Genome-Wide Profiling of DNA Copy Number Variation in CLL Cases Lacking 17p- (TP53) or 11q- (ATM) Abnormalities Selected from the CLL4 Study
Authors: Hockley Sarah L , Gonzalez David , Brito-Babapulle Vasantha , Else Monica , Leone Paola E , Walker Brian A , Matutes Estella , Dearden Claire E , Catovsky Daniel , Morgan Gareth J 
Published: April 2020

Abstract
Chronic lymphocytic leukaemia (CLL) is a heterogenous disease with a highly variable clinical course. A number of recurrent genetic abnormalities associated with CLL have been identified (e.g. 11q-, trisomy 12, 13q-, 17p-), some of which have been shown to be important prognostic markers. Whilst the clinical effects of 17p and 11q deletions are known to be associated with loss of the tumour suppressors TP53 and ATM, respectively, the genes underlying the effects of other genomic aberrations are still yet to be determined. In order to identify additional events that may be crucial to CLL pathogenesis and prognosis we selected 28 cases from the CLL4 study lacking 17p- and 11q- and used high density single nucleotide polymorphism (SNP) arrays to detect novel genomic copy number abnormalities including copy-number-neutral loss of heterozygosity (LOH). DNA was extracted from PBMC samples enriched for CLL cells (CLL&gt;80%) and interrogated using the Affymetrix Human Mapping 500K Array Set. Data were analysed using CNAG 2.0 and dCHIP 2006 to identify regions of genomic imbalance and LOH by comparison to a set of 25 normal controls. In this set of CLL cases without 17p- and 11q-, DNA copy number abnormalities (excluding the IGH and IGL heterogeneic loci) were identified in all 28 cases with a median number of lesions per patient of 7 (range=1–20). Genomic losses were more frequent than gains with a median of 5 deletions/patient compared to a median of 2 gains/patient (p=&lt; 0.0001). The deletions were detected in 96% of cases whereas gains were detected in 79% of cases. As expected, one of the most frequent events identified on the arrays were deletions incorporating 13q14, confirming 12 of 14 cases identified by FISH as having 13q loss. The two deletions not detected by the arrays were shown to be present in less than 20% of CLL cells by FISH. The arrays revealed the minimal deleted region (MDR) to be 13q14.2–14.3 (0.7 Mb) containing the genes DLEU1, DLEU2 and DLEU7. This region also contains the micro-RNAs miR15a and miR16, previously shown to be down-regulated in CLL, further supporting a role for these non-coding RNAs in CLL pathogenesis. Also consistent with FISH data, three cases exhibited trisomy 12. In addition to these known CLL abnormalities, the high resolution of the SNP arrays allowed the identification of novel focal regions of loss containing candidate genes linked to CLL pathogenesis. Interesting focal deletions were observed at 3p13 (15/28 cases), 3q27.3 (9/28 cases), 7q32.3 (20/28 cases), 14q11.2 (10/28 cases), 15q13.3 (3/28 cases) and 18q21.2 (15/28), most of which harboured only a single candidate tumour suppressor gene. Large telomeric regions of LOH without corresponding copy number change, indicative of uniparental disomy (UPD), were present in 4/28 cases of CLL. One case had copy-neutral LOH involving the complete long arm of chromosome 11, which may be an alternative mechanism of loss of ATM, undetectable by FISH. High-resolution copy number analysis has allowed the identification of novel recurrent genetic lesions in CLL, containing tumour suppressor genes that have been implicated in the pathogenesis of other cancers. Further investigation, including gene expression analysis and functional studies of the genes identified, will provide valuable insight into the pathogenesis of CLL and will be presented in the meeting.