scholarly journals A Comparison Among ARIMA, BP-NN, and MOGA-NN for Software Clone Evolution Prediction

IEEE Access ◽  
2017 ◽  
Vol 5 ◽  
pp. 11841-11851 ◽  
Author(s):  
Jayadeep Pati ◽  
Babloo Kumar ◽  
Devesh Manjhi ◽  
K K Shukla
Keyword(s):  
2010 ◽  
Vol 25 (2) ◽  
pp. 165-192 ◽  
Author(s):  
Nils Göde ◽  
Rainer Koschke

2017 ◽  
Vol 26 (6) ◽  
pp. 1132-1138
Author(s):  
Fanlong Zhang ◽  
Siau-Cheng Khoo ◽  
Xiaohong Su

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yi Fang ◽  
Jian Hou

AbstractMultiple myeloma (MM) is the second most common hematologic malignancy, and is characterized by the clonal expansion of malignant plasma cells. Despite the recent improvement in patient outcome due to the use of novel therapeutic agents and stem cell transplantation, all patients eventually relapse due to clone evolution. B cell maturation antigen (BCMA) is highly expressed in and specific for MM cells, and has been implicated in the pathogenesis as well as treatment development for MM. In this review, we will summarize representative anti-BCMA immune therapeutic strategies, including BCMA-targeted vaccines, anti-BCMA antibodies and BCMA-targeted CAR cells. Combination of different immunotherapeutic strategies of targeting BCMA, multi-target immune therapeutic strategies, and adding immune modulatory agents to normalize anti-MM immune system in minimal residual disease (MRD) negative patients, will also be discussed.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 5021-5021
Author(s):  
Evangelia M. Dimitriadou ◽  
Panayiotis Panayiotidis ◽  
Vasiliki Karali ◽  
Konstantinos Lilakos ◽  
Maria K. Angelopoulou ◽  
...  

Abstract It has recently been demonstrated that a considerable subset of CLL patients (>50%) displays intraclonal diversification in their monoclonal Ig sequence, suggesting that the mechanism of ongoing somatic mutations is retained in a significant proportion of B CLL cells. The complexity of studying this phenomenon relies on the enclaved risk of misinterpreting superimposed mutations originating from experimental artifacts. We are still lacking a more detailed picture of inraclonal diversification regarding its frequency and developmental pattern in disease compartments other than blood. In order to clarify some of these questions, we analyzed a total of 675 Ig clones from 11 CLL patients. DNA was extracted from blood in 6 patients (1st group: pt.1 to 6) or from blood/marrow (BM)/lymph nodes (LN) obtained at the same in 5 patients (2nd group: pt.7-11). PCR was performed for 40 cycles with Taq Platinum polymerase and leader or FR1 VH1-6 primers and a consensus JH primer. Monoclonal PCR products were ligated to TA vector and 20 to 70 clones were sequenced. from both orientations. Polymerase mediated base error was 4.4x10−4 after 40 PCR cycles. Base differences observed in two or more clones out of 20, were verified twice and assigned as true intraclonal diversification. This was observed in 6 (pt 2, 6, 7, 9, 10, 11) out of 11 pts (54.5%). Pts 2, 6, 10, 11 were mutated and pt. 7, 9 unmutated in their Ig sequence. Intraclonal diversification was observed in pt. 2 and 6, whereas pt.7, 9, 10, 11 in the 2nd group, displayed intraclonal diversification in some or in all compartments. Base point mutations that were unique in one clone only were observed at the polymerase mediated error rate and were not verified by a second idependent experiment. In the 2nd group pt. 8 displayed lack of diversification both in blood and marrow. Pt.7 displayed diversification only in BM clones (2/64, 3.1%) but not in 71 blood derived or in 53 LN derived clones. Pt. 9 had diversified clones in blood only (2/26, 7.6%) and no diversified clones in 25 BM clones. Pt.10 had diversified clones both in blood and marrow with a distinct pattern: in blood (62 clones) 4 different patterns of diversification were observed in 54 clones (84%); 17/54 were evolving clones. In BM two of the 4 patterns of diversification present in blood were observed in 28/57 clones (51.7%); ten were evolving clones. In pt.11, no diversified clones were present in blood (50 clones) whereas marrow had 4/60 diversified clones (6,66%, two patterns of diversification) and LN had 20/40 diversified clones (50%, two patterns of diversification); 8/20 diversified were evolving clones. The patterns of diversification were different bettween LN and BM in this patient. Base changes in 110 diversified clones were in FRs rather than CDRs (16:1) and resulted in S(silent) rather than R(replacements), S/R 2:1. In conclusion, intraclonal diversification must be considered true if identical base substitutions are observed in minimum two clones. Pattern and frequency are not identical in B CLL cells from different sites (blood vs BM vs LN). Preferance of FRs v CDRs and SvR substitutions implies that diversification procces is not antigen driven. The presence of a functional mechanism of ongoing somatic mutations in leukemic clones and the ability of diversification to target with altered frequency/patterns various disease compartments implies a role of tissue millieu in CLL clone evolution.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4458-4458
Author(s):  
Vassilios Papadakis ◽  
Stefanos Papadhimitriou ◽  
Anna Paisiou ◽  
Chrysoula Belesi ◽  
Agapi Parcharidou ◽  
...  

Abstract T-ALL has increasing incidence during adolescence and it is rarely associated with Philadelphia chromosome positivity. Moreover, extremely rare is the event of Philadelphia chromosome negativity at diagnosis and leukemia clone evolution with t(9;22) at relapse. Such a patient is being described and relevant issues are being raised. A 14 year old boy was diagnosed with leukemia due to malaise and ecchymoses. CBC revealed: WBC 170 k/uL (80% blasts), Hb 13.1 gr/dL, Ht 37.7% and PLT of 26 k/uL. Bone marrow confirmed the diagnosis of ALL (L2 morphology). Bone marrow flow cytometry depicted a T II ALL by EGIL classification (Tdt 54%, cCD3 99%, CD7 96%, CD2 96%, CD4 0%, CD8 2%, CD5 75%, TCRαβ 0%, CD1α 0%, sCD3 31%). Karyotype with G-banding, technically failed. By PCR, blasts were negative for TEL-AML1, E2A-PBXand MLL-AF4 while RNA coding for proteins p190 and p210 was also negative. Additionally, the 9 chromosome was evaluated by FISH technique (centromere and 9p21 areas/genes p16/p14 and p15- Vysis) and an homozygous deletion of 9p16 area was detected in the great majority of the blasts tested. The patient was treated according to the ALL-BFM-95 protocol and proved to be a poor prednisone responder, with residual disease detected on day +15 bone marrow and remission on day +33. He proceeded to the High Risk arm of the protocol. Thirteen months from diagnosis and 5 months on maintenance treatment, the patient suffered a bone marrow relapse. CBC revealed: WBC 30 k/uL (25% blasts), Hb 13.8 gr/dL, Ht 40.9 % and PLT of 201 k/uL. Bone marrow confirmed the relapse (L2 blast morphology) with a more mature T-cell type (cCD/TdT coexpression, with CD3 87% and TCRαβ 53.3% expression). Five of 25 metaphases revealed the following complex karyotype: 46,XY,del(6)(q21),?del(7)(q36), -9, t(9;22)(q34;q11),+mar1. By FISH , monosomy of 9 chromosome was not proved , while homozygous deletion of 9p16 area was again documented and t(9;22) was clearly evident. By PCR, there was no detection of RNA coding for proteins p190 and p210 with standard commercially available probes. The patient is treated with a fludarabine based regimen and imatinib, with the prospective of stem cell transplantation. In conclusion, at diagnosis, T-ALL without t(9;22) but with an homozygous deletion of chromosome 9, was documented. At relapse, there is clone evolution with a more mature T-origin blast detection of a complex karyotype with t(9;22). Ph+ T-ALL is rare, as well as rare is the event of ALL clone evolution, with emergence of Ph+ at relapse. This patient’s data are being completed and there is prospective of further illuminating the underlying pathogenesis. Chromosome 9 deletions are under investigation for contributing in genetic instability. Homozygous 9p16 deletion of ALL blasts at diagnosis and relapse might play a key role in these events.


2021 ◽  
Author(s):  
Lin Wang ◽  
Xinmiao Wang ◽  
Yulin Jia ◽  
Fengyuan Guo ◽  
Shang Zhengjun ◽  
...  

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 11032-11032 ◽  
Author(s):  
Di Wang ◽  
Jie Wang ◽  
Xiaohui Niu ◽  
Zhen Huang ◽  
Zhijie Wang ◽  
...  

11032 Background: Lung metastasis (LM), as the most common metastatic site, is the main reason resulting in treatment failure and death of osteosarcoma (OS). But there was no report about the clone evolution and genomic alteration in the process of LM of OS. Methods: Multiregion whole-genome sequencing and whole-exome sequencing were performed on ten patients with primary OS and matched lung metastatic tumors. A set of high confident somatic nucleotide variants (SNV), small insertion and deletion (indel) and copy number variation (CNV) in each sample were identified, then the n-dimensional Bayesian Dirichlet process was applied to define the constituent mutation clusters as clone or subclone. Neoantigen prediction and HLA typing were performed using NetMHC3.0 and POLYSOLVER algorithm, respectively. Results: There were diversified metastatic progression during lung metastasis of OS including linear evolution (7/10) and parallel evolution (3/10), and metastasis-to-metastasis spread was also found in a patient with multiple metastasis; Mutation accumulative effect during the metastasis of OS was evident, LM had much higher mutation load (fold change = 4.1, P-value < 0.01) and neoantigen burden (fold change = 4.5, P-value < 0.001) than the primary tumor; DNA mismatch repair (MMR) genes relevant deleterious mutation events were found in germline in 8/10 metastatic OS cases and MMR genes mutation were much more in LM than primary cancer; The genome instability of LM was prevalently much more significant than primary tumor, with higher copy number variation frequency (fold change = 7.01, P-value < 0.01). Conclusions: The evolution of OS during LM was very complex with diversified metastatic progression. For the LM of OS, the novel therapy should be considering the much higher mutation load, especially those causing tumor neoantigens, higher genomic instability which were associated with tumor immune therapy. Furthermore, the findings of germline MMR genes mutation in primary OS which had occurred LM and more MMR genes mutation in LM of OS indicated potential clinical benefit on immune checkpoint inhibitor therapy and other small molecular drugs for MMR genes.


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