High-resolution genomic profiling of adult and pediatric core-binding factor acute myeloid leukemia reveals new recurrent genomic alterations

Abstract

To identify cooperating lesions in core-binding factor acute myeloid leukemia, we performed single-nucleotide polymorphism-array analysis on 300 diagnostic and 41 relapse adult and pediatric leukemia samples. We identified a mean of 1.28 copy number alterations per case at diagnosis in both patient populations. Recurrent minimally deleted regions (MDRs) were identified at 7q36.1 (7.7%), 9q21.32 (5%), 11p13 (2.3%), and 17q11.2 (2%). Approximately one-half of the 7q deletions were detectable only by single-nucleotide polymorphism-array analysis because of their limited size. Sequence analysis of MLL3, contained within the 7q36.1 MDR, in 46 diagnostic samples revealed one truncating mutation in a leukemia lacking a 7q deletion. Recurrent focal gains were identified at 8q24.21 (4.7%) and 11q25 (1.7%), both containing a single noncoding RNA. Recurrent regions of copy-neutral loss-of-heterozygosity were identified at 1p (1%), 4q (0.7%), and 19p (0.7%), with known mutated cancer genes present in the minimally altered region of 1p (NRAS) and 4q (TET2). Analysis of relapse samples identified recurrent MDRs at 3q13.31 (12.2%), 5q (4.9%), and 17p (4.9%), with the 3q13.31 region containing only LSAMP, a putative tumor suppressor. Determining the role of these lesions in leukemogenesis and drug resistance should provide important insights into core-binding factor acute myeloid leukemia.

Figure 1

DNA CNAs in 300 newly diagnosed adult and pediatric patients with CBF-AML. (A) Log2 ratio SNP copy number data of diagnostic leukemia cells (median-smoothed with a window of 5 markers; blue indicates deletion and red gain). Each column represents a case, and the SNPs are arranged in rows according to chromosomal location. Cases are arranged by subgroup. Gross changes can be observed for example in chromosome 8 (17 cases with trisomy 8). (B) Analysis via GISTIC of copy number losses (left) and gains (right). False-discovery rate q values are plotted along the x-axis with chromosomal position along the y-axis. Altered regions with significance levels exceeding 0.25 (marked by vertical green line) were deemed significant. Nine significant regions of deletion, and 2 significant regions of amplification were identified. Chromosomal positions are shown for each significant region on the right side of the plots.

Figure 2

Deletions of 7q36.1 involving MLL3. (A) Log2 ratio SNP copy number data in 23 cases at diagnosis with focal or more extensive deletions (P indicates paired normal; and D, diagnosis). (B) Minimally deleted region in 7q36.1 (647 Kb in size) defined by case i16245 containing the 4 genes PRKAG2, GALNTL5, GALNTL11, and MLL3. Each vertical red line represents the genomic position and log2 ratio copy number of an individual marker. (C) Sequencing of MLL3 showing a truncating mutation leading to a premature stop codon in a single case (AE201) without del(7q).

Figure 3

Recurrent deletions at 11p13. The MDR (130 Kb in size) is defined by case i16033 and contains the WT1 and the WIT1 gene (P indicates paired normal; and D, diagnosis).

Figure 4

Recurrent deletion at 17q11.2. The MDR (901 Kb in size) is defined by the 2 cases i16238 and i16306 and contains 10 genes including the tumor suppressor NF1 (P indicates paired normal; and D, diagnosis).

Figure 5

Relapse-associated deletions at 3q13.31 in 4 paired analyzed cases. (A) The MDR is defined by case i16008 that carries a deletion of 46 Kb containing a LSAMP transcript (R indicates relapse; and D, diagnosis). (B) SNP coverage of the locus in case i16008.