Abstract LB329: Pathway-based analysis of genomic alterations in infant ALL
Authors: Byunggil Yoo, Erin Guest, Midhat S. Farooqi
Journal: Cancer Research (2025)

Abstract Introduction: Infant acute lymphoblastic leukemia (ALL) is an aggressive subtype, characterized by early onset and poor clinical outcomes, with about 70% of cases involving KMT2A gene rearrangements (KMT2A-r). This study investigates whether pathway-specific genomic alterations influence prognosis by analyzing sequence variants in infant ALL patients from the Children’s Oncology Group trial AALL0631. Methods: We conducted WGS and WES on DNA extracted from peripheral blood or bone marrow from 48 infant ALL patients across three cohorts at diagnosis and at remission. The three infant ALL cohorts included: Cohort A (infants with KMT2A-r ALL who experienced relapse, n=21), Cohort B (infants with KMT2A-r ALL who remain in remission to date, n=12), and Cohort C (infants with KMT2A germline ALL who remain in remission to date, n=15). Sequencing was conducted using an Illumina HiSeq 4000 or 2500 platform, achieving a minimum coverage depth of 90 Gb for WGS and 15 Gb for WES. Alignment and germline variant calling were performed using BWA and GATK for WGS, and the Illumina Dragen for WES. Somatic variant calling utilized GATK4-Mutect. Genomic variants were classified based on the 2015 ACMG/AMP guidelines. Variants categorized as benign, likely benign, or non-exonic variants of unknown significance were excluded. Further filtering removed germline variants with a population allele frequency exceeding 1% and somatic variants with a frequency above 0.1%. The analysis focused on variants within 22 KEGG pathways, selected for their relevance to cancer mechanisms and DNA repair processes. Variant counts in these pathways were subsequently analyzed to identify potential contributions to disease pathogenesis. Results: Analysis of somatic variants revealed significant differences between Cohort A and Cohort B. Somatic mutations in the non-homologous end-joining (NHEJ) pathway were more frequent in Cohort A (Kruskal-Wallis p = 0.043), while somatic mutations in the Wnt signaling pathway were more common in Cohort B (p = 0.048). For germline variants, mutations in the Notch signaling pathway were more frequently observed in KMT2A-r infant ALL patients. Conclusion: Pathway-specific genomic alterations may impact outcomes in infant ALL. Relapsed KMT2A-r ALL patients showed an enrichment of somatic mutations in the NHEJ pathway, while somatic mutations in the Wnt pathway were more common in patients who remained in remission. Additionally, germline variants in the Notch pathway were prevalent in KMT2A-r cases, suggesting a potential predisposition. These findings offer insights into the molecular mechanisms of infant ALL and highlight potential therapeutic targets. Citation Format: Byunggil Yoo, Erin Guest, Midhat S. Farooqi. Pathway-based analysis of genomic alterations in infant ALL [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB329.