Genomic fusion breakpoints for DNA-based measurable residual disease monitoring in pediatric acute lymphoblastic
Arno H Houtman1,2,3, Chloé Arfeuille1,2,3, Marion Strullu2,3,4
1Service de Génétique du Développement, Unité de Génétique Moléculaire, Hôpital Robert Debré, AP-HP, Paris, France.
Abstract:
Measurable residual disease (MRD) is a key prognostic factor in pediatric acute lymphoblastic leukemia (ALL), but current gold-standard methods based on immunoglobulin/T-cell receptor (IG/TCR) rearrangements are complex and not informative in a subset of patients. Genomic breakpoints of oncogenic fusions (GFBs) are stable, biologically grounded markers that may overcome these limitations and improve MRD assessment. In a cohort of 403 patients with known or suspected fusions, a short-read, capture-based next-generation sequencing strategy coupled with an open-source pipeline identified patient-specific GFBs in 97% of cases. GFB-based MRD assays implemented by qPCR or ddPCR showed very high specificity and allowed lower detection thresholds, resulting in improved sensitivity relative to IG/TCR-based assays. Longitudinal monitoring in 104 patients across multiple pediatric ALL fusion subtypes demonstrated excellent overall concordance between methods in non-BCR::ABL ALL, while revealing fusion-dependent differences. GFB-based MRD was particularly informative in ETV6::RUNX1- and MEF2D-rearranged ALL, where IG/TCR tracking is frequently suboptimal or unreliable due to ongoing rearrangements or the absence of VDJ recombination, respectively. Altogether, this large-scale study establishes GFBs as robust, clinically implementable MRD markers and supports their integration into clinical strategies, provided that subtype-specific biology is considered when selecting markers and interpreting results.
Insights
Genomic fusion breakpoints (GFBs) offer a more sensitive and reliable method for measuring minimal residual disease (MRD) in pediatric acute lymphoblastic leukemia (ALL). This approach improves upon current immunoglobulin/T-cell receptor (IG/TCR) methods, especially in specific ALL subtypes.
Area of Science:
- Oncology
- Genetics
- Molecular Biology
Background:
- Minimal residual disease (MRD) is crucial for prognosis in pediatric acute lymphoblastic leukemia (ALL).
- Current MRD detection methods using immunoglobulin/T-cell receptor (IG/TCR) rearrangements have limitations, including complexity and lack of informativeness in certain patient groups.
- Genomic fusion breakpoints (GFBs) of oncogenic fusions present stable, biologically relevant markers for improved MRD assessment.
Purpose of the Study:
- To evaluate the efficacy of genomic fusion breakpoints (GFBs) as novel markers for minimal residual disease (MRD) detection in pediatric acute lymphoblastic leukemia (ALL).
- To compare the sensitivity and reliability of GFB-based MRD assays against standard IG/TCR methods across various pediatric ALL subtypes.
- To establish GFBs as clinically implementable markers for MRD monitoring in ALL.
Main Methods:
- A cohort of 403 patients with known or suspected fusions underwent next-generation sequencing (NGS) using a short-read, capture-based strategy.
- An open-source bioinformatics pipeline was employed to identify patient-specific GFBs.
- GFB-based MRD assays were developed using quantitative polymerase chain reaction (qPCR) and digital droplet PCR (ddPCR).
- Longitudinal MRD monitoring was performed in 104 patients across different pediatric ALL fusion subtypes.
Main Results:
- Patient-specific GFBs were identified in 97% of cases using the NGS strategy.
- GFB-based MRD assays demonstrated high specificity and achieved lower detection thresholds, leading to improved sensitivity compared to IG/TCR assays.
- High concordance was observed between GFB- and IG/TCR-based methods in non-BCR::ABL ALL.
- GFB-based MRD was particularly advantageous in ETV6::RUNX1- and MEF2D-rearranged ALL, where IG/TCR tracking is often unreliable.
Conclusions:
- Genomic fusion breakpoints (GFBs) are robust and clinically applicable markers for minimal residual disease (MRD) assessment in pediatric acute lymphoblastic leukemia (ALL).
- GFB-based MRD assays offer enhanced sensitivity and reliability, particularly in specific ALL subtypes where conventional methods falter.
- Integration of GFB-based MRD monitoring into clinical practice is supported, with careful consideration of subtype-specific biology for marker selection and result interpretation.
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