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Dynamic APOBEC3A-associated mutagenesis shapes the genomic landscape of ETV6::RUNX1-positive B-cell precursor acute lymphoblastic leukemia

Recent studies have shown that high APOBEC activity is associated with increased therapy evasion in adult cancer. However, APOBEC mutagenesis in pediatric cancer has not been thoroughly characterized. In this study, we determined the prevalence and molecular characteristics of APOBEC mutagenesis in pediatric BCP-ALL using whole genome sequencing, bulk RNA sequencing and single cell RNA sequencing. We show that APOBEC mutagenesis s intrinsic to ETV6::RUNX1-positive samples and can drive clonal heterogeneity through subclonal activity.

Type: Other
Archive: European Genome-phenome Archive (EGA)

3 Datasets

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Dataset ID	Description	Technology	Samples
EGAD00001016426	RNA sequencing was performed on Illumina Novaseq 6000 to generate 150 base-pair paired-end reads of 57 ETV6::RUNX1-positive BCP-ALL samples, aiming for 30M unique reads per sample. CRAMs were generated by read mapping to human reference genome hg38 using STAR-Fusion. The CRAMs were used to quantify the reference transcriptome using featureCounts from Rsubread.		1
EGAD00001016427	Single-cell RNA sequencing data were collected from 19 ETV6::RUNX1-positive BCP-ALL samples, and demultiplexed and aligned to reference transcriptome hg38 (10x Genomics) using the CellRanger pipeline. Resulting FASTQ files were used for transcript quantification and subsequent downstream analyses with Seurat.	Illumina NovaSeq 6000	18
EGAD00001016428	Whole genome sequencing was performed on Illumina Novaseq 6000 to generate 150 base-pair paired-end reads of 57 ETV6::RUNX1-positive BCP-ALL samples. CRAMs were generated by read mapping to human reference genome hg38 using the Burrows-Wheeler aligner (BWA). The CRAMs were used in somatic variant calling with GATK's Mutect2 to analyze mutational patterns in all samples.	Illumina NovaSeq 6000	8