Global Genomic Status At Diagnosis Informs Clinical Outcome in B-Chronic Lymphocytic Leukemia: Stable Versus Progressive Disease
Authors: Dyke Daniel L. Van , Rustin Jeannette G , Smoley Stephanie A. , Passow Jeanette Eckel , Sharma Ruchi G. , Braggio Esteban , Shanafelt Tait D. , Kay Neil 
Published: October 2019

Abstract
Abstract 1772

Background:
B-Chronic Lymphocytic Leukemia (CLL) is notorious for its complex and heterogeneous clinical behavior pattern in a given patient. Panels of prognostic predictors in CLL can be complex but in general have been found to be useful in counseling a given patient. The current most powerful prognostic parameters for disease progression potential are related to leukemic B cell genetic features. Using fluorescent in situ hybridization (FISH) panels, we and others have found a hierarchy of clinical outcome with 17p- and 11q- most aggressive. The limitation of the FISH panel is that while it detects the most common recurring defects, it does not evaluate the global genomic status of the leukemia in terms of less common genetic changes or in terms of genetic complexity. Array comparative genomic hybridization (CGH) has shown that CLL B cells frequently do exhibit greater genetic complexity than is detected by the FISH panel. To further assess the relationship of genomic defects in CLL to disease outcome, we used CGH for genetic analysis of the leukemic cells at or close to the diagnosis in two cohorts of CLL patients who had either stable or progressive disease.

Methods:
We obtained leukemic B cells from patients retrospectively identified as “progressive” (n=47) or “stable” (n=21) CLL patients. The CLL patients had given informed consent to have tissue stored and had robust long term clinical outcome available on our Mayo Clinic CLL Tissue Bank and clinical database. Patients were selected based on whether they were stable as defined by no need for therapy after 5 years from diagnosis, or progressive as defined by requiring therapy within 2 years of the actual CLL diagnosis. All progressive patients had leukemic blood cells sampled within 12 months of diagnosis and prior to treatment. All stable patients had blood cells sampled within 24 months of diagnosis. DNA was extracted and then used for global genomic defect detection using a custom high density 2 × 400k oligonucleotide CGH chip (Agilent). Copy number abnormalities (CNA) and copy number variants (CNV) were assessed. CNA were studied for relationship to clinical outcome for the two cohorts of CLL patients.and CNV were excluded from further analysis.

Results:
The median age was 61 (range 42–81) years in progressive and 67 (range 42–80) in stable patients. Males comprised 77% of the progressive and 57% of the stable patients. CGH was successful in all 68 patients. FISH and CGH were discordant in 8 cases, all with <20% abnormal cells by FISH. Total number of CNA (excluding known benign variants and immunoglobulin rearrangements) was 816, with 597 in progressive (mean 12.7) and 219 in stable patients (mean 10.4). Two stable patients had a normal CGH result. Progressive patients included 15 of 16 trisomy 12, all 4 deletion 17p, and 10 of 11 deletion 11q abnormalities by CGH. Deletion 13q was observed in 39 (83%) progressive and 15 (71%) stable patients, with Rb1 deletion in 11 (23%) progressive and 4 (19%) stable patients. Remarkably, trisomy 18 (2 patients), trisomy 19 (4 patients), and trisomy 21 (1of 2 patients) were observed by CGH in association with trisomy 12. Other recurrent CNA were del(3)(q22q22) in 2 progressive and 1 stable patient and dup(8)(q24.3q24.3) plus dup(11)(p15.4p15.5) in 3 progressive patients; one progressive patient had the dup(8q) without dup (11p). None of the dup(8q) or dup(11p) patients exhibited 11q-, 17p- or +12 defects. Cytogenetic complexity (measured by number of CNA) was greater in progressive than stable patients (p=0.03; odds ratio 1.196), although there was substantial overlap between the groups (range 6–28 CNA in progressive and 5–18 in stable patients). The number of CNA tended to be higher in the presence of 11q- (8–16 CNA) and trisomy 12 (7–21 CNA), and especially 17p- (13–28 CNA).

Conclusions:
CGH and FISH were comparable for the FISH probes tested. CGH revealed that deletion breakpoints were highly variable around the regions targeted by the FISH probes. That trisomy 18, 19, and 21 were confined to the trisomy 12 patients suggests a different mechanism of genetic instability underlying trisomy 12 in CLL. Trisomy 12, deletion 11q and deleton 17p were confined almost exclusively to patients with progressive disease. Likewise, 3 other recurrent CNA (3q-, 8p dup and 11p dup) were over-represented in progressive disease, may comprise high risk genetic defects, and offer new targets for understanding genetic pathways in CLL.

Disclosures:
Kay: Biothera: Research Funding; Clegene: Research Funding; Cephalon: Research Funding; Genentech: Research Funding; Glaxo Smith Kline: Research Funding; Hospira: Research Funding; Novartis: Research Funding; Supergen: Research Funding; Calistoga: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Emergent Biosolutions (Formerly Trubion): Membership on an entity's Board of Directors or advisory committees.