Genome Complexity in Patients with Acute Lymphoblastic Leukaemia Revealed by Array-Based Comparative Genomic Hybridization.
Authors: Strefford Jon C. , Worley Helen , Barber Kerry , Moorman Anthony V. , Harrison Christine J. 
Published: October 2019

Abstract
Chromosomal abnormalities are important for the classification and risk stratification in acute lymphoblastic leukaemia (ALL). However, approximately 30% of childhood and 50% of adults lack abnormalities of clinical relevance. Here, we describe the use of array-based comparative genomic hybridization (aCGH) to determine the genetic profile of these patients (n=96) and examine the secondary changes in those with established abnormalities (n=12). DNA from diagnostic bone marrow was obtained from 108 patients with ALL (88 children and 20 adults). Analysis was performed with either a 1Mb BAC- (n=58) or a 185/244K oligonucleotide-array (n=50). DNA copy number alterations (CNA) were validated with FISH. CNA were common, with a combination of simple and complex patterns of imbalance involving chromosomes 6, 9, 12, 15 and 21. Results were concordant with conventional cytogenetics (CC) and FISH in the majority of cases. Deletions of 6q (n=17) were heterogeneous, ranging from 34.5 to 91.1Mb in size. They shared a common deleted region (CRD) of 1.8Mb (104.2–106Mb), which concurs with previous data and demonstrates the sensitivity of aCGH in measuring CNA in ALL. Six patients with 6q loss harbored a complex series of gains and losses, which in five cases corresponded to the presence of a ring chromosome by CC. CNA involving chromosome 9 were deletions of the short (p) arm (n=36), ranging from 0.7 to 36.7Mb in size. All 9p deletions encompassed the CDKN2A locus, and showed considerable heterogeneity in both the extent and location of the deletion. Hence, the association with prognosis may be dependent on the size of the deletion and the loss of other genes in co-operation with CDKN2A. Twelve patients showed loss of 12p, ranging from 0.7 to 20.9Mb in size, all with a CRD between 10.9 and 11.6Mb, encompassing amongst others, the ETV6 gene. In approximately half the patients, the 12p loss accompanied the ETV6-RUNX1 fusion. CNA involving chromosome 21 occurred in patients with intrachromosomal amplification of chromosome 21 (iAMP21, n=27). Each patient harbored at least one CNA, while several patients had complex patterns of four or more distinct regions of gain or loss. This study corroborated our earlier findings (Strefford et al 2006, PNAS103, 8167–8172) in a larger series and confirmed the variable nature of this abnormality. Five patients showed CNA of chromosome 21 in the absence of iAMP21, suggesting that a genomic rather than a cytogenetic definition may be more appropriate. Chromosome 15 CNA (n=6) were complex, involving several regions, but all with a 6.4Mb CRD. Other recurrent findings included gain of an 11.2Mb region on 17q (n=9) and deletions of 13q between 48.8 and 56.7Mb (n=6). Compared to CC, aCGH showed a three- and four-fold increase in CNA detection per patient (for BAC- and oligo-array, respectively). This is the first report of genome wide detection of CNA in ALL patients using aCGH. It has provided further insight into the size, genomic position, gene content and high-resolution characterization of the breakpoints producing these abnormalities, demonstrating that these changes are often more complex than anticipated. Such precise descriptions of the genetic alterations in ALL may lead to improved molecular diagnosis and prediction of outcome. The sub-microscopic alterations described here may facilitate the identification of novel molecular targets implicated in the pathogenesis of ALL.