Detection of kinase domain mutations in BCR::ABL1 leukemia by ultra-deep sequencing of genomic DNA

Sánchez, Ricardo; Dorado, Sara; Ruíz-Heredia, Yanira; Martín-Muñoz, Alejandro; Rosa-Rosa, Juan Manuel; Ribera, Jordi; García, Olga; Jiménez‐Ubieto, Ana; Carreño‐Tarragona, Gonzalo; Linares, María José Pedraja; Rufian, Laura; Juarez, Alexandra; Carrillo, Jaime; Espino, María José; Cáceres, Mercedes; Exposito, Sara; Cuevas, Beatriz; Vanegas, Raúl; Casado, Luis Felipe; Torrent, Anna; Zamora, Lurdes; Mercadal, Santiago; Coll, Rosa; Cervera, Marta; Hernández‐Rivas, José Ángel; Bravo, Pilar; Serí, Cristina; Anguita, Eduardo; Barragán, Eva; Sargas, Claudia; Ferrer‐Marín, Francisca; Sánchez-Calero, Jorge; Sevilla, Julián; Ruiz, Elena María Villamor; Villalón, Lucı́a; Herráez, María del Mar; Riaza, Rosalía; Magro, Elena; Steegman, J.L.; Wang, Chongwu; Toledo, Paula de; García‐Gutiérrez, Valentín; Ayala, Rosa; Ribera, Josep‐María; Barrio, Santiago; Martínez‐López, Joaquin

doi:10.1038/s41598-022-17271-3

Cited by 7 publications

(4 citation statements)

References 33 publications

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“…The resulting libraries included three biological replicates per biomarker. They were sequenced on the Ion S5 System platform (Life Technologies, Thermo Fisher Scientific) with an estimated depth of 500,000× per amplicon, as previously described ( 24 , 29 , 30 ). The LiqBio-MRD test demonstrated a potential VAF sensibility below 10 −4 ( 24 ).…”

Section: Materials/subjects and Methodsmentioning

confidence: 99%

Personalized monitoring of circulating tumor DNA with a specific signature of trackable mutations after chimeric antigen receptor T-cell therapy in follicular lymphoma patients

et al. 2023

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BackgroundCART therapy has produced a paradigm shift in the treatment of relapsing FL patients. Strategies to optimize disease surveillance after these therapies are increasingly necessary. This study explores the potential value of ctDNA monitoring with an innovative signature of personalized trackable mutations.MethodEleven FL patients treated with anti-CD19 CAR T-cell therapy were included. One did not respond and was excluded. Genomic profiling was performed before starting lymphodepleting chemotherapy to identify somatic mutations suitable for LiqBio-MRD monitoring. The dynamics of the baseline mutations (4.5 per patient) were further analyzed on 59 cfDNA follow-up samples. PET/CT examinations were performed on days +90, +180, +365, and every six months until disease progression or death.ResultsAfter a median follow-up of 36 months, all patients achieved a CR as the best response. Two patients progressed. The most frequently mutated genes were CREBBP, KMT2D and EP300. Simultaneous analysis of ctDNA and PET/CT was available for 18 time-points. When PET/CT was positive, two out of four ctDNA samples were LiqBio-MRD negative. These two negative samples corresponded to women with a unique mesenteric mass in two evaluations and never relapsed. Meanwhile, 14 PET/CT negative images were mutation-free based on our LiqBio-MRD analysis (100%). None of the patients had a negative LiqBio-MRD test by day +7. Interestingly, all durably responding patients had undetectable ctDNA at or around three months after infusion. Two patients presented discordant results by PET/CT and ctDNA levels. No progression was confirmed in these cases. All the progressing patients were LiqBio-MRD positive before progression.ConclusionThis is a proof-of-principle for using ctDNA to monitor response to CAR T-cell therapy in FL. Our results confirm that a non-invasive liquid biopsy MRD analysis may correlate with response and could be used to monitor response. Harmonized definitions of ctDNA molecular response and pinpointing the optimal timing for assessing ctDNA responses are necessary for this setting. If using ctDNA analysis, we suggest restricting follow-up PET/CT in CR patients to a clinical suspicion of relapse, to avoid false-positive results.

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Section: Materials/subjects and Methodsmentioning

confidence: 99%

Personalized monitoring of circulating tumor DNA with a specific signature of trackable mutations after chimeric antigen receptor T-cell therapy in follicular lymphoma patients

et al. 2023

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“…Though there are many good myeloid panels available on the market from Thermofisher, Qiagen, Illumina, Archer, etc., they are not enriching the transcript P210 or P190 before sequencing. A recent study that used a DNA-based method to detect kinase domain mutations found that the method had a 92% sensitivity and an 81.6% specificity 49 . The use of DNA as a starting material may have contributed to a decrease in the assay's specificity.…”

Section: Discussionmentioning

confidence: 99%

Validation of a novel NGS based BCR::ABL1 kinase domain mutation detection assay in Indian cohort

Chaudhary,

Patel

et al. 2024

Sci Rep

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The efficacy and treatment outcome of a CML patient are heavily dependent on BCR::ABL1 kinase domain (KD) mutation status. Next-generation sequencing technology is a bright alternative to the previously used sanger sequencing method due to its global presence in diagnostic setups, massive parallel sequencing ability, and far better sensitivity. In the present study, we have demonstrated a new protocol for kinase domain mutation analysis using the next-generation sequencing (NGS) method using the ion torrent sequencing platform. This protocol uses RNA as the starting material, followed by nested PCR to amplify the fusion transcript, which is subsequently used as a template for NGS. Initial validation and comparison of this assay with the sanger sequencing (SS) method yielded 95.23% agreement. CML samples (n = 121) with a failure to TKI response were subjected to this newly developed NGS-based assay to detect KD mutations, from which samples were found to have mutations with a sensitivity ranging from 2.32 to 93.41%. A total of 34.71% of samples (n = 42) were found to be positive for one or more KD mutations, whereas 65.29% of samples (n = 81) were found to be negative. Nine samples out of 42 positive samples, i.e., 21.42%, were found to have compound mutations. This is one of the first studies from India, which includes more than 160 samples and is analyzed by the NGS approach for KD mutation analysis.

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“…In contrast by using DNA both ABL1 and BCR::ABL1 alleles would be sequenced—which would usually result in an inferior LoD because the number of BCR::ABL1 alleles (present only in leukemic cells) are far fewer than the number of ABL1 alleles (present in both leukemic and normal cells). Use of high sensitivity techniques like error-corrected NGS or digital PCR might theoretically enable this issue to be circumvented [ 144 ], and indeed the utility of DNA-based targeted dPCR for T315I has been described in patients with advanced disease [ 145 ], but a systematic comparison would be needed before generally endorsing DNA-based strategies.…”

Section: Bcr::abl1 Mutations and Mechanisms Of Resistance To Tkismentioning

confidence: 99%

European LeukemiaNet laboratory recommendations for the diagnosis and management of chronic myeloid leukemia

Cross,

Ernst,

Branford

et al. 2023

Leukemia

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From the laboratory perspective, effective management of patients with chronic myeloid leukemia (CML) requires accurate diagnosis, assessment of prognostic markers, sequential assessment of levels of residual disease and investigation of possible reasons for resistance, relapse or progression. Our scientific and clinical knowledge underpinning these requirements continues to evolve, as do laboratory methods and technologies. The European LeukemiaNet convened an expert panel to critically consider the current status of genetic laboratory approaches to help diagnose and manage CML patients. Our recommendations focus on current best practice and highlight the strengths and pitfalls of commonly used laboratory tests.

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Detection of kinase domain mutations in BCR::ABL1 leukemia by ultra-deep sequencing of genomic DNA

Cited by 7 publications

References 33 publications

Personalized monitoring of circulating tumor DNA with a specific signature of trackable mutations after chimeric antigen receptor T-cell therapy in follicular lymphoma patients

Personalized monitoring of circulating tumor DNA with a specific signature of trackable mutations after chimeric antigen receptor T-cell therapy in follicular lymphoma patients

Validation of a novel NGS based BCR::ABL1 kinase domain mutation detection assay in Indian cohort

European LeukemiaNet laboratory recommendations for the diagnosis and management of chronic myeloid leukemia

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