High Resolution Genomic Analysis In CLL Demonstrates Genomic Stability In Untreated Patients and Novel Markers of Progression In Treated Patients
Authors: Brown Jennifer R , Hanna Megan , Tesar Bethany , Werner Lillian , Reynolds Hazel , Fernandes Stacey M , Macconaill Laura , Wang Yaoyu , Correll Mick , Neuberg Donna , Freedman Arnold S. 
Published: October 2019

Abstract
Abstract 2426
Chronic lymphocytic leukemia is the most common leukemia of adults but still incurable. Prognosis at diagnosis is widely variable, and the key cytogenetic abnormalities determined by FISH remain one of the best predictors of prognosis and treatment response. We therefore undertook very high resolution genomic analysis of 161 CLLs with matched germline samples using Affymetrix 6.0 SNP arrays, in an effort to identify additional predictors of prognosis, and have also performed gene expression profiling on most of this patient cohort. The median age at diagnosis for the cohort was 55 (31–79), and the median time to sampling was 4.6 months (0.5–291). 22% of the cohort was previously treated, with an additional 21% of patients receiving treatment during the follow-up period, for a total of 43% treated, with a median time from diagnosis to treatment of 41 months (0.4-161.2 months). The genomic data were analyzed both by GISTIC, which identifies significant deletions and amplifications based on analysis of the frequency and amplitude of each aberration in the tumor samples alone, as well as by paired copy number analysis of each tumor and its cognate germline, using Birdseed, PLINK and PennCNV. Our results show that the CLL genome is overall quite stable, with a median of only one acquired copy number aberration per sample, excluding rearrangements at the immunoglobulin gene loci. GISTIC analysis on the entire population identified the known common CLL abnormalities at frequencies that would be expected in a largely untreated cohort: 57% del 13q, 6.2% deletion 11q, 5.0% deletion 17p, and 12% trisomy 12. The presence of two or more acquired copy number aberrations (CNAs) of any type was associated with a significantly shorter time to first therapy (p<0.0001). A higher number of CNAs was strongly associated with deletions of 11q or 17p, but the predictive power of a higher number of CNAs was still present in those CLLs without deletions 11q or 17p. Detailed analysis of 13q deletion revealed no association of longer deletions or homozygous deletions with time to first therapy. However, any additional somatic copy number aberration in addition to 13q deletion significantly reduced the time to first therapy, making it comparable to non-13q patients. In order to identify genetic markers of progression, we compared treated to untreated patients using GISTIC. This analysis revealed that untreated patients showed peaks largely limited to deletion 13q and trisomy 12. Treated patients however showed three additional significant peaks: a deletion peak at 8p, as well as significant amplification peaks at 3q26.32 and 8q24.21. The deletion peak at 8p was observed in 8 of 161 samples tested (5.0%), and was large, with a common region of deletion spanning 11.0–29.6 Mb. Six of eight of these patients were untreated at the time of sampling but had a very short time to treatment thereafter, independent of whether they had coexistent deletions of 17p or 11q, suggesting that this deletion carries a very poor prognosis in itself. Another notable region of amplification was found on 3q26.32 in nine patients (9/161 or 5.6%). Although many of these amplified regions were large, three of the nine patients carrying this amplification demonstrated focal somatic amplification of the final exon of PIK3CA, the alpha catalytic subunit of PI3K. Finally the amplification on 8q24 was present in 6 of 161 CLLs (3.7%), two of which were focal and amplified only the gene desert region previously implicated in CLL risk by genome-wide association study and located approximately 335 kb centromeric to MYC. Analysis of gene expression profiling comparing patients with and without amplifications demonstrated upregulation of MYC mRNA expression and alteration of downstream targets of MYC in samples with amplification. We conclude that very high resolution copy number analysis with matched germline comparison in CLL reveals a quite stable genome in untreated patients, and identifies amplifications of 3q26 and MYC at 8q24 as progression events.

Disclosures:
No relevant conflicts of interest to declare.