogenic, 3 as likely pathogenic and 18 as variants of unknown significance. Targeted NGS gene panel increased the diagnostic yield by fourfold over iterative SS in our diagnostics facility. Conclusion: We have identified 29 potentially causative variants in an Australian and New Zealand cohort of suspected HM cases and found that the ATP1A2 gene was the most commonly mutated gene. Our results suggest that screening using NGS multigene panels to investigate ATP1A2 alongside CACNA1A and SCN1A is a clinically useful and efficient method.

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