scholarly journals Sensitive Monitoring of BCR-ABL1 Kinase Domain Mutations By Next Generation Sequencing for Optimizing Clinical Decisions in Philadelphia-Positive Acute Lymphoblastic Leukemia in the Graaph-2014 Trial

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1295-1295 ◽  
Author(s):  
Jean-Michel Cayuela ◽  
Francois Lay ◽  
Yves Chalandon ◽  
Philippe Rousselot ◽  
Xavier Thomas ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Acute Lymphoblastic Leukemia ◽  
Limit Of Detection ◽  
Lymphoblastic Leukemia ◽  
Intensive Therapy ◽  
Kinase Domain ◽  
Rapid Expansion ◽  
Next Generation ◽  
Low Level ◽  
Generation Sequencing

A high proportion of Ph-positive Acute Lymphoblastic Leukemia (Ph+ ALL) patients still undergo relapses despite the use of Tyrosine Kinase Inhibitors (TKIs) in addition to chemotherapy as frontline therapy. In this leukemia subtype, the role of BCR-ABL1 kinase domain (KD) mutations as a driver of resistance to TKIs has already been documented by previous studies and such mutations have been reported in up to 80% of the patients at relapse. Next-generation sequencing (NGS) has been proposed to characterize these mutations with a higher sensitivity than Sanger. We report here a prospective study aiming at detecting potentially resistant cell populations by NGS in Ph+ ALL patients enrolled in the GRAAPH 2014-trial. Between March 2016 and February 2019, 156 patients aged 18 to 59 years with newly diagnosed Ph+ and/or BCR-ABL1 positive ALL have been included in the GRAAPH 2014 trial (NCT02619630). BCR-ABL1 isoforms were E1A2 69%, B2A2/B3A2 29%, atypical 2%. After a prephase of steroid, treatment consisted of 4 blocks of chemotherapy + nilotinib. 118 patients (76%) underwent allogeneic or autologous stem cell transplantation (SCT). 22 medullary relapses were recorded within a median time of 9 months (range, 2 - 35). Blood and marrow samples harvested at diagnosis, after each treatment block, before and 3 months after SCT, and at relapse, were sequenced if BCR-ABL1/ABL1 ratio were above 0.001. Mutated BCR-ABL1 transcripts were detected by sequencing the KD of BCR-ABL1 transcripts by NGS with a limit of detection (LOD) of 0.03. T315I allele specific oligonucleotide (ASO) droplet digital RT-PCR (ddRT-PCR) with a LOD of 0.0005 was also performed at diagnosis on a subset of 63 patients, including 5 who have subsequently developed a T315I clone. NGS. At diagnosis, no KD mutation was found by NGS in pretreatment samples of 137 patients. During follow-up (FU), only 12 mutations were found by NGS in 7 out of the 88 patients tested (81, 45, 30, 20, 19, 9 after block 1, 2, 3, 4, before and 3 months after SCT, respectively). Mutations were T315I (N=6), Y253H (N=1), E255K (N=2), E255V (N=1), Q252H (N=1), Y253F (N=1). At relapse, 16 mutations were identified by NGS in 12 patients out of the 17 tested (71%). Mutations were T315I (N=7), Y253H (N=n=3), F359V (N=2), E255K (N=1), E255V (N=1), Q252H (N=1), Y253F (N=1). More than 1 mutated clone were present in 2 patients (E255V+T315I+F359V and Y253H+F359V), and a compound mutation was found in 1 patient (Q252H/Y253F). Out of the 7 patients found mutated during FU, 5 have relapsed with a rapid expansion (1 to 3 months) of the mutated clone. One patient harboring a sub-clonal (10%) E255K at MRD1 has relapsed 9 months later without any detectable mutation. One patient identified with 3 mutated clones (E255K 10%, E255V 10%, T315I 80%) underwent SCT and has not relapsed so far. We failed to anticipate expansion of any mutated clone in the 7 remaining patients found mutated at relapse. T315I ASO ddRT-PCR on diagnostic samples. Low-level T315I mutated BCR-ABL1 transcripts (0.00051 to 0.0013) were detected in 14 out of 63 patients (24%) tested. Only one has expanded a T315I clone later on. In the context of the GRAAPH 2014 trial, 71% of the 17 relapses tested so far were associated with BCR-ABL1 KD mutations. Expansion of the mutated clone could have been characterized before the onset of hematological relapses in only 5 out of 12 patients (42%). Unfortunately in these cases, lags between first detection and relapse were very short (1 to 3 months). On the contrary, occurrences of relapses associated with expansion of KD-mutated clones could not have been anticipated in 58%. All mutations identified, including T315I, F359V, E255K/V and Y253F/H, Q252H/Y253F are known for conferring resistance to nilotinib. NGS is a valuable method for KD mutation detection in Ph+ ALL. It allows a quantitative characterization of KD mutations at relapse. However in our hands and in the context of an intensive therapy combining chemotherapy, nilotinib and SCT, its enhanced sensitivity as compared to Sanger (3% vs 20%) does not translate into the capacity of anticipating expansion of KD-mutated clones. Moreover, in this study, NGS did not detect any mutation in pre-therapeutic samples while T315I mutated BCR-ABL1 transcripts were found at low-level in 24% of these samples by ddRT-PCR. However it should be emphasized that when detected, low-level T315I mutated sub-clones present at diagnosis failed to expand in most instances. Disclosures Cayuela: Incyte: Honoraria, Speakers Bureau; Novartis: Consultancy, Honoraria, Speakers Bureau. Chalandon:Pfizer: Consultancy, Honoraria; Bristol-Myers Squibb: Consultancy, Honoraria; Incyte Biosciences: Consultancy, Honoraria; Novartis: Consultancy, Honoraria. Rousselot:Pfizer: Research Funding. Thomas:PFIZER: Honoraria; ABBVIE: Honoraria; INCYTE: Honoraria; DAICHI: Honoraria. Huguet:Amgen: Honoraria; Servier: Honoraria; Jazz Pharmaceuticals: Honoraria; BMS: Honoraria; Pfizer: Honoraria; Incyte Biosciences: Honoraria; Novartis: Honoraria. Chevallier:Incyte: Consultancy, Honoraria; Jazz Pharmaceuticals: Honoraria; Daiichi Sankyo: Honoraria. Boissel:NOVARTIS: Consultancy. Vey:Novartis: Consultancy, Honoraria; Janssen: Honoraria. Berthon:PFIZER: Other: DISCLOSURE BOARD; JAZZPHARMACEUTICAL: Other: DISCLOSURE BOARD; CELGEN: Other: DISCLOSURE BOARD.

scholarly journals Next-Generation Sequencing in Acute Lymphoblastic Leukemia

2019 ◽  
Vol 20 (12) ◽  
pp. 2929 ◽  
Author(s):  
Nicoletta Coccaro ◽  
Luisa Anelli ◽  
Antonella Zagaria ◽  
Giorgina Specchia ◽  
Francesco Albano
Keyword(s):  
Next Generation Sequencing ◽  
Acute Lymphoblastic Leukemia ◽  
Residual Disease ◽  
Age Of Onset ◽  
Lymphoblastic Leukemia ◽  
Genomic Analysis ◽  
Next Generation ◽  
Acute Leukemias ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and accounts for about a quarter of adult acute leukemias, and features different outcomes depending on the age of onset. Improvements in ALL genomic analysis achieved thanks to the implementation of next-generation sequencing (NGS) have led to the recent discovery of several novel molecular entities and to a deeper understanding of the existing ones. The purpose of our review is to report the most recent discoveries obtained by NGS studies for ALL diagnosis, risk stratification, and treatment planning. We also report the first efforts at NGS use for minimal residual disease (MRD) assessment, and early studies on the application of third generation sequencing in cancer research. Lastly, we consider the need for the integration of NGS analyses in clinical practice for genomic patients profiling from the personalized medicine perspective.

scholarly journals Next-Generation Sequencing in Adult B Cell Acute Lymphoblastic Leukemia Patients

2017 ◽  
Vol 23 (4) ◽  
pp. 691-696 ◽  
Author(s):  
Olga Sala Torra ◽  
Megan Othus ◽  
David W. Williamson ◽  
Brent Wood ◽  
Ilan Kirsch ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Acute Lymphoblastic Leukemia ◽  
B Cell ◽  
Lymphoblastic Leukemia ◽  
Next Generation ◽  
Cell Acute Lymphoblastic Leukemia ◽  
Generation Sequencing

Next-Generation Sequencing Of The BCR-ABL1 Kinase Domain May Be Beneficial In Decision Making Among Chronic Myeloid Leukemia Patients With Tyrosine Kinase Inhibitor Resistance

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 384-384 ◽  
Author(s):  
Yucel Erbilgin ◽  
Ahmet Emre Eskazan ◽  
Ozden Hatirnaz Ng ◽  
Ayse Salihoglu ◽  
Tugrul Elverdi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Myeloid Leukemia ◽  
Kinase Inhibitor ◽  
Kinase Domain ◽  
Next Generation ◽  
Time Points ◽  
Low Level ◽  
Development Of Resistance ◽  
Tki Resistance ◽  
Generation Sequencing

Abstract Background and Aim BCR-ABL1 mutation testing is recommended for chronic myeloid leukemia (CML) patients who have suboptimal response and/or treatment failure with tyrosine kinase inhibitor (TKI) therapy. BCR-ABL1 mutations in the kinase domain (KD) of ABL1 account for at least 40-50% of all TKI resistant cases. Thus, detection of low-level mutations after development of resistance may offer critical information to guide subsequent therapy selection. The current gold standard for BCR-ABL1 mutation detection is Sanger sequencing (SS), which has an analytical sensitivity of approximately 10-20%. In this study, our aim was to detect low level BCR-ABL1 variants in follow up samples of CML patients with TKI resistance using next-generation sequencing (NGS) approach. Methods Eight patients with CML who were resistant to imatinib had been routinely sequenced with SS for BCR-ABL1 KD mutations between December 2009 and December 2012. We then retrospectively analyzed these samples with NGS. RT and long range PCR was performed to amplify BCR-ABL1 fusion transcripts and the PCR products sequenced bidirectional after library preparation. We performed a fusion transcript based BCR-ABL1 mutation assay using Roche 454 amplicon deep-sequencing technology that is suited for detecting low level variants in pooled amplicon samples. Sequencing data was analyzed with GS Amplicon Variant Analyzer (AVA) software, and the variant frequency cut-off was adjusted to 1%. Results Clinical features, sequencing results, and the outcomes of the patients were summarized in Table 1. Four patients were male, and the median age was 37 years (range, 20-60 years). The patients were all in chronic phase at the time of the diagnosis. After imatinib resistance, 4 patients had received dasatinib (DAS), and 2 were given nilotinib (NIL) as second line TKI treatment. The remaining two patients had both received DAS and NIL (Table 1). In a set of 20 clinical samples, at different time points, NGS not only identified all the mutations detected by SS, but additionally identified low level variants present between 1 – 28.12 %. T315I and E255K/V were the most common mutations, which were detected in four patients, both by SS and NGS at the same time points (Table 1). Two patients (patient #1 and #4) had T315I, and they both progressed to blastic phase and died. E255K was detected in patients #2 and #3, and patient #2 had achieved and maintained complete cytogenetic and major molecular responses with 100 mg daily DAS, whereas patient #3 had received both NIL and DAS, but she was deceased due to myeloid blastic crisis. Among 4 patients (patients #5, #6, #7, and #8), mutation analysis was performed at eleven different time points, and these patients were wild-type with SS. We also did not detect any clinically significant mutations in these patients by NGS. Most probably mechanisms other than KD mutations were responsible for the TKI resistance among these four patients. Conclusions Polyclonal mutations in BCR-ABL1 KD are commonly identified in TKI resistant patients. Thus, detection of low-level mutations after development of resistance offers critical information to guide subsequent therapy selection. An inappropriate kinase inhibitor selection could highly increase the risk of treatment failure with clonal expansion of the resistant mutant. In our imatinib resistant cohort, we detected low level variants accompany to known mutations which may constitute background genetic variations. Although we had expected to detect mutations earlier by NGS (i.e. before these mutations can be detected by SS), we did not observe such finding in our patients. The patients' samples may not show a stable mutation spectrum between time points. Hence, it is not always possible to spot a mutation before patients show resistance to therapy. Regular NGS analysis might detect these mutations in earlier phases, which might help clinicians to choose the most suitable individual treatment modality for the patients. Acknowledgment The authors would like to thank the Interlaboratory Robustness of Next-generation sequencing (IRON) Phase II study group members, especially to Simona Soverini and Alexander Kohlmann who designed BCR-ABL primers and plates. We also would like to thank the Research Fund of the Istanbul University (Project no. 24244) and Turkish Society of Hematology for supporting the study. Disclosures: Sayitoglu: Roche Diagnostics: Research Support Other.

scholarly journals Capture-Based Next-Generation Sequencing Improves the Identification of Immunoglobulin/T-Cell Receptor Clonal Markers and Gene Mutations in Adult Acute Lymphoblastic Leukemia Patients Lacking Molecular Probes

Cancers ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1505
Author(s):  
Roberta Cavagna ◽  
Marie L. Guinea Montalvo ◽  
Manuela Tosi ◽  
Michela Paris ◽  
Chiara Pavoni ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Acute Lymphoblastic Leukemia ◽  
T Cell ◽  
T Cell Receptor ◽  
Lymphoblastic Leukemia ◽  
Cell Receptor ◽  
Molecular Probes ◽  
Next Generation ◽  
Mutational Status ◽  
Generation Sequencing

The monitoring of minimal residual disease (MRD) in Philadelphia-negative acute lymphoblastic leukemia (ALL) requires the identification at diagnosis of immunoglobulin/T-cell receptor (Ig/TCR) rearrangements as clonality markers. Aiming to simplify and possibly improve the patients’ initial screening, we designed a capture-based next-generation sequencing (NGS) panel combining the Ig/TCR rearrangement detection with the profiling of relevant leukemia-related genes. The validation of the assay on well-characterized samples allowed us to identify all the known Ig/TCR rearrangements as well as additional clonalities, including rare rearrangements characterized by uncommon combinations of variable, diversity, and joining (V-D-J) gene segments, oligoclonal rearrangements, and low represented clones. Upon validation, the capture NGS approach allowed us to identify Ig/TCR clonal markers in 87% of a retrospective cohort (MRD-unknown within the Northern Italy Leukemia Group (NILG)-ALL 09/00 clinical trial) and in 83% of newly-diagnosed ALL cases in which conventional method failed, thus proving its prospective applicability. Finally, we identified gene variants in 94.7% of patients analyzed for mutational status with the same implemented capture assay. The prospective application of this technology could simplify clonality assessment and improve standard assay development for leukemia monitoring, as well as provide information about the mutational status of selected leukemia-related genes, potentially representing new prognostic elements, MRD markers, and targets for specific therapies.

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