Stone, Annjanette

Abstract Abstract 1245 Poster Board I-267 Introduction Chronic lymphocytic leukemia (CLL) patients with del(11q) by fluorescence in situ hybridization (FISH) have a poor prognosis. These patients often have younger age of onset, bulky lymphadenopathy, and short clinical response to treatment with purine analogues. Deletion of 11q in CLL is thought to involve loss-of-function of ataxia-telangiectasia mutated (ATM), a protein kinase central to DNA damage responses. As part of a larger study of early-intermediate stage, high risk CLL patients, we applied whole genome copy number variation (CNV) analysis to characterize the genomic alterations in CLL patients with and without del(11q) by FISH. Patients and Methods We studied 17 patients aged 29-67 with early-intermediate stage, untreated CLL who had high risk for disease progression based on evaluation of molecular and immunophenotypic markers. Of these patients, six had del(11q) by FISH analysis. No patients in this study had del(11q) as a sole FISH abnormality. CLL cells and normal cells were separated by magnetic bead selection from patient peripheral blood samples with absolute lymphocyte counts that ranged from 7.4 to 106 × 109/L. CNV analysis was performed on purified genomic DNA from the CLL cells and from normal cells for each patient in order to distinguish acquired CNVs in malignant cells from polymorphic CNVs in the human genome. We used the Illumina human660w-quad beadchip, a single nucleotide polymorphism (SNP)-based microarray for whole-genome genotyping and CNV analysis that contains more than 550,000 tag SNPs and approximately 100,000 additional markers that target regions of common CNV. CNV data was analyzed using CNV partition (Illumina Genome Studio software) and PennCNV. Results CNV analysis reveals hemizygous deletions of 11q in all 6 patients positive for del(11q) by FISH. The size of the deletion varies from ∼980 Kb to ∼44 Mb. All deletions include the region of the ATM gene at 11q22.3. No large homozygous deletions of 11q were detected. The three largest interstitial deletions (∼39 Mb, ∼41 Mb, ∼44 Mb) span 11q14.1-q23.3. A slightly smaller deletion of ∼33 Mb spans 11q14.2-q23.3. One deletion of ∼8.6 Mb covers 11q22.1-q22.3. The smallest deletion of ∼980 Kb is found within 11q22.3, centered on the ATM gene. Three out of 6 patients show complex interstitial deletions of 11q that consist of two or more discontinuous segments of loss of heterozygosity (LOH) separated by short undeleted regions. Five out of 6 patients with 11q deletions also show 13q hemizygous deletion by CNV analysis and by FISH. In 4 of these patients, the 11q and 13q interstitial deletions are the only acquired CNV events detected in the CLL genome. In one patient with 11q and 13q interstitial deletions, CNV analysis also shows chromosome 12 copy number (CN)=3 (also detected by FISH), CN=3 at 3q24-telomere (tel), and LOH events consistent with hemizygous deletion at 11p13 and 7p15.2-tel. Most noteworthy are 2 patients negative for any FISH abnormality who show copy-neutral LOH of most of 11q. The region of copy-neutral LOH includes 11q12-tel in one patient and 11q13.1-tel in the other patient. The copy-neutral LOH event involves close to 100% of the CLL cells in one patient, but only about 50% of the CLL cells in the other patient. Conclusions Whole genome CNV analysis by SNP-based microarrays greatly expands our ability to detect acquired genomic events in CLL cells and provides a powerful tool for CLL clinical research. Applying this new genomic technology to CLL patients with 11q deletions reveals marked complexity in the size and structure of hemizygous deletion events, which include the region of the ATM gene at 11q22.3 and can be discontinuous, indicative of complex genomic events. We identified copy-neutral LOH of 11q in 2 patients, a finding not previously described in CLL cells. Copy-neutral LOH of 11q is a genetic mechanism by which biallelic mutations of ATM, in cooperation with the loss of other tumor suppressor genes on 11q, may contribute to poor outcomes in some CLL patients without detectable FISH abnormalities. Additional studies, including sequencing of the ATM gene in 11q copy-neutral LOH patients, are required to confirm this hypothesis. Disclosures Shanafelt: Genentech, Hospira, Polyphenon E International, Celgene, Cephalon, Bayer Health Care Pharmaceuticals: Research Funding. Kay:Genentech, Celgene, Hospira, Polyphenon Pharma, Sanofi-Aventis: Research Funding; Biogenc-Idec, Celgene, Genetech, Genmab: Membership on an entity's Board of Directors or advisory committees. Zent:Genentech: Research Funding; Bayer: Research Funding; Genzyme: Research Funding; Novartis: Research Funding.

Abstract Abstract 2420 Introduction: Interstitial deletion of chromosome 11q (11q-) detected by fluorescence in situ hybridization (FISH) is an unfavorable prognostic marker in chronic lymphocytic leukemia (CLL). CLL patients with 11q- often have younger age of onset, bulky lymphadenopathy, and poorer overall survival. The ataxia-telangiectasia mutated (ATM) gene, which encodes a protein kinase central to DNA damage response, is thought to be the critical gene in CLL 11q- through loss of ATM function. A subgroup of CLL patients with 11q- has been shown by other investigators to have a mutation in the remaining ATM allele, supporting a loss-of-function hypothesis. In an ongoing study, we are using SNP-based whole genome copy number variation (CNV) analysis to characterize in detail the 11q deletions in CLL patients. In addition, we have reported uniparental disomy (UPD) of 11q in CLL patients negative for FISH abnormalities. Here we report direct DNA sequence analysis of the ATM gene in CLL patients with 11q- and with UPD of 11q. Patients and Methods: We performed CNV analysis and ATM sequencing on 10 patients aged 29–67 with early-intermediate stage, untreated CLL who had high risk for disease progression based on molecular and immunophenotypic markers. Eight patients had 11q- and 2 patients had UPD of 11q. CLL cells and normal cells were separated from patient peripheral blood samples by immunomagnetic beads. CNV analysis was performed on purified genomic DNA from CLL and normal cells for each patient to distinguish acquired copy number changes in malignant cells from polymorphic CNVs in the human genome. We used the Illumina 660w-quad beadchip, a SNP-based microarray for CNV analysis. CNV data was analyzed by CNV partition and PennCNV software. DNA sequence analysis of the ATM gene was performed by the dideoxy chain termination method using an ABI 3730 DNA Analyzer. All coding regions of the ATM gene (exons 4–65) and associated splice site junctions were amplified by PCR using purified genomic DNA from CLL cells. DNA sequence of the PCR products was determined on both strands. Sequence data was analyzed by Sequencher software. Results: In the 8 CLL patients with 11q−, CNV analysis demonstrates hemizygous interstitial deletions that vary from 980 Kb to 43.2 Mb. All deletions include the region of the ATM gene at 11q22.3. Two out of these 8 patients have a mutation in the residual ATM allele. One patient (CLL010) has a point mutation in exon 61 of ATM (c.8600G>A (gly2867glu)) that likely involves the substrate-binding region of the PI3-kinase domain. One patient (CLL029) has a frameshift mutation in exon 12 of ATM (c.1401_1405delCAAGA; asp467fs) that causes a premature stop signal at codon 484, presumably resulting in a truncated protein. In the 2 CLL patients with UPD of 11q, CNV analysis demonstrates copy-neutral loss of heterozygosity that extends from either 11q12.1 (CLL008) or 11q13.1 (CLL009) to the terminus of 11q. Both patients with UPD of 11q display homozygous mutation of the ATM gene. One patient (CLL008) has a point mutation in exon 58 of ATM (c.8161G>A (asp2721asn)) that likely involves the ATP binding site in the catalytic domain. One patient (CLL009) has a frameshift mutation in exon 24 of ATM (c.3238_3247del10bp/ins11bp; asp1080fs) that creates a premature stop signal at codon 1095, presumably resulting in a truncated protein. Conclusions: We report a new finding that ATM gene mutation occurs in CLL patients with UPD of 11q. Our study further expands observations reported by others concerning the role of ATM mutations in CLL. ATM mutations that we characterized include point mutations that may interfere with kinase activity and frameshift mutations that may result in a truncated ATM protein. Our sequence analysis supports a loss-of-function mechanism for ATM in a subgroup of high-risk, untreated CLL patients. The absence of detectable ATM mutations in the majority of CLL patients with 11q- may imply the existence of hidden ATM mutations not found by our targeted exon sequencing approach or epigenetic mechanisms that result in loss of gene expression. The finding that untreated CLL patients with UPD of 11q have homozygous ATM mutation supports a clonal selection hypothesis for identical alleles of mutated ATM in the absence of mutagenic chemotherapy. Selection of a CLL subclone with mutated ATM may confer a proliferative advantage through increased cell division and/or resistance to apoptosis following DNA damage. Disclosures: Zent: Genzyme: Research Funding; Genentech: Research Funding; Novartis: Research Funding; G.S.K.: Research Funding.

Abstract Abstract 1265 Poster Board I-287 Introduction Fluorescence in situ hybridization (FISH), in combination with other markers, is used as a prognostic tool for CLL patients at diagnosis. The presence or absence of trisomy 12 and deletions at 13q, 11q, and 17p helps to predict disease progression and to stratify patients for therapeutic decisions. We hypothesized that whole genome single nucleotide polymorphism (SNP)-based copy number variation (CNV) analysis would capture all of the information in current CLL FISH panels and would reveal new CNV features in the CLL genome. Patients and Methods Nineteen early-intermediate clinical stage, untreated CLL patients aged 29 to 77 were determined to be at high risk for disease progression by FISH, IgVH mutation status, ZAP-70, and CD38 prognostic markers. CLL cells and normal cells were separated by magnetic bead selection from patient peripheral blood samples with absolute lymphocyte counts that ranged from 7.4 to 162 × 109/L. CNV analysis was performed on purified genomic DNA from the CLL cells and from normal cells for each patient in order to distinguish acquired CNVs in malignant cells from polymorphic CNVs in the human genome. We used the Illumina human660w-quad beadchip, a SNP-based microarray for whole-genome genotyping and CNV analysis that contains more than 550,000 tag SNPs and approximately 100,000 additional markers that target regions of common CNV. CNV data was analyzed using CNV partition (Illumina Genome Studio software) and PennCNV. Results 100% concordance is found between del(13q), del(11q), and del(17p) FISH abnormalities and loss of heterozygosity (LOH) at 13q, 11q, and 17p by CNV analysis. All three patients with trisomy 12 by FISH show copy number(CN)=3 of chromosome 12 by CNV analysis. Of 15 patients with del(13q) by FISH, 12 out of 15 have regions of hemizygous deletion on 13q that vary from ∼830 Kb to ∼38 Mb. The smallest region of LOH is located within 13q14.3. Three out of 15 patients show homozygous deletion within 13q14.3. One of these 3 patients has copy-neutral LOH of the entire 13q arm with an embedded 835 Kb segment of homozygous deletion at 13q14.3. Two patients have large discontinuous segments of LOH on 13q, indicating complex interstitial deletion events. Two out of 5 patients with del(13q) as a sole FISH abnormality show additional CNV events in the CLL genome. One of these patients has copy neutral LOH at 2q33.1-telomere(tel). One other patient with sole del(13q) FISH shows LOH events at 10q23.31-23.33 and at 15q15.1. Five out of six patients with del(11q) by FISH have either 13q LOH (n=4) or chromosome 12 CN=3 (n=1) without any other CNV events detected in the CLL genome. One patient with trisomy 12 and del(11q) by FISH has three additional acquired CNV abnormalities in the CLL genome: LOH at 7p15.2-tel, LOH at 11p13, and CN=3 at 3q24-tel. In contrast to patients with del(11q), del(13q), and trisomy 12, patients with del(17p) by FISH have numerous acquired CNV abnormalities in the CLL genome. These include LOH events at 1p34.3-p34.2, 2q34-q36.3, 3p21.31-tel, 4p13, 4p15.1-tel, 15q11.2-q14 and 15q14-q15.3, 16p13.3-tel, 16p13.11, 16p13.2, 18p11.21-tel, 20p11.21-tel, and 20q13.2-q13.31. CN=3 at 2p12-tel is detected in 2 out of 5 patients with 17p hemizygous deletion. One out of 5 patients with 17p hemizygous deletion shows CN=3 at 10q22.2-tel. One other patient also with 17p hemizygous deletion shows CN=3 at 22q12.2-tel. Conclusions Whole genome CNV analysis by SNP-based microarrays greatly expands our ability to detect acquired genomic events in CLL cells. These events include hemizygous deletion, homozygous deletion, copy-neutral LOH, and CN=3 duplication. Detection of copy-neutral LOH is not possible by FISH or array comparative genomic hybridization technology. The current study reveals a high number of acquired CNV events in earlier stage, untreated CLL patients with 17p hemizygous deletion. This observation, indicative of genomic instability, is consistent with the known poor prognosis of del(17p) patients. The new somatic CNV abnormalities detected in CLL cells may help to discover additional genes or signaling pathways involved in CLL initiation and progression. In addition, the new CNV markers may be used in larger clinical studies to improve CLL prognosis and patient stratification for therapy. Disclosures Shanafelt: Genentech: Research Funding; Hospira: Membership on an entity's Board of Directors or advisory committees, Research Funding; Polyphenon E International: Research Funding; Celgene: Research Funding; Cephalon: Research Funding; Bayer Health Care Pharmaceuticals: Research Funding. Kay:Genentech, Celgene, Hospira, Polyphenon Pharma, Sanofi-Aventis: Research Funding; Biogenc-Idec, Celgene, Genentech, genmab: Membership on an entity's Board of Directors or advisory committees. Zent:Genentech, Bayer, Genzyme, Novartis: Research Funding.