Patient-specific assays based on whole-genome sequencing data to measure residual disease in children with acute lymphoblastic leukemia – a proof-of- concept study

Arthur, Cecilia; Rezayee, Fatemah; Mogensen, Nina; Saft, Leonie; Rosenquist, Richard; Nordenskjöld, Magnus; Harila‐Saari, Arja; Tham, Emma; Barbany, Gisela

doi:10.21203/rs.3.rs-1403708/v1

Cited by 2 publications

(2 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We are also grateful to the staff at the Clinical Genomics Platform at Science for Life Laboratory (SciLife Lab), Stockholm, particularly to Valtteri Wirta and Jesper Eisfeldt, for expert assistance regarding WGS and bioinformatics. A manuscript preprint is available at Research Square ( 48 ).…”

Section: Acknowledgmentsmentioning

confidence: 99%

Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia: A Proof of Concept Study

et al. 2022

View full text Add to dashboard Cite

Risk-adapted treatment in acute lymphoblastic leukemia (ALL) relies on genetic information and measurable residual disease (MRD) monitoring. In this proof of concept study, DNA from diagnostic bone marrow (BM) of six children with ALL, without stratifying genetics or central nervous system (CNS) involvement, underwent whole-genome sequencing (WGS) to identify structural variants (SVs) in the leukemic blasts. Unique sequences generated by SVs were targeted with patient-specific droplet digital PCR (ddPCR) assays. Genomic DNA (gDNA) from BM and cell-free DNA (cfDNA) from plasma and cerebrospinal fluid (CSF) were analyzed longitudinally. WGS with 30× coverage enabled target identification in all cases. Limit of quantifiability (LoQ) and limit of detection (LoD) for the ddPCR assays (n = 15) were up to 10−5 and 10−6, respectively. All targets were readily detectable in a multiplexed ddPCR with minimal DNA input (1 ng of gDNA) at a 10−1 dilution, and targets for half of the patients were also detectable at a 10−2 dilution. The level of MRD in BM at end of induction and end of consolidation block 1 was in a comparable range between ddPCR and clinical routine methods for samples with detectable residual disease, although our approach consistently detected higher MRD values for patients with B-cell precursor ALL. Additionally, several samples with undetectable MRD by flow cytometry were MRD-positive by ddPCR. In plasma, the level of leukemic targets decreased in cfDNA over time following the MRD level detected in BM. cfDNA was successfully extracted from all diagnostic CSF samples (n = 6), and leukemic targets were detected in half of these. The results suggest that our approach to design molecular assays, together with ddPCR quantification, is a technically feasible option for accurate MRD quantification and that cfDNA may contribute valuable information regarding MRD and low-grade CNS involvement.

show abstract

Section: Acknowledgmentsmentioning

confidence: 99%

Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia: A Proof of Concept Study

et al. 2022

View full text Add to dashboard Cite

show abstract

“…The CNS involvement is more common in ALL than in adult acute myeloid leukemia (2). Long-term outcomes in childhood ALL have improved over the past half century, largely due to the greater precision in the risk stratification of patients based on the initial diagnostic risk factors and the early treatment response as assessed by minimal residual disease (MRD) (3)(4)(5). In addition, the identification of genetic abnormalities associated with prognosis and treatment, along with effective targeted therapies, also plays an important role (6).…”

Section: Introductionmentioning

confidence: 99%

Analysis of RAS gene mutations in adverse events during first induction chemotherapy in childhood acute lymphoblastic leukemia

Chen¹,

Wu²,

Lv³

et al. 2023

Transl Pediatr

View full text Add to dashboard Cite

Background The rat sarcoma virus ( RAS ) pathway controls cell proliferation, differentiation, and apoptosis, which have been implicated in the pathogenesis of various hematological malignancies. Prognostic importance of RAS gene mutation, relatively frequently in childhood acute lymphoblastic leukemia (ALL), has been debated. We aimed to study RAS gene mutation profile and prognosis in 93 children with newly diagnosed ALL. Methods We retrospectively analyzed clinical characteristics, treatment, and outcomes of 93 ALL children during first induction chemotherapy in Anhui Provincial Children’s Hospital under the Chinese Children’s Leukemia Group-acute lymphoblastic leukemia 2018 (CCLG-ALL-2018). All genomic DNA samples were obtained from bone marrow mononuclear cells upon new diagnosis. RAS gene mutation was performed by polymerase chain reaction (PCR). All children were stratified into standard-, medium-, and high-risk groups, and then treated with risk-based regimens according to CCLG-ALL-2018 protocol. Results Of 93 ALL children, 26 (27.9%) were positive for RAS mutation, among whom 19 had N- RAS mutation, 8 had K- RAS mutation, and 1 had a double mutation. The ETV6/RUNX1 fusion gene was the most common genetic alteration (n=16, 17.2%). The most common adverse events during first induction chemotherapy were coagulation abnormalities (n=76, 81.7%), followed by fever (n=71, 76.3%) and alanine transaminase (ALT) elevation (n=34, 36.6%). Compared with negative RAS mutation group, the risk of hyperbilirubinemia was significantly reduced in RAS mutation group (P=0.018), and there was no significant difference in any other adverse events. The average duration of agranulocytosis during first induction chemotherapy was 6 days, and the average duration of agranulocytosis in RAS mutation group and RAS negative group was 6 and 5 days, with no significant difference. Multivariate linear regression analysis showed that in RAS mutation group, when body mass index (BMI) exceeded the median value of this ALL population (BMI >15.38), the risk of agranulocytosis was significantly increased (P=0.003). Conclusions Newly diagnosed ALL in children with RAS mutation is less likely to be associated with fusion gene expression. RAS mutation increases the risk of agranulocytosis duration during first induction chemotherapy, lowers BMI and reduces the risk of hyperbilirubinemia in ALL children.

show abstract

Patient-specific assays based on whole-genome sequencing data to measure residual disease in children with acute lymphoblastic leukemia – a proof-of- concept study

Cited by 2 publications

References 24 publications

Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia: A Proof of Concept Study

Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia: A Proof of Concept Study

Analysis of RAS gene mutations in adverse events during first induction chemotherapy in childhood acute lymphoblastic leukemia

Contact Info

Product

Resources

About