Integrative genomic analysis of childhood acute lymphoblastic leukaemia lacking a genetic biomarker in the UKALL2003 clinical trial

Abstract

Incorporating genetics into risk-stratification for treatment of childhood B-progenitor acute lymphoblastic leukaemia (B-ALL) has contributed significantly to improved survival. In about 30% B-ALL (B-other-ALL) without well-established chromosomal changes, new genetic subtypes have recently emerged, yet their true prognostic relevance largely remains unclear. We integrated next generation sequencing (NGS): whole genome sequencing (WGS) (n = 157) and bespoke targeted NGS (t-NGS) (n = 175) (overlap n = 36), with existing genetic annotation in a representative cohort of 351 B-other-ALL patients from the childhood ALL trail, UKALL2003. PAX5alt was most frequently observed (n = 91), whereas PAX5 P80R mutations (n = 11) defined a distinct PAX5 subtype. DUX4-r subtype (n = 80) was defined by DUX4 rearrangements and/or ERG deletions. These patients had a low relapse rate and excellent survival. ETV6::RUNX1-like subtype (n = 21) was characterised by multiple abnormalities of ETV6 and IKZF1, with no reported relapses or deaths, indicating their excellent prognosis in this trial. An inferior outcome for patients with ABL-class fusions (n = 25) was confirmed. Integration of NGS into genomic profiling of B-other-ALL within a single childhood ALL trial, UKALL2003, has shown the added clinical value of NGS-based approaches, through improved accuracy in detection and classification into the range of risk stratifying genetic subtypes, while validating their prognostic significance.

Fig. 1. Classification of B-other-ALL cohort according to technique.

Sankey plot showing the number of patients tested by each technique and those classified into genomic subtypes of B-other-ALL, as defined in Table 1. *Cases tested by FISH and/or MLPA, not all cases by all kits and probes. **Excludes 9 patients with other subtype defining abnormalities. WGS Whole genome sequencing, t-NGS Targeted next generation sequencing, FISH Fluorescence in situ hybridisation, MLPA Multiplex Ligation-dependent Probe Amplification.

Fig. 2. Genomic and clinical features of the PAX5alt subtype.

A Oncoplot showing the distribution of clinical features and genetic abnormalities within the PAX5alt subtype and associated copy number profile risk status (UKALL-CNA [36] and IKZF1_plus [40]). Coexistence of CRLF2-r is indicated in red in the B-other-ALL subtype row. Copy number profile status was unavailable for patients lacking Multiplex Ligation-dependent Probe Amplification (MLPA) data. *The SALSA P335-ALL-IKZF1 and P327-iAMP21-ERG MLPA kits were used to determine gene copy number. Relapses were defined as follows: very early, < 18 months from diagnosis; early, within 6 months of end of treatment; late >6 months after end of treatment. B Circos plot illustrating the range of PAX5 translocation partner genes in PAX5-r. C Stacked bar plot showing the distribution of PAX5alt abnormalities amongst different age groups. NCI National Cancer Institute, WBC White blood cell count, MRD Minimal residual disease, t-NGS Targeted next-generation sequencing, WGS Whole genome sequencing, PAX5-r PAX5 rearranged, PAX5-ITD PAX5 internal tandem duplication, CNA Copy number alteration.

Fig. 3. Genomic and clinical features of the ETV6::RUNX1-like subtype.

A Oncoplot showing the distribution of clinical features and genetic abnormalities within the ETV6::RUNX1-like subtype and associated copy number profile risk status (UKALL-CNA [36] and IKZF1_plus [40]). Coexistence of CRLF2-r is indicated in red in the B-other subtype row. Copy number profile status was unavailable for patients lacking Multiplex Ligation-dependent Probe Amplification (MLPA) data. *The SALSA P335-ALL-IKZF1 and P327-iAMP21-ERG MLPA kits were used to determine gene copy number. Relapses were defined as follows: very early, < 18 months from diagnosis; early, within 6 months of end of treatment; late > 6 months after end of treatment. B Circos plot illustrating the constellation of ETV6 translocation partner genes which characterise ETV6::RUNX1-like. Only the recurrent translocation partners are labelled with gene names. C Heatmap of MLPA ratios for copy number detection of ETV6 and IKZF1 across the ETV6::RUNX1-like subtype.

Fig. 4. Relapse rate and overall survival of B-other-ALL subtypes.

Kaplan-Meier survival curves showing the relapse rate (A) and overall survival (B) for patients treated on UKALL2003 classified into the six most prevalent genomic subtypes of B-other-ALL.