Clinical Relevance of Genes Commonly Deleted in Childhood B-Cell Precursor ALL (BCP-ALL)
Authors: Schwab Claire , Chilton Lucy , Enshaie Amir , Morrison Heather , Jones Lisa , Al-Shehhi Halima A , Erhorn Amy , Russell Lisa J , Vora Ajay J , Mitchell Christopher D , Richards Sue M , Goulden Nicholas , Kinsey Sally , Moorman Anthony V. , Harrison Christine J 
Published: October 2019

Abstract
Abstract 290
Multiplex Ligation-dependent Probe Amplification (MLPA) provides an accurate and reliable high throughput method to screen for copy number abnormalities (CNA) of the significant genes in BCP-ALL. We have screened a consecutive cohort of 1427 childhood BCP-ALL patients treated on UKALL97 and UKALL2003 using the P335 SALSA MLPA kit IKZF1 (MRC Holland, The Netherlands). We here report the association of CNA involving these genes with clinical features. The overall breakdown of CNA was CDKN2A/B 28% (395), ETV6 22% (312), PAX5 19% (272), IKZF1 14% (196), RB1 6% (92), BTG1 6% (89) and EBF1 2% (30), as well as the rearrangement, P2RY8-CRLF2 4% (63). The cohort comprised 762 (54%) males and 665 (46%) females. There was no shift in the gender balance according to CNA. The median age of the entire cohort was 5 years (range 1–23) with 24% of patients being ≥10 years. There was some correlation between the distribution of CNA and patient age. Patients with IKZF1 and CDKN2A/B deletions were significantly older at 7 years (p<0.0001) and 6 years (p<0.0001), respectively, with 39% and 33%, respectively, of deletions occurring in patients ≥10 years old. The incidence of these deletions increased with age, a trend which continued into adulthood. There was a peak in incidence of ETV6 deletions in children aged 2–4 years, explained by their strong association with ETV6-RUNX1, which has a peak incidence in this age group. There was no significant change in incidence linked to age for deletions of the other genes tested. The median WCC of the cohort was 11.8 x109/l with 44% of patients having a count of <10 x109/l. Patients with IKZF1, PAX5 or CDKN2A/B deletions were more likely to have a WCC of >50×109/L (each p<0.001). The association of IKZF1, PAX5 and/or CDKN2A/B aberrations with age and WCC meant that there was a significantly higher incidence of patients with these deletions classified as NCI HR compared to SR (each p<0.001).
There is particular interest in IKZF1 and CRLF2 in relation to outcome in BCP-ALL. We have previously shown an intermediate outcome for patients with CRLF2 rearrangements. We here examined the prognostic effect of IKZF1 deletions in this patient cohort; but excluded Down syndrome and BCR-ABL1 positive patients from survival analyses. Among 469 ALL97 patients, 13% (63) had IKZF1 deletions and after a median follow-up time of 9.5 years, 49% (31) had relapsed and 40% (25) had died. In the NCI standard risk (SR) group, patients with IKZF1 deletions had a significantly inferior event free survival (EFS) at 5 years (61% v 85%, p=0.0006). However, the effect appeared to be largely confined to patients with intermediate risk cytogenetics (63% v 85%, p=0.025) rather than those with good risk cytogenetics (75% v 87%, p=0.2915). As expected the NCI high risk (HR) patients with IKZF1 deletions had an inferior EFS: 50% v 68%, p=0.0112. In ALL2003, 776 patients with a median follow-up time of 3.9 years were available for analysis. Among 11% (87) patients with IKZF1 deletions, 13% (11) had relapsed and 5% (4) died in remission, resulting in a significantly inferior 5 year EFS: 78% v 90% p=0.0025. Of note, 8/11 IKZF1 deleted patients who relapsed were MRD positive (>0.01%) at day 28 and only 1/22 patients with good risk cytogenetics and IKZF1 deletion relapsed. There was no evidence that the type of deletion (deletion of exons 4–7 vs others) was linked to outcome in either the ALL97 or ALL2003 cohort.
In conclusion, we have shown that IKZF1, PAX5 and/or CDKN2A/B aberrations are significantly associated with NCI HR, which may point to an associated poor outcome. Indeed, we showed that patients with IKZF1 deletions had an inferior outcome overall. However, there was evidence to suggest that the effect was pleiotropic and, importantly, IKZF1 deleted patients treated on ALL2003 in general achieved a respectable EFS rate of 75% at 5 years. Although in most studies IKZF1 deletions have been associated with a poor prognosis in BCP-ALL, while the risk relating to CRLF2 has been variable, thus far these findings, including those from this study, do not support changes to treatment for patients with these abnormalities.

Disclosures:
No relevant conflicts of interest to declare.