scholarly journals Whole-exome sequencing in relapsing chronic lymphocytic leukemia: clinical impact of recurrent RPS15 mutations

Blood ◽  
2016 ◽  
Vol 127 (8) ◽  
pp. 1007-1016 ◽  
Author(s):  
Viktor Ljungström ◽  
Diego Cortese ◽  
Emma Young ◽  
Tatjana Pandzic ◽  
Larry Mansouri ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Poor Prognosis ◽  
Clinical Impact ◽  
Lymphocytic Leukemia ◽  
Whole Exome ◽  
Key Points ◽  
Frequent Mutations

Key Points Whole-exome sequencing of CLL patients who relapsed after FCR treatment revealed frequent mutations in RPS15. RPS15 mutations are likely to be early clonal events and confer poor prognosis.

Mutations of the SF3B1 splicing Factor in Chronic Lymphocytic Leukemia: Association with Progression and Fludarabine-Refractoriness

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 464-464
Author(s):  
Davide Rossi ◽  
Alessio Bruscaggin ◽  
Valeria Spina ◽  
Silvia Rasi ◽  
Hossein Khiabanian ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Lymphocytic Leukemia ◽  
Splicing Factor ◽  
Potential Contribution ◽  
Critical Component ◽  
Newly Diagnosed ◽  
Whole Exome ◽  
Recurrent Mutations

Abstract Abstract 464 Fludarabine-refractoriness of chronic lymphocytic leukemia (CLL) is due to TP53 disruption in ∼40% of refractory cases, but in a sizeable fraction of patients the molecular basis of this aggressive clinical phenotype remains unclear. Our initial findings from whole exome sequencing of fludarabine-refractory CLL led to the identification of recurrent mutations of SF3B1, a critical component of the cell spliceosome, prompting further investigations of these alterations in a large CLL panel. The study population comprised 3 clinical cohorts representative of: i) fludarabine-refractory CLL (n=59), including cases (n=11) subjected to whole exome sequencing; ii) newly diagnosed and previously untreated CLL (n=301); and iii) clonally related RS (n=33). Tumor samples were obtained: i) for fludarabine-refractory CLL, immediately before starting the treatment to which the patient eventually failed to respond; ii) for newly diagnosed and previously untreated CLL, at disease presentation. All RS studies were performed on RS diagnostic biopsies. Mutation analysis of SF3B1 was performed on genomic DNA by a combination of Sanger sequencing and targeted next generation sequencing. SF3B1 was altered in 10/59 (17%) fludarabine-refractory CLL by missense mutations (n=9) or in-frame deletions (n=1) clustering in the HEAT3, HEAT4 and HEAT5 repeats of the SF3B1 protein. Two sites that are highly conserved inter-species (codon 662 and codon 700) were recurrently mutated in 3 and 5 cases, respectively. SF3B1 mutations were monoallelic, and were predicted to be functionally significant according to the PolyPhen-2 algorithm. Mutations occurred irrespective of IGHV mutation status, CD38 expression and ZAP70 expression. At the time of fludarabine-refractoriness, SF3B1 mutations were enriched in cases harboring a normal FISH karyotype (p=.008) and distributed in a mutually exclusive fashion with TP53 disruption (mutual information I =0.0609; p=.046). By combining SF3B1 mutations with other genetic lesions enriched in chemorefractory cases (TP53 disruption, NOTCH1 mutations, ATM deletion), fludarabine-refractory CLL appeared to be characterized by multiple molecular alterations that, to some extent, are mutually exclusive. We then compared the prevalence of mutations observed at the time of fludarabine-refractoriness to that observed in other disease phases. At diagnosis, SF3B1 mutations were rare (17/301; 5%), and showed a crude association with short treatment free survival (p<.001) and overall survival (p=.011). Remarkably, 5/17 (29%) CLL mutated at diagnosis were primary fludarabine-refractory patients. In CLL investigated at diagnosis, the hotspot distribution and molecular spectrum of SF3B1 mutations, as well as their mutual relationship with other genetic lesions, were similar to those observed in fludarabine-refractory CLL. SF3B1 mutations were restricted to 2/33 (6.0%) clonally-related RS. Across the different disease phases investigated, mutations were somatically acquired in all cases (n=18) for which germline DNA was available. These data document that mutations of SF3B1, a splicing factor that is a critical component of the spliceosome; i) recurrently associate with fludarabine-refractory CLL; ii) occur at a low rate at CLL presentation; iii) play a minor role in RS transformation, corroborating the notion that CLL histologic shift is molecularly distinct from chemorefractory progression without RS transformation. The identification of SF3B1 mutations points to the involvement of splicing regulation as a novel pathogenetic mechanism in CLL. The pathogenicity of SF3B1 mutations in CLL is strongly supported by clustering of these mutations in evolutionarily conserved hotspots localized within HEAT domains, which are tandemly arranged curlicue-like structures serving as flexible scaffolding on which other components can assemble. Also, the observation that SF3B1 regulates the alternative splicing program of genes controlling cell cycle progression and apoptosis points to a potential contribution of SF3B1 mutations in modulating tumor cell proliferation and survival. In addition to pathogenetic implications, SF3B1 mutations might also provide a therapeutic target for SF3B1 inhibitors, that are currently under pre-clinical development as anti-cancer drugs. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole-Exome Sequencing of 262 Primary CLL Samples

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1952-1952 ◽  
Author(s):  
Dan A. Landau ◽  
Chip Stewart ◽  
Johannes G. Reiter ◽  
Michael Lawrence ◽  
Carrie Sougnez ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Exome Sequencing ◽  
Gene Mutations ◽  
Clinical Impact ◽  
Lymphocytic Leukemia ◽  
Driver Mutations ◽  
Driver Gene ◽  
Discovery Process ◽  
Driver Genes ◽  
Whole Exome

Abstract Unbiased high-throughput massively parallel sequencing methods have transformed the process of discovery of novel putative driver gene mutations in cancer. In chronic lymphocytic leukemia (CLL), these methods have yielded several unexpected findings, including the driver genes SF3B1, NOTCH1 and POT1. Recent analysis, utilizing down-sampling of existing datasets, has shown that the discovery process of putative drivers is far from complete across cancer. In CLL, while driver gene mutations affecting >10% of patients were efficiently discovered with previously published CLL cohorts of up to 160 samples subjected to whole exome sequencing (WES), this sample size has only 0.78 power to detect drivers affecting 5% of patients, and only 0.12 power for drivers affecting 2% of patients. These calculations emphasize the need to apply unbiased WES to larger patient cohorts. To this end, we performed a combined analysis of CLL WES data joining together our previously published cohort of 159 CLLs with data from 103 CLLs collected by the International Cancer Genome Consortium (ICGC). The raw sequencing reads from these 262 primary tumor samples (102 CLL with unmutated IGHV, 147 with mutated IGHV, 13 with unknown IGHV status) were processed together and aligned to the hg19 reference genome. Somatic single nucleotide variations (sSNVs) and indels were detected using MuTect. Subsequently, inference of recurrently mutated genes was performed using the MutSig algorithm. This method combined several characteristics such as the overall mutation rate per sample, the gene specific background mutation rate, non-synonymous/synonymous ratio and mutation clustering to detect genes that are affected by mutations more than expected by chance. This analysis identified 40 recurrently mutated genes in this cohort. This included 22 of 25 previously identified recurrently mutated genes in CLL. In addition, 18 novel candidate CLL drivers were identified, mostly affecting 1-2% of patients. The novel candidates included two histone proteins HIST1H1D and HIST1H1C, in addition to the previously identified HIST1H1E. Another was IKZF3, affected by a recurrent sSNV resulting in a p.L162R change in its DNA binding domain, in close proximity to a region recently identified as critical for lenalidomide resistance in multiple myeloma (MM). An additional recurrently mutated gene was nuclear RNA export factor 1 (NXF1), which along with previously known recurrently mutated genes (SF3B1, XPO1, DDX3X), highlights the importance of RNA processing to CLL biology. Finally, this search for putative CLL driver genes also identified ASXL1 and TRAF3, already characterized as drivers in acute myeloid leukemia and MM, respectively. Of the 59 of 262 samples for which RNA-seq data were available, 76% of the identified driver mutations were detected and thereby validated. Validation using RNAseq detection of driver mutations and targeted sequencing within the entire cohort are ongoing. The larger size of our cohort enabled the separate application of the somatic mutation discovery process to samples with mutated or unmutated IGHV. Among the 147 samples with mutated IGHV, only 5 driver genes (TP53, SF3B1, MYD88, CHD2, RANBP2) retained significance. In contrast, analysis of the 102 IGHV unmutated samples revealed a distinct and more diverse pattern of recurrently mutated genes (lacking MYD88 and CHD2, and including NOTCH1, RPS15, POT1, NRAS, EGR2, BRAF, MED12, XPO1, BCOR, IKZF3, MAP2K1, FBXW7 and KRAS). This extended cohort also allowed for better resolution of the clinical impact of those genetic variants with greater than 4% prevalence in the cohort. For example, samples with POT1 mutations were found to be associated with shorter time from sample to therapy compared with those with wild-type POT1 (P= 0.02). Our study demonstrates that with larger cohort size, we can effectively detect putative driver genes with lower prevalence, but which may nonetheless have important biological and clinical impact. Moreover, our interrogation shows that subset analysis can reveal distinct driver patterns in different disease subsets. In particular, the marked clinical difference between CLLs with mutated and unmutated IGHV may reflect the higher likelihood of the latter group to harbor a broader spectrum of driver mutations with a more complex pattern of co-occurrence. Disclosures Brown: Sanofi, Onyx, Vertex, Novartis, Boehringer, GSK, Roche/Genentech, Emergent, Morphosys, Celgene, Janssen, Pharmacyclics, Gilead: Consultancy.

scholarly journals Whole‐exome sequencing identified mutational profile of a case with T‐cell chronic lymphocytic leukemia

2020 ◽  
Vol 8 (11) ◽  
pp. 2251-2254
Author(s):  
Kenji Nozaki ◽  
Takafumi Yokota ◽  
Eri Itotagawa ◽  
Kazuhito Tsutsumi ◽  
Shinsuke Kusakabe ◽  
...  
Keyword(s):  
T Cell ◽  
Chronic Lymphocytic Leukemia ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Lymphocytic Leukemia ◽  
Whole Exome ◽  
Cell Chronic Lymphocytic Leukemia

scholarly journals Whole Exome Sequencing Reveals Multiple Driver Events in Chronic Lymphocytic Leukemia Patients with Acquired Ibrutinib Resistance

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1287-1287
Author(s):  
Chingiz Underbayev ◽  
Inhye E Ahn ◽  
Hailey Harris ◽  
Lauren T Vaughn ◽  
Mehdi Pirooznia ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Chronic Lymphocytic Leukemia ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Chromosomal Aberrations ◽  
Research Funding ◽  
Single Agent ◽  
Lymphocytic Leukemia ◽  
Driver Mutations ◽  
Whole Exome

Disease progression in chronic lymphocytic leukemia (CLL) patients receiving single-agent ibrutinib has been associated with either histological transformation or acquired mutations in BTK and PLCG2 genes which are found in up to 85% of patients with progressive CLL (PD-CLL), less commonly in patients with histologic transformation. Variant allele frequencies of these mutations are highly variable and in some patients remain low and thus cannot fully explain the emergence of drug-resistant clones. Cooperation between mutant and "wild-type" clones has been proposed to explain expansion of clones that have no BTK or PLCG2 mutation. Alternatively, additional drivers have been suggested, including 8p deletion. Here we performed a comprehensive analysis of resistant samples' clonal composition using droplet digital polymerase chain reaction (ddPCR) and whole exome sequencing across multiple time points and compartments to reveal additional hits responsible for drug resistance. Eighty-four CLL patients have been enrolled to a phase II study for ibrutinib monotherapy. Eligible patients had either TP53 aberration or age ≥65 years regardless of prior treatment status. All patients received single-agent ibrutinib 420 mg once daily until disease progression or intolerable side effects occurred. At a median follow-up of 5.5 years, 23 (27.4%) patients developed progressive disease (PD) including 17 patients with PD-CLL, five with Richter's transformation and one with prolymphocytic leukemia. Majority of PD-CLL patients had TP53 aberration (88.2%) and relapsed or refractory CLL (58.8%). The median time-to-progression was 38.8 months for all PD patients and was shorter for those with histologic transformations compared to those with PD-CLL (7.0 vs 44.2 months). We tested for BTK/PLCG2 mutations in 17 PD-CLL patients using archival samples collected at baseline, during response to ibrutinib and at progression using variant-specific ddPCR assays. Fifteen PD-CLL patients (88%) had detectable BTK and/or PLCG2 variants at the time of progression. Notably, only 5 PD-CLL patients (29.4%) demonstrated a strong BTK/PLCG2-driven resistance with cumulative clonal fraction (cCF) above 50% at PD and a significant tumor burden in the peripheral blood (PB). Seven patients (41.2%) demonstrated partial BTK/PLCG2-associated resistance (cCF ranging 4-40%) with additional sub-clonal variants (TP53, NFKBIE, SF3B1, BIRC3, KRAS) and chromosomal aberrations (del8p, del6q, amp2p) as putative drivers in concurrently evolving subclones at PD. Finally, 29.4% of patients had very low (<4%, 3 patients) or undetectable (2 patients) frequencies of BTK/PLCG2 variants but often carried multiple chromosomal aberrations (del17p, del8p, del3p, del2p, del13q) and known CLL driver mutations (NOTCH1, SF3B1) in the resistant clone(s). In all PD-CLL patients, the resistant clones were detected in at least one of the 3 compartments: PB, lymph node (LN) or bone marrow (BM). Expanding clones were present in all 3 sites in three patients (18%), in PB and either LN or BM in 10 (59%) patients, and in LN and/or BM but not in PB in 4 patients (23%). In summary, BTK/PLCG2 mutations are present in most patients progressing on ibrutinib but in many cases these mutations cannot completely account for drug resistance. Exome sequencing followed by clonal decomposition analysis revealed additional genetic alterations in ibrutinib-resistant clones including acquisition of multiple copy number alterations and/or additional known CLL driver mutations. In most patients resistant clones are equally detected in blood and tissue sites. Disclosures Wiestner: Acerta: Research Funding; Merck: Research Funding; Nurix: Research Funding; Pharmayclics: Research Funding.

scholarly journals Whole-Exome Sequencing Revealed No Recurrent Mutations within the PI3K Pathway in Relapsed Chronic Lymphocytic Leukemia Patients Progressing Under Idelalisib Treatment

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 2770-2770 ◽  
Author(s):  
Paolo Ghia ◽  
Viktor Ljungström ◽  
Eugen Tausch ◽  
Andreas Agathangelidis ◽  
Annika Scheffold ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Research Funding ◽  
Somatic Mutations ◽  
Lymphocytic Leukemia ◽  
Employment Equity ◽  
Phase 3 ◽  
Whole Exome ◽  
Equity Ownership

Abstract Introduction: Idelalisib (IDELA) is an ATP-competitive, reversible, and selective small molecule inhibitor of the delta isoform of phosphatidylinositol 3-kinase (PI3Kδ) approved for the treatment, in combination with rituximab, of patients with relapsed chronic lymphocytic leukemia (CLL). In the relapsed CLL randomized, controlled trials, IDELA + rituximab showed high response rates with improved progression-free and overall survival as compared with placebo + rituximab. While IDELA therapy has significant efficacy, disease progression after response occurs, indicating that escape mechanisms may develop. However, the molecular basis for relapse or progressive disease (PD) in CLL patients treated with IDELA has not yet been characterized. Methods: Peripheral blood mononuclear cells (PBMCs) were collected from 13 CLL patients enrolled in the phase 3 studies; NCT01539512 (study 116; IDELA + rituximab vs placebo + rituximab), 116 extension study NCT01539291 (study 117) and NCT01659021 (study 119; IDELA + ofatumumab). Sample selection criteria included treatment period of at least 180 days (range: 243-703 days), achieving at least partial nodal response followed by PD, PD did not occur within a drug interruption window, PD was not associated with Richter's transformation, and PBMC samples were available from both baseline and time of PD. Whole-exome sequencing (WES) was conducted on the matched samples from 13 subjects fitting the above criteria. In 6/13 cases, DNA was available from CD19+/CD5+ enriched tumor cells, and neutrophils or T-lymphocytes served as a source of germline DNA. These 6 patients were considered as a discovery set for mutational analysis. Established bioinformatics tools were used for detection of somatic mutations and for the comparison of baseline and PD samples. Results: Baseline clinical patient profiles indicated that 12 of 13 patients with PD had unmutated IGHV genes and 8 patients carried TP53 aberrations (ie, 17p deletion and/or TP53 mutation). WES resulted in a mean read depth of 106X within the targeted coding region across samples. In the discovery set, on average 25 somatic mutations (range: 4-44) at baseline and 32 mutations (range: 15-81) at progression were identified. By comparing baseline and PD samples, we identified 88 PD-associated mutations. These specific mutations were tested for in a complete set of 13 patient samples; however, no recurrent progression-associated mutations were identified in more than 1 patient. In particular, no progression-associated mutations were identified in the PI3K signaling pathway or in any other related pathway. Conclusion: Across 3 phase 3 studies in relapsed CLL, WES on 13 samples from patients with PD while on IDELA treatment were evaluated. This analysis detected no relapse-associated mutations in common across this patient set; in particular, no mutations were identified in the drug-binding site (ie, "gateway mutation") or in any other related signaling pathway. Based on these results, we conclude there is no common mutational mechanism of IDELA resistance in this patient group. Disclosures Ghia: Gilead: Consultancy, Honoraria, Research Funding, Speakers Bureau; Janssen: Consultancy, Honoraria, Speakers Bureau; Roche: Honoraria, Research Funding; Adaptive: Consultancy; Abbvie: Consultancy, Honoraria. Tausch:Gilead: Other: Travel support, Speakers Bureau; Celgene: Other: Travel support; Amgen: Other: Travel support. Owen:Roche: Honoraria, Research Funding; Pharmacyclics: Research Funding; Celgene: Honoraria, Research Funding; Abbvie: Honoraria; Lundbeck: Honoraria, Research Funding; Novartis: Honoraria; Janssen: Honoraria; Gilead: Honoraria, Research Funding. Barrientos:Gilead: Consultancy, Research Funding; Janssen: Consultancy; AbbVie: Consultancy, Research Funding. Munugalavadla:Gilead Sciences: Employment, Equity Ownership. Degenhardt:Gilead Sciences: Employment, Equity Ownership. Kim:Gilead Sciences: Employment, Equity Ownership. Dubowy:Gilead Sciences: Employment, Equity Ownership. Dreiling:Gilead Sciences: Employment, Equity Ownership. Rosenquist:Gilead Sciences: Speakers Bureau. Stilgenbauer:Hoffmann-La Roche: Consultancy, Honoraria, Other: Travel grants , Research Funding; AbbVie: Consultancy, Honoraria, Other: Travel grants, Research Funding; GSK: Consultancy, Honoraria, Other: Travel grants , Research Funding; Pharmacyclics: Consultancy, Honoraria, Other: Travel grants , Research Funding; Janssen: Consultancy, Honoraria, Other: Travel grants , Research Funding; Mundipharma: Consultancy, Honoraria, Other: Travel grants , Research Funding; Celgene: Consultancy, Honoraria, Other: Travel grants , Research Funding; Amgen: Consultancy, Honoraria, Other: Travel grants, Research Funding; Novartis: Consultancy, Honoraria, Other: Travel grants , Research Funding; Sanofi: Consultancy, Honoraria, Other: Travel grants , Research Funding; Genzyme: Consultancy, Honoraria, Other: Travel grants , Research Funding; Genentech: Consultancy, Honoraria, Other: Travel grants , Research Funding; Gilead: Consultancy, Honoraria, Other: Travel grants , Research Funding; Boehringer Ingelheim: Consultancy, Honoraria, Other: Travel grants , Research Funding.

The Genome of Chronic Lymphocytic Leukemia

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 51-51
Author(s):  
Giulia Fabbri ◽  
Vladimir Trifonov ◽  
Davide Rossi ◽  
Oliver T Elliot ◽  
Joseph M Chan ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Copy Number ◽  
Lymphocytic Leukemia ◽  
Gene Copy ◽  
Additional Patient ◽  
Array Analysis ◽  
Whole Exome ◽  
Copy Number Changes

Abstract Abstract 51 Chronic lymphocytic leukemia (CLL) is a malignancy of CD5+ mature B cells that includes two distinct subtypes marked by the differential presence of immunoglobulin gene mutations and a distinct clinical course. The pathogenesis of CLL is largely unknown: in contrast to other types of B cell malignancies, CLL is not associated with recurrent, balanced chromosomal translocations, nor genes have been found that are specifically targeted by somatic mutations, with the exception of ATM and p53 in 6–12% of cases. Instead, more than 80% of CLL patients carry genomic deletions of chromosomal regions 13q14, 11q22–23, and 17p13, or trisomy 12. Of these, the 13q14.3 deletion, encompassing the DLEU2/miR-15a/miR-16-1 cluster (Calin and Croce, Nat Rev Cancer 2006), has been recently shown to promote the development of CLL in mice (Klein et al., Cancer Cell 2010), suggesting its pathogenetic role in the human disease. To determine the extent of somatic genetic lesions (mutations and gene copy number changes) that are present in the CLL genome, we have integrated next generation whole-exome sequencing analysis (Nimblegen/Roche FLX454) and genome-wide high-density single nucleotide polymorphism array analysis (Affymetrix SNP 6.0) in 5 cases representative of the two CLL immunogenetic subgroups and their paired normal DNAs. Candidate tumor-specific nonsynonymous mutations were verified by Sanger sequencing in the same tumor/normal pairs, and all genes validated as mutated were then screened in an independent panel of 48 CLL DNAs by PCR amplification/direct sequencing of their entire coding region. The whole-exome sequencing approach revealed a total of 36 mutations, corresponding to 36 distinct genes at an average of 7 mutations/case (range, 5–9 mutations/case). The majority of these events were represented by single base pair substitutions (N=34, of which 30 missense mutations and 4 nonsense mutations), while frameshift insertion/deletions were rare (N=2 deletions of 4 and 32 base pairs, respectively; 5.5%). Analysis of the mutation features showed a prevalence of transitions versus transversions (64% vs 36%) and an elevated G+C over A+T ratio (66% vs 44%), analogous to the mutation spectrum observed in the genome of epithelial tumors such as colorectal, pancreatic and brain cancer. SNP array analysis in 4 of the 5 “discovery” cases confirmed the presence of the 13q14 deletion in 2 samples and identified 25 additional regions of copy number changes, corresponding to ∼7 lesions/case (range: 3 to 10) and mostly represented by deletions (N=16/27, ∼60%). When screened in the extended CLL panel, several of the 36 genes identified through the whole exome sequencing approach appeared to be mutated in at least one additional patient. Overall, these data indicate that the coding genome of CLL contains on average ∼14 somatic gene alterations per case. When classified based on functional annotation, most of these lesions appeared to converge on discrete signaling pathways, which likely represent important pathogenetic and possibly therapeutic targets in CLL. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Genomic Landscape of Chinese Patients with Chronic Lymphocytic Leukemia By Whole-Exome Sequencing

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 2784-2784
Author(s):  
Yi Miao ◽  
Yi Xia ◽  
Chun Qiao ◽  
Huayuan Zhu ◽  
Jiazhu Wu ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Somatic Mutations ◽  
Median Number ◽  
Lymphocytic Leukemia ◽  
Chinese Patients ◽  
Western Countries ◽  
Whole Exome ◽  
Genomic Landscape

Introduction: Through previous studies using Sanger sequencing and targeted gene sequencing, we found that the frequencies of certain genes in Chinese patients with chronic lymphocytic leukemia (CLL) were different from those in CLL patients from the western countries. However, until now, there are no published whole-exome sequencing (WES) studies in Chinese CLL patients. To better define the genomic landscape of CLL cases in China, we conducted WES studies of CLL cases in our center. Methods: This study include 43 CLL patients, of whom 40 were untreated at the time of sampling. The median age of the 43 patients were 61 years, the male-to-female ratio was 2:1. We isolated peripheral blood mononuclear cells, then CD19 positive cells were purified by using magnetic microbeads in some cases. The buccal cells or the leukocytes that were depleted of CD19 positive cells were used as germline controls. We purified genomic DNA and used the purified DNA for library construction, after which we sequenced the library using the Illumina HiSeq2500 platform. After sequencing, software including Burrows-Wheeler Aligner (BWA) and GATK were used for the bioinformatic analysis. Results: In the 43 Chinese patients with CLL, the median number of somatic mutations was 67 (range:10-128) and the median number of nonsynonymous mutations was 26 (range: 5-55). We found that the number of mutations in patients older than 60 was significantly higher than that in the younger patients. Somatic mutations were detected across 991 different genes, of which 24 genes were identified as drivers in the study from the Dana-Faber Cancer Institute (DFCI). The 24 genes included NOTCH1, SF3B1, MYD88, POT1, TP53 and so on. Seventy-nine genes were recurrently mutated and 13 genes were found to be mutated in 3 or more cases. The most frequently mutated gene was NOCTH1 (6 cases, 14.0%). FBXW7, another gene that is involved in the regulation of the NOTCH1 pathway, was also mutated in 3 cases. IGLL5, MUC4 and MYD88 were also among the most frequently mutated genes, with each of them being mutated in 5 cases (11.6%). We found that the frequencies of mutations in IGLL5 (11.6% vs. 2.2%, P=0.0056), MYD88 (11.6% vs. 3.0%, P=0.0147), BCOR (9.3% vs. 2.2%, P=0.0246), and SF3B1 (4.7% vs. 21.0%, P=0.0084) were significantly different between Chinese CLL patients and patients from western countries. BCOR-mutated patients had more frequent aberrations involving NOTCH1 pathway (NOTCH1 and/or FBXW7 mutation) than BCOR-unmutated patients (3/4 [75.0%] vs. 6/39 [15.4%], P=0.0242) (Figure 1A). Analysis of 10967 tumor samples from the Cancer Genome Atlas (TCGA) program revealed that tumors with BCOR mutations had a higher frequency of NOTCH1 aberrations (NOTCH1 and/or FBXW7 mutation) than those without BCOR mutations (116/349 [33.2%] vs. 722/10618 [6.8%]; odds ratio: 6.824, 95%CI: 5.393-8.634, P<0.0001) (Figure 1B). These data suggest BCOR mutations and NOTCH1 aberration may cooperate in the pathogenesis of CLL and other types of tumors. NFKBIA mutations were identified in 2 cases (Figure 1C) and we found that the mRNA level of NFKBIA was significantly lower in the NFKBIA mutated CLL cells than in the normal B cells (Figure 1D-E); in the MEC-1 cell line, significant activation of NF-кB pathway was observed after knockdown of NFKBIA using siRNA (Figure 1F). Conclusion: Patients with CLL in China and patients with CLL in the western countries have different mutational landscapes. BCOR gene mutations may cooperate with aberrations involving the NOTCH1 pathway in the pathogenesis of CLL. NFKBIA could be a potential tumor suppressor in the pathogenesis of CLL. Figure 1 Disclosures No relevant conflicts of interest to declare.

scholarly journals Association of polygenic risk score with the risk of chronic lymphocytic leukemia and monoclonal B-cell lymphocytosis

Blood ◽  
2018 ◽  
Vol 131 (23) ◽  
pp. 2541-2551 ◽  
Author(s):  
Geffen Kleinstern ◽  
Nicola J. Camp ◽  
Lynn R. Goldin ◽  
Celine M. Vachon ◽  
Claire M. Vajdic ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
B Cell ◽  
Risk Score ◽  
Clinical Impact ◽  
Lymphocytic Leukemia ◽  
Polygenic Risk Score ◽  
Polygenic Risk ◽  
Key Points ◽  
High Discrimination

Key Points PRS, based on the known CLL loci, predicts CLL risk with high discrimination. This PRS predicts risk of monoclonal B-cell lymphocytosis, a precursor to CLL and a condition that has clinical impact beyond risk for CLL.

Abstract 756: Whole exome sequencing identifies frequent mutations of PTPRB and KDR in secondary angiosarcoma

2019 ◽  
Author(s):  
Tenzin Gayden ◽  
Brendan C. Dickson ◽  
Hamid Nikbakht ◽  
Pierre-Olivier Fiset ◽  
Nicolas De Jay ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome ◽  
Frequent Mutations ◽  
Secondary Angiosarcoma

Somatic activating ARAF mutations in Langerhans cell histiocytosis

Blood ◽  
2014 ◽  
Vol 123 (20) ◽  
pp. 3152-3155 ◽  
Author(s):  
David S. Nelson ◽  
Willemijn Quispel ◽  
Gayane Badalian-Very ◽  
Astrid G. S. van Halteren ◽  
Cor van den Bos ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Langerhans Cell Histiocytosis ◽  
Langerhans Cell ◽  
Braf V600e ◽  
Novel Mutations ◽  
Whole Exome ◽  
Key Points ◽  
Inhibitor Treatment

Key Points Whole exome sequencing reveals novel mutations in ARAF that activate the kinase and are inhibitable by vemurafenib in a patient with LCH. Requiring the presence of BRAF V600E in LCH to qualify for rat fibrosarcoma inhibitor treatment may be overly exclusionary.

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