Clinically Significant Mutations, Deletions and Translocations Involving ETV6 Identified by Whole Genome and Whole Exome Sequencing; Report From NCI/COG Target AML Initiative

Abstract 125

Despite identification of genomic alterations in AML, clinically actionable variants are limited. Further, mutations identified in adult AML are less frequent or not found in childhood AML. TARGET AML initiative, a collaboration between National Cancer Institute Office of Cancer Genomics (NCI/OCG) and Children's Oncology Group (COG) provided resources to perform multi-platform analysis of a large number of pediatric AML cases in order to identify therapeutic targets in childhood AML. As part of this effort, diagnostic, remission and relapse specimens from a large cohort of children with AML were subjected to whole genome sequencing (WGS). In addition, all specimens underwent characterization by expression profiling, SNP genotyping, methylation profiling and miRNA sequencing. Specimens from a subset of patients also underwent whole exome sequencing (WES) and whole transcript sequencing (RNA Seq). Here we present data from an interim analysis of the data that identified clinically significant, novel somatic mutations, deletions and translocations involving the ETV6 gene in pediatric patients with AML. Non-silent somatic mutations of ETV6, including missense, splice site mutations and indels were identified by WGS and WES. Large deletions involving ETV6 gene were identified by WGS and SNP/CGH arrays, and novel fusion transcripts (cryptic translocations) involving ETV6 were identified by WGS and RNA Seq. We present the prevalence and clinical significance of genomic alterations of ETV6 that were identified as part of TARGET AML study.

WGS and WES data were available from 54 and 22 pediatric AML patients, respectively. In these 76 selected cases, somatic mutations in ETV6 were identified and verified in 3 patients. Frequency validation was performed by sequencing of the entire coding region of the ETV6 gene in diagnostic specimens from 180 children with AML. Somatic mutations of ETV6 gene were identified in 6% of patients, of which none had cytogenetic or molecular risk features. Those with somatic ETV6 mutations had an overall survival (OS) of 20% vs. 76% for those without mutations (p=0.002) with a corresponding relapse risk (RR) of 80% vs. 29% (p=0.004), demonstrating the potential impact of ETV6 mutations in pediatric AML.

Deletions involving ETV6 gene (del ETV6) were detected in 3 patients by WGS and confirmed by SNP genotyping array and by fluorescent in situ hybridization (FISH). Subsequent interrogation of the SNP genotyping data identified deletions of 12p13 involving ETV6 in 19/242 patients (8%) ranging from 0.25 Mb to >20 Mb. Those with del ETV6 lacked cytogenetic (−7, or −5/del5q) or molecular (FLT3/ITD) high-risk features, but 50% of those with del ETV6 had core binding factor (CBF) AML. All patients with del ETV6 achieved a morphologic complete remission (CR) and had no evidence of minimal residual disease at the end of induction chemotherapy. Relapse risk for patients with and without del ETV6 was 63% vs. 45% (p=0.3) with a corresponding disease-free survival (DFS) of 32% vs. 53% (p=0.2). Due to the high prevalence of CBF AML in patients with del ETV6, we inquired whether this alteration might impact outcome in patients with CBF AML. In patients with CBF AML, del ETV6 was associated with adverse outcome, where CBF patients with and without del ETV6 had an event-free survival of 0% vs. 63%, respectively (p=0.002). Of the CBF AML patients who achieved an initial CR, those with compared to those without a del ETV6 had a RR of 88% (vs. 38%, p=0.08) with a DFS of 0% (vs. 61%, p=0.009) respectively.

Cryptic ETV6 translocations involving at least two distinct translocation partners represented a third class of ETV6 alterations identified by WGS and RNA Seq. FISH evaluation of select patients was available and identified 16 patients with positive FISH for ETV6 variants. Those who had ETV6 alterations by FISH had a median age at diagnosis of 3.7 years. Evaluation of remission induction rate as well as post remission outcome demonstrated that all but 3 of these 16 patients either failed to achieve a CR (N=4) or relapsed after an initial remission (82% failure rate). These data identified varying genomic alterations of ETV6 by whole genome sequencing that identify a significant proportion of pediatric AML cases with adverse outcome who may be targeted for altered therapy.