Citations

Abstract Purpose: Glioblastoma is the most frequent and lethal primary brain tumor. Development of novel therapies relies on the availability of relevant preclinical models. We have established a panel of 96 glioblastoma patient-derived xenografts (PDX) and undertaken its genomic and phenotypic characterization. Experimental Design: PDXs were established from glioblastoma, IDH-wildtype (n = 93), glioblastoma, IDH-mutant (n = 2), diffuse midline glioma, H3 K27M-mutant (n = 1), and both primary (n = 60) and recurrent (n = 34) tumors. Tumor growth rates, histopathology, and treatment response were characterized. Integrated molecular profiling was performed by whole-exome sequencing (WES, n = 83), RNA-sequencing (n = 68), and genome-wide methylation profiling (n = 76). WES data from 24 patient tumors was compared with derivative models. Results: PDXs recapitulate many key phenotypic and molecular features of patient tumors. Orthotopic PDXs show characteristic tumor morphology and invasion patterns, but largely lack microvascular proliferation and necrosis. PDXs capture common and rare molecular drivers, including alterations of TERT, EGFR, PTEN, TP53, BRAF, and IDH1, most at frequencies comparable with human glioblastoma. However, PDGFRA amplification was absent. RNA-sequencing and genome-wide methylation profiling demonstrated broad representation of glioblastoma molecular subtypes. MGMT promoter methylation correlated with increased survival in response to temozolomide. WES of 24 matched patient tumors showed preservation of most genetic driver alterations, including EGFR amplification. However, in four patient–PDX pairs, driver alterations were gained or lost on engraftment, consistent with clonal selection. Conclusions: Our PDX panel captures the molecular heterogeneity of glioblastoma and recapitulates many salient genetic and phenotypic features. All models and genomic data are openly available to investigators.

AbstractObjectivesPrevious studies noted discordance of programmed death‐1 (PD‐1) and one of its ligands (PD‐L1) across patient‐matched primary and metastatic clear cell renal cell carcinoma (ccRCC). There are inconsistencies if the primary or metastatic tumor has higher expression, and whether metastatic tumor expression is associated with patient outcome. Thus, we examined PD‐1 and PD‐L1 in patient‐matched tumors using a large number of ccRCC patients with long follow‐up.Materials and MethodsWe analyzed PD‐1 and PD‐L1 using immunohistochemistry in patient‐matched primary and metastatic tumors from 110 ccRCC patients. Concordance was assessed among longitudinal metastatic tumors, as well as across patient‐matched primary and metastatic tumors. Cox proportional hazards regression was used to evaluate the associations of metastatic tumor expression with cancer‐specific survival.ResultsWe observed inter‐metastatic tumor heterogeneity of PD‐1 in 25 (69%) of the 36 patients and of PD‐L1 in seven (19%) patients. Concordance between patient‐matched primary and metastatic tumors was 73% (Kappa = 0.16, 95% CI: −0.003‐0.32). Similarly, concordance of PD‐L1 between metastatic and patient‐matched primary tumors was 78% (Kappa = 0.27, 95% CI: 0.09‐0.46). Both markers demonstrated higher expression in primary vs metastatic tumors. Metastatic tumor expression of PD‐1 was significantly associated with metastatic location (P < .0001) and ccRCC‐specific survival (HR = 2.15, 95% CI: 1.06‐4.36, P = .035).ConclusionsThe expression of PD‐1 and PD‐L1 is discordant across patient‐matched ccRCC tumors, with higher expression in primary tumors. Higher PD‐1 expression was associated with metastatic location and lower cancer‐specific survival. If validated, these results highlight the importance of evaluating these biomarkers in metastatic tissue specifically.

Abstract Motivation DNA methylation can be measured at the single CpG level using sodium bisulfite conversion of genomic DNA followed by sequencing or array hybridization. Many analytic tools have been developed, yet there is still a high demand for a comprehensive and multifaceted tool suite to analyze, annotate, QC and visualize the DNA methylation data. Results We developed the CpGtools package to analyze DNA methylation data generated from bisulfite sequencing or Illumina methylation arrays. The CpGtools package consists of three types of modules: (i) ‘CpG position modules’ focus on analyzing the genomic positions of CpGs, including associating other genomic and epigenomic features to a given list of CpGs and generating the DNA motif logo enriched in the genomic contexts of a given list of CpGs; (ii) ‘CpG signal modules’ are designed to analyze DNA methylation values, such as performing the PCA or t-SNE analyses, using Bayesian Gaussian mixture modeling to classify CpG sites into fully methylated, partially methylated and unmethylated groups, profiling the average DNA methylation level over user-specified genomics regions and generating the bean/violin plots and (iii) ‘differential CpG analysis modules’ focus on identifying differentially methylated CpGs between groups using different statistical methods including Fisher’s Exact Test, Student’s t-test, ANOVA, non-parametric tests, linear regression, logistic regression, beta-binomial regression and Bayesian estimation. Availability and implementation CpGtools is written in Python under the open-source GPL license. The source code and documentation are freely available at https://github.com/liguowang/cpgtools. Supplementary information Supplementary data are available at Bioinformatics online.

Abstract Genome-wide association studies (GWAS) have revealed that 25 regions in 24 genes are associated with adult diffuse glioma development. These regions were identified by performing GWAS of glioma overall and GWAS by pathology (GBM and nonGBM). Subsequently, these regions have been evaluated for associations with specific molecular subtypes. The 2016 WHO Classification of Tumors of the Central Nervous System utilizes two somatic alterations to molecularly-classify adult diffuse glioma: IDH mutation and 1p/19q codeletion. TERT promoter mutation has also been shown to be associated with age at diagnosis and patient outcome. We hypothesized that germline variants may increase susceptibility to, or interact with, these somatic alterations to accelerate the development of specific molecular subtypes of glioma. To test our hypothesis, we performed a GWAS by glioma molecular subtype – as defined by presence or absence of IDH and TERT somatic mutation and 1p/19q codeletion – utilizing a two-stage design and subsequent meta analysis that included 3001 total glioma cases and 2697 total controls. Data were imputed using the Michigan Server and logistic regression was used, adjusting for age and sex. The Cancer Genome Atlas (TCGA) data were used to perform an expression quantitative trait loci (eQTL) analysis on candidate germline variants. Variants in 2q37 and 7p22 were associated with IDH-mutated glioma (meta analysis p< 5x10-8). The eQTL analyses demonstrated significant associations between 2q37 variants and expression of nearby genes as well as associations between 7p22 variants and nearby genes (p< 0.0001). In conclusion, we identified and validated novel germline variants in two genes that are associated with etiology of IDH-mutated adult diffuse glioma.

Abstract BACKGROUND Oligodendrogliomas are classified as either WHO grade II or III depending on histologic features. Grade often influences treatment decisions. However, there is variability in patient outcome within tumors of similar grade. We hypothesized that copy number burden (CNB) and specific copy number variants (CNV) might be associated with oligodendroglioma grade and prognosis. METHODS Copy number array analyses were performed on 285 molecular oligodendrogliomas (IDH-mutant, 1p/19q-whole arm-codeleted) from the Mayo Clinic internal and consult neuropathology practice and 167 TCGA molecular oligodendrogliomas. CNB was defined as the total number of copy number alterations. The association of CNB and CNV with grade and overall survival (when available) was assessed. All Mayo and TCGA data were evaluated using the ChAS software suite (Thermo- Fisher) and blindly reviewed by a clinical cytogeneticist (RBJ). RESULTS The mean CNB was 5.0 and 10.4 in the Mayo WHO grade II and III oligodendrogliomas, respectively (p = 5.4 x 10–17). Among the TCGA WHO grade II and III oligodendrogliomas the mean CNB was 4.4 and 5.3, respectively (p = 0.034). Common CNVs (occurring in at least 5% of cases) were -4/4q-, +8/8q+, -9/9p-/cnLOH 9p, +11/11q+, -14/14q-, -15 and -18/18q-. Of these, -9/9p-/cnLOH 9p was significantly associated with higher grade in both the Mayo and TCGA cohorts (p = 8.3 x 10-10 and 0.018, respectively). In the TCGA cohort the presence of >10 CNVs or +11/11q+ was associated with a poorer survival (p = 0.016 and 0.006, respectively). CONCLUSIONS CNB is significantly associated with WHO grade in IDH-mutant, 1p/19q co-deleted oligodendrogliomas. The presence of a significantly elevated CNB in some WHO grade II tumors may be suspicious for the presence of unappreciated grade III histologic features. Longer follow-up will be necessary to determine if CNB or single CNVs are associated with survival.

Abstract Abstract 2838 The combination of novel agents and chemo-immunotherapy (CIT) has led to a significant increase in both overall and complete response rates for chronic lymphocytic leukemia (CLL). There is, however, significant clinical heterogeneity in the overall effectiveness of CIT. Specifically, some patients are long-term responders who experience durable clinical remission while others, even though responding well initially, have less durable remissions. It is unclear if this heterogeneity is a reflection of an incomplete cytotoxic effect or whether certain leukemia sub-populations (i.e. subclones) are resistant to the effects of CIT. Comprehensive analysis of tumor cells has provided, in some malignancies, evidence of extraordinary genomic complexity and intraclonal genetic diversity. Conversely, little is known of the genetic architecture of the leukemic clone in CLL patients and the extent to which CLL tumor cells differentiate genetically at the subclonal level. In order to gain insight into the genetic architecture and clonal evolution underlying disease progression/relapse, we performed a sequential, longitudinal whole genome analysis by array-based comparative genomic hybridization (aCGH) in 22 CLL cases with evidence of clinical progression and/or clinical relapse post therapy. These patients received standard purine analogue, cyclophosphamide and rituximab (PCR) for progressive disease. For the purposes of this study, we classified samples as; time point 1 (TP1) collected >6 months before starting first-line CIT for disease progression; time point 2 (TP2) consisting of tumor samples at the time of initial progression requiring treatment; and time point 3 (TP3) consisting of tumor samples collected >6 months after initial treatment but prior to subsequent treatments. Overall, aCGH assay was performed in 54 samples from 22 cases (2 to 4 time points analyzed per patient): 6 cases were analyzed at TP1 and TP2, 8 at TP2 and TP3, 2 at TP1 and TP3, and the remaining 6 cases were analyzed at TP1, TP2 and TP3. In cases showing genetic changes between time points, FISH analyses were performed in 32 additional samples to assess intra-clonal diversity and provide a quantification of the clone size. There was a small increase in genomic complexity in later time points with a mean of 4 (median 4, range 0–12) CNAs detected at the first time point for each patient, increasing to a mean of 5.3 (median 4.5, range 0–21) CNAs at the last time point analyzed. Diverse patterns of changes in genetic architecture were observed. The simplest change in genetic architectures was the linear sequence, found in 2 cases (9%) and characterized by the maintenance of the initial abnormalities and the subsequent acquisition of additional CNAs in the same subclone. The pattern of changes in genetic architecture in another 4 patients (18%) demonstrated marked heterogeneity including multiple genetic subclones evolving either in succession or in parallel. In all 4 cases with multiple subclones, a marked shift in the dominant subclone was observed at the time of disease relapse, with the minor subclones at TP1 and TP2 becoming the dominant subclones at TP3. In addition, the subclonal evolution continued following secondary therapies, and in all 4 cases the emerging subclone showed resistance to multiple treatments. This argues strongly in favor of subclones with specific genetic structures becoming dominant with the selective evolutionary pressure imposed by therapy. In summary, this sequential genetic study reveals that CLL leukemic B cells exhibit an unanticipated level of heterogeneity including a variable number of genetically distinct subclones, which display dynamic behavior in disease progression. The characterization of this intraclonal architecture is of critical importance to better understand the mechanisms of disease progression and relapse as well as to ultimately inform us of individualized treatment strategies. Disclosures: Fonseca: Consulting :Genzyme, Medtronic, BMS, Amgen, Otsuka, Celgene, Intellikine, Lilly Research Support: Cylene, Onyz, Celgene: Consultancy, Research Funding.

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.

Abstract Abstract 3538 Background: Cytogenetics detection of common recurring genetic defects by FISH is an important clinical prognostication tool in CLL and is frequently used by clinicians for counseling and risk stratification. Thus, any improvement in FISH technology is a welcome advance in our care for CLL patients. Mayo Clinic CLL FISH analyses are prepared directly from buffy coat samples rather than mononuclear cells or lymphocytes. FISH probes (deletion 6q, 11q, 13q, 17p, +12 & IGH/CCND1) are scored among consecutive nuclei without selection for nuclear morphology (so called clinical scoring). CLL B-cells are observed, microscopically, primarily as round lymphocytes with round nuclei, and we found (ASH 2010, #3606) that the % abnormal nuclei in the CLL round cell population is significantly higher than that of the non-round nuclei population. In 79 of 87 (91%) patients, the % abnormal nuclei was greater in round vs unselected nuclei (mean difference 24%; range 1.5 – 57%). Round nuclei (p = 0.004) correlated better with % B-cells by flow cytometry than either consecutive unselected nuclei (p = 0.046) or the lobed (non-round) nuclei (p = 0.40). Utilizing this “Poor Man's” sorting technique, we proposed that scoring consecutive round nuclei would improve sensitivity of detection of CLL FISH defects in patients, especially those with low B-cell counts. In a retrospective study of Mayo Clinic patients with normal baseline FISH who had a FISH defect in follow-up, we showed that by re-scoring 28 baseline cases for round nuclei exclusively, 12 originally normal samples remained normal but 16 (57%) were abnormal using the “Poor Man's” scoring technique. In the present study, we prospectively compared FISH scoring on unsorted samples using the “Poor Man's” technique vs the clinical technique. Methods: After IRB approval, we collected 63 consecutive unsorted Mayo Clinic patient blood samples referred for CLL FISH testing with an absolute lymphocyte count (ALC)< 30K × 109/L, and scored each sample using both the “Poor Man's” round nuclei method and the standard clinical method. The kappa statistic was used to adjust for chance agreement. Bland Altman plots of difference (“Poor Man's” result minus clinical result) vs the average of the two methods were generated. Results: Median age of the 40 males (64%) and 23 females (36%) was 66 years (range 36–87), and median ALC was 6.803 (range 0.980–29.750). The most common FISH defects were 11q-, trisomy 12 & 13q- by clinical technique (14%, 22% & 46% respectively) as well as by “Poor Man's” method (16%, 24% & 49% respectively). A high degree of agreement was observed between the two methods when positive/negative comparisons were made (p<0.0001). Additional FISH defects were observed in 12 of 63 (19%) patients (one 11q-, one +12; six 13q-, and four 17p-) when we utilized the “Poor Man's” method that were not observed by the clinical method. Discussion: The “Poor Man's” sorting method compares well with the clinical method for the presence and absence of FISH defects. The abnormal CLL FISH patterns are truly confined to round nuclei. The “Poor Man's” method is more sensitive than the clinical method, resulting in higher reported abnormal cells and detection of more defects. Importantly, additional FISH defects were identified in 12 patients via “Poor Man's” method that were not observed by clinical technique and 6 of these involved a change in the patients' hierarchical (Döhner) classification due to detection of the more unfavorable prognostic markers of trisomy 12 or deletion 11q or 17p. Thus, selectively scoring FISH in the round nuclei increases the sensitivity for detection of a genetic defect in CLL and provides a practical framework for prognostication in CLL patients with low lymphocyte counts and, we would speculate, including those in clinical remission or with minimal residual disease. 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.

Abstract Abstract 3605 CLL is a malignant B-cell disorder characterized by the accumulation of small B lymphocytes with a mature appearance in blood, marrow and lymph nodes. Despite effective treatment options, all patients with CLL will eventually relapse after therapy. This could be due in part to the presence of subclones of the CLL cell population that harbor genetic abnormalities, which confer resistance to treatment. The aims of this study were to investigate the clonal evolution in longitudinal samples of CLL patients and to identify genetic alterations associated with disease progression and resistance to therapy. Sequential analyses were performed in 51 samples from 23 patients who were included in a previously reported clinical trial of pentostatin, cyclophosphamide and rituximab (PCR) given every 3 weeks for 6 cycles in previously untreated CLL (Blood 109:2007). In all cases the first sample analyzed was prior to therapy. In 5 of 23 patients, three time points were analyzed: >6 months prior to entry onto PCR trial (time point A), just before starting with the PCR regimen (time point B), and the time of relapse after PCR trial (time point C). Seven patients were analyzed at time points A and B; 9 at time points B and C and 2 at time points A and C. The median time between points A and B was 17.5 months (range 8–48 months) and between points B and C was 20.5 months (7–60 m). All samples were examined by array-based comparative genomic hybridization (aCGH) using the Agilent Sureprint G3 (1 million probe) array. aCGH findings were confirmed by interphase FISH using probes for D13S319 (MIR16–1/MIR15A), RB1, MDM2, CEP12, CEP6, MYB, TP53, NFKBIA, PERP and FGFR1 loci. Overall, we observed a small increase in the number of copy-number abnormalities (CNA) with disease progression. Twenty-two of the 23 patients with paired samples harbored at least one CNA that persisted in all samples, indicating clonal relationship between the sequential samples. In 15 of the 23 patients the tumor clone was stable and no CNA differences between time points were identified. Conversely, genomic evolution was found in 8 patients. In 3 cases the genetic differences were observed pre treatment (between time points A and B) and in the other 5 cases, the observed changes were found after therapy (between time points A and C or between B and C). One remarkable case with genome evolution exhibited two subclones sharing trisomies 12 and 19, but with several unique CNA confined to each subclone. The first subclone was characterized by deletions of 6q, RB1, MIR16-1/MIR15A and 3 other losses, while the second subclone showed homozygous deletion of MIR16–1/MIR15A and 5 other monoallelic deletions. The first subclone was predominant at time points A and B (60–70% of cells), but was present in only 10–20% of cells at time point C as confirmed by FISH. Conversely, the second subclone was observed in ~20% of cells at time points A and B and became predominant after therapy, found in ~80% of cells at time point C. Another case was characterized by deletion 11q32 (including ATM and others) as the sole abnormality at time point B. Significant genomic complexity was observed at time point C, including deletions of 11q32, 9p21 (CDKN2A), 9q12-q33, 14q13.2 (NFKBIA) and 17p (TP53), and gains of 2p16 (REL) and 9q34. Interestingly, the deletion 11q32 from both time points arose independently at each time point, as they exhibited different chromosomal breakpoints and copy number variants. Moreover, the other CNA found at relapse were not identified at diagnosis (confirmed by aCGH and FISH). For evolution of specific CNA, trisomy 12 was found in 5 cases at the first sample analyzed and was stable with no changes between time points. The frequency of deletions 13q14.3 (MIR16-1/MIR15A) and 17p increased at the later time points. Conversely, –6q decreased in frequency across time points (3 cases in time points A–B and 1 case in time point C). In summary, at least 35% of CLL patients exhibited clonal evolution and at least 9% showed evidence of multiple subclones. This subgroup of CLL patients provides an exceptional framework for comprehensive analysis of genome evolution during disease progression before and after therapy. Our observations also support the hypothesis of a common CLL progenitor cell can give rise to clonally related, but genetically evolving subpopulations of tumor cells. Finally, this study may bring novel information regarding the drug resistance pathways utilized by CLL B cell clones post therapy. Disclosures: Kipps: GlaxoSmithKline: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Genentech: Research Funding; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Research Funding; Genzyme: Research Funding; Memgen: Research Funding; Igenica: Consultancy, Membership on an entity's Board of Directors or advisory committees; Sanofi Aventis: Research Funding; Abbott Laboratories: Research Funding. Fonseca:Genzyme: Consultancy; Medtronic: Consultancy; BMS: Consultancy; AMGEN: Consultancy; Otsuka: Consultancy; Celgene: Consultancy, Research Funding; Intellikine: Consultancy; Cylene: Research Funding; Onyx: Research Funding; FISH probes prognostication in myeloma: Patents & Royalties.

Abstract Abstract 3606 Background: Cytogenetic abnormalities are important prognostic indicators in CLL. At Mayo Clinic, CLL FISH analyses are derived from buffy coat samples not purified for lymphocytes. Scoring is therefore performed on consecutive qualifying nuclei regardless of cell size, shape or morphology. This scoring may not reflect the percent of abnormal nuclei of the affected cell type, but rather the entire population of cells present in the sample. We sought to determine whether the percent abnormal nuclei in only the affected cell type (e.g. lymphocytes) of patients with CLL differed from that of the general cell population. Scoring only B-lymphocytes could increase the sensitivity of the test in patients with low B-cell counts, either early in their disease or after treatment. Cell sorting techniques could be used to reach this goal but can be expensive, labor intensive and add to completion time. We propose a “Poor Man's Cell Sorting” technique based on cell morphology when stained with 4',6-diamidino-2-phenylindole (DAPI). In CLL samples, both round and so called “lobed” cells are seen by DAPI staining but we hypothesize that the CLL B-cells typically present as perfectly round in shape (Fig. 1). Thus our hypothesis: if only the round cells are scored for a genetic defect, would this more accurately represent the malignant leukemic B-cell population and allow for enhanced disease status by FISH? Methods: After IRB approval, we identified 87 CLL patients (75% male; 25% female, mean age 62.4 y, range 43–89 y) in the Mayo Clinic CLL Database, who were seen at Mayo Clinic between March, 2002 - July, 2010. We selected patients known to have low level FISH abnormalities and who therefore should have a significant population of both lymphocytes and neutrophils. Selection criteria included <20×106 B-cells per microliter (by flow cytometry) of peripheral blood and ≤40% of interphase nuclei expressing a specific FISH abnormality. Although most of the 87 patients exhibited more than one FISH abnormality, we focused on only one FISH defect per patient for this study. The original specimen (slide or fixed cell pellet) was rescored for % abnormal nuclei among 100 consecutive round and 100 consecutive lobed (or multilobular) nuclei, using DAPI to identify nuclear architecture. These scores were compared to each other and to the original clinical FISH analysis (scored for 200 consecutive nuclei and not selected for nuclear morphology). Results: Among 87 cases, FISH signals were scored for 6q-(1), 11q-(9), +12(15), 13q-(58), 17p-(2) and 2 IGH rearrangements. In 86/87 cases, the abnormal lobed nuclei did not have FISH defects. One patient exhibited 35% +12 by clinical assay, 52% +12 in the round nuclei, and 11% by lobed nuclei. For all cases, the mean percentage of abnormal nuclei was greater in the round cells (46%) vs original scoring (23.6%). In 79/87 patients (91%), the % of abnormal nuclei was greater in the round cells vs original FISH (mean increase 24.3%; range 1.5–57%). One patient's score was the same in round cells vs original, and 7 patients exhibited fewer abnormal nuclei in the round cells vs original. For these 7 cases, the mean % abnormal nuclei was 5.6% for round nuclei vs 8.4% for original score (score differences ranged from 1 – 5.5%). Overall, by univariate regression analysis, round cells (p=0.0043) have a better correlation with % B-cells, ascertained by flow cytometry, than either the current clinical approach (p=0.0462) or the lobed-cell approach (p=0.4058). Discussion: In virtually all cases (99%), the abnormal FISH patterns were confined to the round nuclei, and the lobed nuclei were virtually always normal by FISH. For patients with <20×106 lymphocytes, selecting for round nuclei uniformly resulted in identification of a higher percentage of abnormal cells. Further studies, including comparison of our round nucleus approach to CLL FISH analysis to actual sorted B-lymphocyte cell selection and the association of this leukemic restricted estimation of abnormal FISH levels to clinical outcome are necessary. Given our findings, we believe that estimating FISH defects restricted to the leukemic B-cell population will become an important adjunct to cytogenetic analysis for patients with low lymphocyte counts, including those in clinical remission and those with minimal residual disease. Disclosures: No relevant conflicts of interest to declare.