Sequential SNP6.0 Microarray Analysis In Rai Stage 0 CLL Patients with Either Stable or Progressive Identifies Genomic Evolution In Both Cohorts
Authors: Rose-Zerilli Matthew JJ , Rajibali Miqdad , Parker Helen , Parker Anton , Gardiner Anne Catherine , Davis Zadie , Mold Sarah , Glide Sharron , Chaplin Tracy , Young Bryan D , Oscier David Graham , Strefford Jonathan C. 
Published: October 2019

Abstract
Abstract 1696
Sequential karyotypic and/or FISH analysis in patients with CLL show evidence of genomic evolution in 10 – 20% of cases. Common secondary abnormalities include loss of the second allele of 13q14, additional trisomies or translocations involving the immunoglobulin gene loci in patients with trisomy 12 and complex karyotypic abnormalities in patients with loss and/or mutation of the p53 and ATM genes. However the clinical significance of genomic evolution in patients presenting with early stage disease remains uncertain. Nor is it clear whether the use of high resolution genomic arrays can detect additional clinically relevant abnormalities in this cohort of patients. To address these issues we performed sequential genomic studies using the affymetrix SNP 6.0 platform (Affymetrix, Santa Clara, CA), G-banding and FISH in 29 patients presenting with either stage A0 CLL or MBL in whom IGVH gene mutational status and CD38 and ZAP 70 expression were known. In each case, Partek Genomic Suite (Partek Incorporated, St Louis, MS) was used to identify acquired copy number alterations (CNAs) and copy number neutral LOH events (CNNLOH) by comparing the disease presentation (PT) and subsequent (FU) SNP tumor profiles to each other and to matched germ-line DNA extracted from buccal cells. Patients were subdivided into those that subsequently exhibited stable disease for a minimum of 5 years (n=9) with a median time between sampling of 8 years (range 2 – 15) or those that developed progressive disease (n=20) with a median time between sampling of 4 years (range 1 – 10). 8 patients with progressive disease were treated prior to the follow up sample. All stable cases and 13/20 with progressive disease had mutated IGHV genes. The concordance between G-banding, FISH and SNP array data was >99%. In each case, a more complex genome was present at FU. The acquisition of additional CNAs was not associated with IgVH mutation status, ZAP-70, CD38 positivity or whether a patient had been treated. When these data were stratified for whether a patient subsequently exhibited stable or progressive disease, the following observations were made. Firstly, there was no difference in the acquisition of small CNAs (<1Mb) between stable or progressive patients. However, the mean number of additional large CNAs (>1Mb) per patient and the total genomic size of these additional changes were greater in progressive cases; stable and progressive cases exhibited a mean of 0.67 and 1.1 additional CNAs at FU and a mean total imbalance of 2.33Mb and 16.9Mb, respectively. In this limited series these differences did not reach statistical significance. Interestingly, the frequency of copy number variations (CNV, annotated in the Database of Genomic Variation; http://projects.tcag.ca/variation/) was higher in cases that went on to develop progressive disease (P=0.002). The size of established recurrent CNAs also changed between time-points. Most notably, several cases exhibited larger 13q14 deletions at FU. Two patients with deletion or CNNLOH of 17p displayed a more complex genome at FU, characterized by multiple CNAs larger than 1Mb. One patient acquired CNNLOH on 17p at FU in addition to five additional CNAs (>1Mb). Conversely, the degree of complexity did not increase in a patient with an ATM deletion. Six cases without an apparent abnormality of ATM or TP53 showed complex genomes at PT and additional CNAs (mean 2.8) at FU. A series of novel, recurrent CNAs were observed exclusively in FU samples, including duplications of 13q and 15q observed in 38% and 53% of patients, respectively. In conclusion, using high resolution microarray analysis we show genomic evolution in early stage patients with predominantly good risk biomarkers who pursued either an indolent or progressive course. However, our data suggests that larger acquired CNAs may be more prognostically relevant than smaller regions. We show preliminary data implicating CNVs in the pathogenesis of CLL and we have also identified a series of novel acquired regions of CNAs that may harbor cancer genes which it is hoped will contribute to our understanding of the pathophysiology of CLL and/or have clinical relevance.

Disclosures:
No relevant conflicts of interest to declare.