Slager, Susan L.

Abstract Background Next Generation sequencing (NGS) is a powerful tool to identify somatic mutations associated with tumor onset and drug response. While it is well suited for high quality fresh/frozen samples, NGS is not proven for FFPE tissue which is the most common type of clinical specimen. Since the nucleic acids can be readily extracted from FFPE samples for a variety of genomic analyses, a comparative mutational analysis of paired frozen and FFPE tissues is urgently needed. Our long term goal is to establish a lab protocol to detect mutations in FFPE tumors using a targeted capture and sequencing approach for genes of interest. This pilot study focuses on the comparison of FFPE and frozen samples to test the validity of using FFPE tissues in such application. Methods Gene Selection: 128 genes associated with known pathogenic mutations in lymphoma Sample Selection: 9 diffuse large B-cell lymphoma (DLBCL) cases with FFPE, frozen and germline samples, as well as 10 frozen normal lymphatic tissues as references for CNV detections Capture Probe Design: We targeted coding exons and UTR, as well as the evolutionarily conserved intronic regions. The capture probes were designed using the Agilent eArray tool. The titling density of the probes was set to 3 probes overlapping with every base in the target region to improve the capture efficiency in FFPE samples. The least stringent masking of the repeat regions was allowed to include regions with small repeats that are shorter than the length of the sequencing reads (100-bp). In addition, boosting parameters were picked to set various levels of probe replication in different regions in order to minimize the local coverage differences (e.g. between regions of different GC contents) Sequencing and Bioinformatics: The target capture and sequencing were performed by the Mayo Clinic Medical Genome Facility. The reads were mapped to Human Reference Genome Build 37 using Novalign, and SNVs were called using GATK. The CNVs were identified using an in-house developed algorithm, patternCNV. Results The designed probes covered 99.65937% of the target regions. We generated 2.2-6.7 Gbp of reads per sample, 57.4-71.5% of which were on target. This equalled an average coverage of 2100-6700 folds which is 10-30 times higher than the minimal coverage recommended by Agilent. Due to this high coverage, we observed duplicate reads that accounted for 7.7-73.5% of the total reads. When we analysed the data with and without the duplicated reads, the concordance of the called SNVs was between 84-93% out of 207-249 mutated positions per trio-sample. There were 7.8-8.9% and 1.1-2.2% unique SNVs per sample by excluding or including duplicate reads, respectively. The dis-concordances were mostly missed calls, where a SNV was observed in only 1 or 2 of the trio samples. The missed calls from frozen samples ranged from 0-10.4% compared to 1.4-10.4% from the FFPE tissues, with 0.88-2.4% more SNVs missed in FFPE. Further analyses showed that all of the missing calls came from the lack of or low coverage of the corresponding positions. There were also differences of the called SNVs between the trio samples. However, this was extremely rare. Only 2 out of the 9 trio samples at a total of 3 positions had disagreements in called SNVs between FFPE and frozen tissues, all due to the allelic imbalance where the percentage of reads supporting the alternative alleles were below 20%. Therefore, this dis-concordance can be removed by back-filling of the read-level information for each position. Unfortunately only 11.9-47.4% of the CNVs called in frozen tissues were identified in FFPE samples, due to the widely various coverage in FFPE samples. The consequent large noises of the log ratio values between the FFPEs and normal references significantly reduced the sensitivity for CNV calling. Conclusions This pilot study compared the performance of SNV and CNV detection in FFPE and paired frozen tissues using a target capture and sequencing approach. With a capture probe design strategized to benefit FFPE samples, we observed SNV detection rates in FFPE that were only slightly lower (0.88-2.4%) than those of frozen tissues due to poor coverage of some positions in FFPE samples. With a proper back-filling step, there was no dis-concordance of the called SNVs between FFPE and frozen samples. However, CNV detections in FFPE were more problematic due to the un-predictable regional coverage in FFPE samples. Disclosures: No relevant conflicts of interest to declare.

Abstract Background: Over the last decade, increasing numbers of families with at least 2 cases of CLL or other B-cell lymphoproliferative disorders have been described. Methods: Families seen at Mayo Clinic with at least one individual diagnosed with CLL and one or more first or second degree relative diagnosed with CLL or a B-cell lymphoproliferative disorder(LPD) were identified. Clinical characteristics and risk stratification test results (cytogenetic abnormalities by FISH, level of CD38 expression, and IgVH gene mutation status) were extracted and reviewed. Serum, intracellular and CLL B cell secreted levels of pro- and anti-angiogenic cytokines (VEGF, BFGF, and TSP) were also compared between cases of familial and sporadic CLL. Results: Seventy-one families seen at Mayo Clinic were identified meeting criteria for familial CLL. Of the 71 index CLL families, 78.9% (n=56) had at least one other first or second-degree relative with CLL or a B cell LPD, 15.5% (n=11) had 2 other affected members, and 5.6% (n=4) had 3 or more affected members. Of affected family members with B-cell LPDs other than CLL, 64% (n=25) had non-Hodgkin lymphoma, 21% (n=8) had Hodgkin disease, 10% (n=4) had multiple myeloma or Waldenstrom macroglobulinemia, and 5% (n=2) had another lymphoid leukemia (1 ALL, 1 hairy cell leukemia). The median age was 62, with 63% males and 37% females. The majority of individuals had an early Rai stage at diagnosis (stage 0–66%, stage I-19%). Results of cytogenetic testing by FISH, CD38 status, IgVH gene mutation status appear similar in familial and sporadic CLL cases seen at Mayo clinic during the same time interval. No clear pattern of IgVH gene mutation status, IgVH gene family usage, level of CD38 expression, or cytogenetic abnormalities by FISH was seen among multiple affected members from the same family. There were also no significant differences noted in serum, intracellular, and CLL B cell secreted levels of VEGF, BFGF or TSP in the familial samples when compared to a cohort of non-familial samples. Conclusions: Expression of cytogenetics by FISH, immunophenotype, IgVH mutation status and levels of serum, intracellular and cytoplasmic pro- and anti-angiogenic factors(VEGF, BFGF, and TSP) were similar in individuals with familial and sporadic CLL.

Abstract Abstract 2409 Background: Serum free light chain (FLC) quantitation has prognostic value in MGUS, multiple myeloma (MM), solitary plasmacytoma, and amyloid light chain (AL) amyloidosis, and it has been incorporated in response criteria for both MM and AL amyloidosis. Two recent studies have shown FLC abnormalities are present in 39–54% of CLL patients and are associated with shorter time to treatment (TTT) and inferior overall survival (OS) in CLL. Here we report the largest study to date of FLC abnormalities in a prospective cohort of CLL patients and explore the effects of both monoclonal and polyclonal FLC elevations. Methods: Newly diagnosed CLL patients were prospectively enrolled in the University of Iowa/Mayo Clinic SPORE Molecular Epidemiology Resource (MER). Serum FLC was quantitated from stored research serum samples using the Freelite FLC assay (The Binding Site, Ltd., Birmingham, UK). Elevated FLC was defined as either kappa or lambda above the reference range (k>19.4 mg/L, l>26.3 mg/L). Monoclonal FLC elevation was defined as elevated FLC with an abnormal FLC ratio. Polyclonal FLC elevation was defined as elevated FLC with a normal FLC ratio (0.26–1.65). Patients with normal FLC but abnormal FLC ratio were evaluated as a distinct group (Abnormal FLC Ratio). Clinical data was abstracted using a standard protocol for the MER and patients were followed systematically for TTT and OS. Cox proportional hazards models were used to assess the association of FLC with TTT and OS. Results: 385 CLL patients diagnosed between September 2002 and February 2008 with available serum were assayed. At a median follow-up of 47 months (range 1–94), 135 patients (35%) have been treated and 43 patients have died (11%). Abnormalities in FLC were present in nearly half of the CLL patients (48.8%). Although 32.4% had an elevated kappa or lambda, only 14.0% had a monoclonal FLC elevation while the remaining 18.4% had a polyclonal FLC elevation. An additional 16.4% had an abnormal ratio without elevated FLC. Monoclonal FLC elevation was associated with high risk features of CD38+, CD49D+, ZAP70+, IGHV unmutated and having high risk FISH (del 17p13; del 11q22). Monoclonal FLC elevation was highly associated with shorter TTT (HR=3.24, p=0.0007) and poor overall survival (HR=4.14, p=0.0006). These associations remained statistically significant after adjusting for stage and prognostic factors. Abnormal FLC ratio without elevated FLC was also associated with shorter TTT (HR=1.74, p=0.03), though this association did not hold after adjustment for stage and prognostic factors. Polyclonal FLC elevations were associated high risk FISH and poor overall survival (HR=6.41, p<0.0001, adjusted HR = 4.82, p=0.0002) but not with TTT. Conclusions: In the largest series of newly diagnosed CLL patients reported to date, nearly half of CLL patients have abnormal FLC concentrations. Monoclonal FLC elevation is an independent predictor of shorter TTT and inferior overall survival in CLL, is associated with high risk markers, and may be a marker of an aggressive tumor. Polyclonal FLC elevation without abnormal FLC ratio is independently associated with poor overall survival but not TTT suggesting it may be a non-specific marker of host frailty/comorbidity rather than disease specific outcomes. Regardless of cause, CLL patients with elevated FLC have poor outcome and FLC may have utility as a biomarker in CLL. Disclosures: Zent: Genzyme: Research Funding; Genentech: Research Funding; Novartis: Research Funding; G.S.K.: Research Funding.

Abstract Abstract 2443 Background: There is strong and consistent evidence that a genetic component contributes to the etiology of chronic lymphocytic leukemia (CLL). A recent genome-wide association (GWA) study of CLL identified genetic variants located on chromosomes 2q13, 2q37.1, 6p25, 11q24, 15q23, and 19q13 that increased the risk of CLL within a European population. We replicated 5 of these 6 loci in an independent sample of CLL cases and controls from the United States. We now investigate whether these loci also influences MBL, a reported precursor condition of CLL. In addition, a follow-up analysis of the initial GWA study identified four more CLL-susceptibility loci on 2q37.3, 8q24.21, 15q21.3, and 16q24.1. Herein, we also evaluate the association of these four loci with risk of CLL. Methods: Peripheral blood samples were obtained from three ongoing studies: the Genetic Epidemiology CLL (GEC) Consortium, the Mayo Clinic non-Hodgkin lymphoma (NHL)/ CLL study, and the Mayo Clinic Biobank. We implemented rigorous genotyping quality-control measures, and successfully genotyped a total of 407 CLL patients, 965 controls, and 60 MBLs from these studies. Within each locus, the previously reported single nucleotide variants (SNPs) or variants in high linkage disequilibrium (LD) with the previously reported SNPs were evaluated with risk of MBL or CLL. Tests for association was done using the Cochran-Armitage trend test, and unconditional logistic regression was used to estimate odds ratios (ORs) and corresponding 95% confidence intervals (CIs) for CLL or MBL risk Results: In our evaluation of the six initially reported CLL-susceptibility loci (2q13, 2q37.1, 6p25, 11q24, 15q23, and 19q13) with MBL risk, we found three of the six had suggestive associations (p-value < 0.20) with ORs comparable to and in the same direction as those observed from CLL risk. Our strongest finding was with rs13397985 at locus 2q37.1 (OR= 1.56; 95% CI: 1.05, 2.31; p-trend = 0.041), followed by rs17483466 at locus 2q13 (OR= 1.49; 95% CI: 0.99, 2.24; p-trend = 0.074). As expected given our previously reported findings with CLL risk, the association between rs11083846 on chromosome 19q13 and MBL risk was not significant (p-trend = 0.70). Of the four recently reported CLL-susceptibility loci SNPs located on 2q37.3, 8q24.21, 15q21.3, and 16q24.1, we found all to be associated with CLL risk but one. Specifically, the strongest association was seen for locus 8q24.21 (best tagged SNP rs1021955; OR = 1.37; 95% CI: 1.10, 1.70; p-trend = 0.005), followed by locus 16q24.1 (best tagged SNP rs305065; OR= 0.77; 95% CI: 0.61, 0.97; p-trend = 0.024). However, we found no associations for locus 15q21.3 for the previously reported SNP nor for any SNPs in LD with the previously reported SNP. Conclusions: Our MBL results provide additional robust genetic evidence that MBL is a precursor to CLL and that it shares similar underlying genetic predisposition. Also our results confirm three of the four recently reported CLL-susceptibility loci and further support the role of a genetic basis in the etiology of CLL. More research is needed to elucidate the potential manner in which these genetic loci function in CLL or MBL. Disclosures: No relevant conflicts of interest to declare.

Abstract Abstract 4610 Introduction Infections are a major cause of morbidity and mortality in patients with chronic lymphocytic leukemia (CLL). Up to 50% of CLL patients develop infectious complications, and 30–50% of all deaths in CLL patients are attributed to infections. Despite these data, the available research on infectious complications in CLL is primarily limited to patients participating in clinical trials of chemotherapy, obscuring the distinction between the risk of infection due to the disease’s natural history relative to the risk associated with therapy related immune suppression. METHODS: The Mayo Clinic Rochester (MCR), a tertiary referral center in rural southeastern Minnesota, is also the primary hematology center for southeastern Minnesota, northern Iowa, and western Wisconsin. There are no metropolitan areas or hematology specialty centers within a ∼50 mile radius. To explore the natural history of infection in a community-based cohort of CLL patients, we used the Mayo Clinic CLL database to identify all patients with newly diagnosed CLL who resided within 50 miles of MCR and diagnosed between January, 1999 and December, 2009. The comparison cohort consisted of 689 adult patients who also resided within 50 miles of MCR who were seen for a general medical examination between September, 2002 and December, 2009 and who were enrolled as controls in a case-control study of non-Hodgkin lymphoma. All hospitalizations at MCR among both cohorts were audited to document hospitalization with infection and cross-referenced with the Mayo Clinic infection database, which includes all culture results obtained from hospitalized MCR patients. Serologies and viral assays were also reviewed. Patients whose cultures were negative but who were given a clinical diagnosis of infection (e.g. pneumonia) and who were treated with a full course of antibiotic therapy were considered to have a culture negative infection. RESULTS: In May 2010, there were 2022 CLL patients in the Mayo Clinic CLL Database diagnosed between 1999 and 2009. Of these, 174 (9%) were local CLL patients residing within 50 miles of MCR. Median age at diagnosis for these non-referred CLL patients was 69 years (range 27–97). Most had early stage disease (60% stage 0; 32% stage I-II). On prognostic evaluation, 121 (75%) patients were CD38 negative, 66 (61%) ZAP-70 negative, 47 (50%) IGHV mutated, and 56 (62%) had either no abnormality or 13q14- as a sole abnormality on FISH analysis. 64 (37%) patients progressed to require treatment for CLL during follow-up. After median follow-up of 4.0 years (range 0–11), 32 (18.4%) CLL patients were hospitalized with infection at least once as compared to 20/689 (2.9%) individuals in the control cohort (odds ratio=7.5; p<0.0001) Figure 1A. Even prior to receiving treatment for CLL, the rate of hospitalization for infection remained higher than the control cohort (p=0.002; Figure 1B). The 32 CLL patients hospitalized with infection were admitted with infection a total of 89 times (median 1 hospitalization for infection per patient). A specific infectious organism was identified by cultures or serologies in 60 (63%) of the 89 infections in CLL cases and 10/27 (37%) infections among controls. Hospitalization for an opportunistic infection (e.g. cytomegalovirus, cryptococcus, filamentous fungi, mycobacteria, Pneumocystis) occurred in 5/174 (3%) CLL patients during follow-up compared to 0/689 controls (p<0.001). Finally, we performed a pooled multivariable analysis of all patients (n=863) to identify factors (age, sex, CLL diagnosis, CLL treatment) associated with infection risk. Most factors were independently associated with hospitalization for infection [Age (per year, OR=1.03, p=0.02), sex (male, OR=4.0, p<0.001), diagnosis of CLL (OR=2.1, p=0.09), and treatment for CLL (OR=5.9, p<0.001)]. In univariate analysis of CLL patients [sex (OR=4.2, p=0.01), higher Rai stage (p=0.046), unfavorable (del 17p13; del 11q23) FISH [OR=4.6, p=0.02] and unmutated IGHV [OR=2.8, p=0.07]) were associated with risk of infection. CONCLUSIONS: In this cohort study, patients with newly diagnosed CLL had a 7.5-fold risk of hospitalization for infection relative to the control cohort. After 4 year follow-up, ∼1 in 5 CLL patients required hospitalization for infection. Although CLL treatment was a substantial risk factor for infection, the risk of infection among untreated patients remained higher than controls. 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. Zent:GlaxoSmithKline: Research Funding; Genentech: Research Funding; Genzyme: Research Funding.

Abstract Background Although its prevalence is not well defined, transformation to Hodgkin lymphoma (HL) is a rare but well recognized complication in patients with CLL. Prior studies have reported a median survival of 0.8-1.7 years in these patients. Prior therapy of CLL, especially with purine analogs, has been shown to have adverse impact on survival after development of HL. We used the Mayo Clinic CLL database to describe outcomes of CLL patients seen at our institution who developed HL. Methods The Mayo Clinic CLL database includes all consenting patients with a pathologic diagnosis of CLL. Patients who developed biopsy-proven HL were included in this analysis. For patients referred from an outside institution, pathology review at Mayo Clinic was mandatory to be included. Clinical characteristics, therapy and overall survival (OS) were analyzed for all HL patients. Results Among 3124 CLL patients seen at Mayo Clinic from 1/1995 to 7/2011, 26 developed HL. In a nested cohort of 1644 patients who were seen within 12 months of CLL diagnosis and followed prospectively, the prevalence of HL was 0.05%/year (10 year risk=0.5%). All 26 patients had classical HL. The median duration between CLL diagnosis and development of HL was 6.2 years (range, 0-24.5 years). The median age at diagnosis of HL was 68 years (range, 45-88 years) and 21 (81%) were male. At the time of HL diagnosis, the median WBC count was 7.8 x 109/L (range, 1.3-87.3), median hemoglobin was 11 gm/dL (range, 7.2-13), median platelet count was 220x109/L (range, 53-627), median serum lactate dehydrogenase was 249 U/L (range, 133-658), and median serum albumin was 3.4 gm/dL (range, 2.6-4.2). According to the Ann Arbor staging system for HL, 10 (38%) were Stage II, 2 (8%) were Stage III, 11 (42%) were Stage IV, and undetermined in 3 (12%) patients. Sixteen patients (61%) received HL therapy with doxorubicin, bleomycin, vinblastine and dacarbazine (ABVD), seven (27%) received other chemotherapy, and treatment was unknown in 3 (12%) patients. No patient underwent stem cell transplantation as therapy for HL. After a median follow-up of 8.7 years from CLL diagnosis date, 16 (61%) patients have died. The median OS from date of HL diagnosis was 3.9 years (95% CI, 1.0 – 5.0 years). The International Prognostic score (IPS) for HL, originally proposed by Hasenclever in 1998, identified seven prognostic factors: serum albumin <4 gm/dL, hemoglobin <10.5 gm/dL, male sex, age >45 years, stage IV disease, WBC≥15 x 109/L, and lymphocytopenia in patients with newly diagnosed HL. When we applied these prognostic parameters (available in 22/26 patients, 85% in our cohort), the IPS score predicted median survival as follows: score of ≤2 (18% of the patients), median survival not reached; score of 3 (23% of the patients), 6.2 years; score of 4 (36% of the patients), 2.4 years; and score ≥5 (23% of the patients), 0.3 years (p-value=0.005, Figure 1). In contrast, the Richter syndrome prognostic score developed for CLL patients who transform to diffuse large B-cell lymphoma failed to predict survival in these patients (Tsimberidou, JCO, 2006). Of the 26 patients with HL, 16 (61%) had received therapy for their CLL prior to developing HL, including 12 (46%) who had received more than one line of therapy. Purine analogs had been administered for treatment of CLL prior to development of HL in 13/26 (50%) patients. The median survival of HL patients who had previously received CLL therapy was significantly worse compared to those who were untreated for CLL (2.8 years vs. 7.6 years, p-value=0.02). There was a trend toward shorter survival for HL patients who had received previous purine analog therapy for CLL compared to those who received alternate therapies (1.8 years vs. 5 years, p-value: p-value=0.07). Of the 9 HL biopsy samples in which Epstein Barr virus (EBV) in-situ hybridization studies were performed, EBV was detected in 6 (67%) patients. No association was observed between prior purine analog therapy and EBV status (p-value=1.0). There was no difference in survival according to the EBV status of HL (p-value=0.33). Conclusion The 10 year incidence of transformation to Hodgkin transformation among patients with newly diagnosed CLL is 0.5% (∼1/200 CLL patients). In this single-institution analysis, median survival of CLL patients who developed Hodgkin transformation of CLL was approximately 4 years after HL diagnosis. The IPS accurately predicted survival in our cohort of HL patients. Disclosures: Zent: Novartis: Research Funding; GlaxSmithKline: Research Funding; Biothera: Research Funding; Genzyme: Research Funding; Genentech : Research Funding. Shanafelt:Glaxo-Smith-Kline: Research Funding; Cephalon: Research Funding; Hospira: Research Funding; Celgene: Research Funding; Polyphenon E International: Research Funding; Genentech: Research Funding.

Abstract BACKGROUND: Studies have suggested that patients with CLL are at a significantly increased risk of developing other lymphoid malignancies. Whether the risk of developing a 2nd lymphoproliferative disorder (LPD) is more strongly related to characteristics of the leukemia cell or to other factors such as prior chemotherapy is unknown. This distinction is important given increasing momentum to pursue early treatment of CLL patients based on recently identified prognostic markers, e.g. ZAP-70, IgVH mutation status. We used the Mayo Clinic CLL Database (DB) to conduct an observational cohort study to evaluate the relationship between clinical, biologic, and treatment characteristics and the risk of secondary LPD. METHODS: The Mayo Clinic CLL DB was established in 1999 and included 962 patients at the time of the present analysis. Clinical information regarding date of diagnosis, prognostic parameters, treatment history, disease-related complications, and co-morbidities was abstracted from clinical records on all patients at the time of study enrollment and maintained on an ongoing basis. For the present study, cases of secondary LPD were identified by chart review and cross referencing patient clinic numbers from the CLL DB with the Mayo Clinic Lymphoma and Leukemia/Myelodysplasia databases. Additionally, all clinic numbers were cross-referenced with an electronic hematopathology database that has recorded results of all bone marrow and lymph node biopsies of all Mayo Clinic patients since 1992. RESULTS: A second LPD was identified in 26 (2.7%) of the 962 CLL patients during a median follow-up of 7.12 years (range 0.1–21.0). The median time from diagnosis to development of secondary LPD was 4.4 years (range 0–19 years). Diffuse large B-cell lymphoma was the most common subtype of secondary LPD (12 of 26 cases). Gender was associated with increased risk of developing 2nd hematologic cancer where 1% of women compared to 3.4% of men (p=0.051) developed a 2nd LPD. Treatment history was also related to development of a 2nd LPD. 2nd LPD developed among 4% of previously treated CLL patients compared to 2% of untreated patients (p=0.08). Among the 362 patients who were treated for CLL prior to developing a second LPD, the median time to first treatment was shorter for those who developed a 2nd LPD (2.43 years vs. 6.22 years; p<0.001). No statistically significant association was observed between other clinical or biologic leukemia cell characteristics and development of 2nd LPD including IgVH gene mutation status, ZAP-70 status, CD38 status, cytogenetic abnormalities by FISH, B2M, stage at diagnosis, or ALC at diagnosis. CONCLUSIONS: In this observational cohort study, prior treatment demonstrated a stronger correlation with the risk of developing a 2nd LPD than did leukemia cell characteristics including IgVH gene mutation status, FISH, ZAP-70, B2M, and CD38. This finding suggests Richter’s transformation may relate more to therapy than characteristics of the leukemia cell itself. Until the results of clinical trials evaluating the role of early treatment based on prognostic parameters are available, this result underscores the importance of delaying administration of chemotherapy until patients meet established criteria for treatment.

Abstract Patients with CLL complicated by autoimmune diseases causing cytopenias (AID) are often considered to have clinically advanced disease (Rai stage III - IV, Binet C). With the use of automatic differential counts and flow cytometric immunophenotyping of peripheral blood, CLL is now most often diagnosed in asymptomatic patients with early stage disease. These changes in clinical practice could have an impact on clinical presentation and prognosis of CLL patients with AID. To more fully define AID complicating CLL, we conducted an observational study of a large cohort of CLL patients. Methods All 1737 patients with chronic B cell lymphoproliferative diseases seen in the Division of Hematology at Mayo Clinic Rochester from January 1, 1995 to December 30, 2004 were included. Lymphoid malignancies were classified using WHO and modified NC-WG 1996 criteria (CLL = 1649, “atypical” CLL = 4, leukemic phase of lymphoma = 9, chronic B cell lymphoproliferative disorders (not otherwise classified) = 75). Autoimmune hemolytic anemia (AIHA) was defined as a Hgb ≤ 10 g/dL with at least one appropriate marker of hemolysis (elevated indirect bilirubin, LDH, or reticulocyte count; or increased bone marrow erythropoiesis without bleeding) and evidence of an autoimmune mechanism (positive DAT, cold agglutinins), or at least 2 markers of hemolysis in absence of evidence of bleeding or hypersplenism. Immune thrombocytopenia (ITP) was defined as a platelet count of ≤100 x 109/L with normal/ increased bone marrow (BM) megakaryocytes or normal/increased absolute reticulocyte count. Pure red blood cell aplasia (PRBCA) was defined as a Hgb ≤ 10 g/dL, reticulocytopenia, and an isolated absence of BM erythrocyte precursors. Autoimmune granulocytopenia (AIG) was defined as sustained neutropenia (< 0.5 x 109/l) in the absence of chemotherapy for at least 8 weeks and with decreased/absent BM granulocyte precursors. Results Seventy four (4.5%) CLL patients had AID (78% male, median age at diagnosis 67 yr). The diagnosis of AID preceded CLL in 12% and was concomitant with the diagnosis of CLL in 15% of patients. Of the CLL patients with AID, 55% had AIHA, 47% ITP, 10% PRBCA and 4% AIG; 10% had coincident AIHA and ITP (Evans syndrome). Most AIHA (74%) patients presented with symptomatic anemia but 68% of the ITP patients were asymptomatic at diagnosis. Forty one patients (55%) developed AID prior to receiving any treatment for CLL. Only 9 of the 33 patients who developed AID after treatment for CLL had received purine analogues. Eighteen (24%) patients with CLL and AID died; the estimated median survival was 12.4 yr. Discussion In this CLL population with predominantly early stage disease at diagnosis (> 60% Rai stage 0), AID is clinically distinct from that previously reported in patients with more advanced disease. A higher proportion of patients had ITP which was usually asymptomatic. Most patients with AID had not previously required therapy for CLL. Purine analogue therapy did not appear to be a major cause of AID in this population. Overall survival was considerably more favorable than that previously reported with CLL induced bone marrow failure (Rai stage III-IV, Binet C). We conclude that the earlier diagnosis and subsequently longer follow up of patients with CLL has altered the clinical presentation and prognostic consequences of AID. A more detailed analysis of the correlation between novel prognostic risk factors and the risk of AID in CLL patients is planned.

Abstract Tumors arise and evolve by iterative steps of mutation, subclonal selection, and clonal expansion due to growth advantage of the fittest subclones and external mutation induction and selection pressure from radiation and drug therapies. Various studies have shown that greater clonal complexities in primary tumors are correlated with poor clinical outcome of tumor progression and/or drug resistance. Recently, we have reported that very few of the driver mutations, all of which were clonal, detected in primary diffuse large B-cell lymphoma (DLBCL) were associated with DLBCL outcome as measured by 24-month event-free survival (EFS24). In the current project, we identified and studied subclonal mutations in primary DLBCL tumors and assessed their associations with EFS24, as well as the role of activation-induced cytidine deaminase (AID) in genomic mutations occurred in DLBCL tumors. The detection of subclonal mutations is still a significant bioinformatics challenge. In addition, identification of clonal mutations in samples with lower tumor purities faces similar challenges due to the low concentration of reads supporting the mutant alleles. The current methods of somatic mutation calling are not sufficiently sensitive to identify the low concentration mutations in tumor DNA sequencing data. We implemented a bioinformatics workflow for low-concentration and subclonal mutation detection which is based on the positional read pile-up data and a back-fill approach (PUB). The pile-up files were first generated using the re-aligned and re-calibrated BAM files after read alignment using Burrows-Wheeler Aligner (BWA). The variant positions with alternative bases were annotated by attributes defined in the Variant Quality Score Recalibration (VQSR). PUB then used a boosting method and a generalized linear model (GLM) to train a model of 'good quality' variants using common variants from HapMap, and prioritized and called clonal and subclonal variants based on the trained model. The VQSR attributes related to alternative allele depth were less-weighed in order to call subclonal mutations. The somatic mutations were then identified by Fisher's Exact Test using sequencing depths of the reference and alternative alleles from paired tumor and germline sequencing data. The exome sequencing data of paired tumor and peripheral blood from 48 newly diagnosed DLBCL patients were analyzed using PUB. Thirty-six of the 48 patients achieved EFS24 with the other 12 patients experienced primary treatment failure. Most of the tumors studied had tumor purities between 40-70%. PUB identified substantially higher number of somatic mutations, both clonal and subclonal, compared to those detected using existing somatic callers. We observed that the prevalence of mutations in previously reported driver genes were higher using thresholds of mutation concentration ≥ 5% and Fisher's Exact Test p ≤ 0.05, including EZH2 (mutated in 26% of DLBCL tumors analyzed by PUB, compared to 12.7% as previously reported), MLL2 (72% vs. 31%), CD79B (22% vs. 14%), TNFRSF14 (36% vs. 20%), MEF2B (22% vs. 16.4%), CARD11 (46% vs. 21.8%), and MYD88 (18% vs. 11%). In addition, other genes involved tumorigenesis that have not been previously linked to DLBCL also harbored both clonal and subclonal mutations with substantial prevalence, including FGFR3 (12%), KIT (24%), and ATM (28%). Furthermore, association of genes displaying clonal and subclonal mutations with EFS24 identified potential biomarkers for DLBCL outcome. Among these, two genes EPGN and ASTE are involved in epithelial growth factor receptor signaling and had association p values of 0.0001 and 0.0016, respectively. The oncogene MAFB was also associated with EFS24 (p= 0.0016). We searched for AID induced mutations among all identified variant positions and concluded that there was no evidence of AID site enrichments compared to a simulated data set. In summary, we developed and applied a sensitive bioinformatics pipeline for the identification of both clonal and low concentration somatic mutations in primary DLBCL exome sequencing data which further revealed the clonal complexity of the primary DLBCL tumors. Several of the genes were identified as potential biomarkers for DLBCL outcome. Disclosures Maurer: Kite Pharma: Research Funding. Ansell:Bristol-Myers Squibb: Research Funding; Celldex: Research Funding. Link:Genentech: Consultancy, Research Funding; Kite Pharma: Research Funding. Cerhan:Kite Pharma: Research Funding.

Abstract Abstract 1540 Background: Diffuse Large B-cell Lymphoma (DLBCL) is the most common lymphoma in the western world. Outcomes have improved with the standard initial therapy of rituximab and anthracyline based chemotherapy (immunochemotherapy). However, 20–40% of patients will either fail to achieve remission or relapse following initial immunochemotherapy. Most relapses occur early, and long-term outcome of relapsed/refractory patients is generally poor despite salvage regimens and stem cell transplant. Traditionally, studies for DLBCL have been evaluated using progression-free and/or overall survival. However, the event rate in DLBCL slows significantly approximately 12–18 months after diagnosis, and late events are often due to competing (non-DLBCL related) risks, especially in older patients. Here we examine outcome of DLBCL patients based on their event status at 12 months. Methods: Newly diagnosed DLBCL patients were prospectively enrolled in the University of Iowa/Mayo Clinic Lymphoma SPORE Molecular Epidemiology Resource (MER). Clinical data were abstracted from medical records using a standard protocol. Patients were actively followed for events (progression, re-treatment, or death due to any cause) and overall survival (OS). Event-free status at 12 months after diagnosis (EFS12) was assessed as a dichotomous variable. Cause of death was determined by medical record and death certificate review using prospectively determined definitions. Expected survival was based on age and sex matched survival using the Minnesota population death rates. Confirmation cohorts were from a Lyon, France hospital based registry and NCCTG clinical trial N0489. Results: 680 patients with newly diagnosed DLBCL and treated with rituximab + anthracycline based chemotherapy were enrolled in the MER from 2002 to 2009. The median age was 62 years (range 18–92). 53% were male. At a median follow-up of 59 months (range 8–116), 266 patients (39%) had an event and 188 patients (28%) died. 162 patients (24%) had an event in the first 12 months after diagnosis, comprising 60% of all events. Patients with an event in the first 12 months had poor survival with death almost exclusively due to disease (Figures 1a, 2a). In contrast, patients who were event-free at 12 months had comparable survival to the age and sex matched general population (Figure 2b) and were more likely to die of other causes than DLBCL (Figure 1b). Overall survival rates by EFS12 status were validated in patients from a French hospital-based registry (N=265) and the NCCTG N0489 clinical trial (N=87) with additional replication studies underway. Conclusions: DLBCL patients who are event-free at 12 months after diagnosis have an excellent prognosis with an overall survival similar to that of an age- and sex- matched general population and are more likely to die of other causes than DLBCL. This finding has implications for clinical management, new clinical trials, and follow-up testing in this patient population. In contrast, patients with an event within the first 12 months after diagnosis have a poor prognosis with almost all deaths secondary to DLBCL. EFS status at 12 months identifies patients with poor outcomes due to disease. This can be utilized as an endpoint in biologic studies and clinical trials to address early treatment failures. EFS status at 12 months should be incorporated into prognostic models to identify high risk patients in newly diagnosed DLBCL. Disclosures: No relevant conflicts of interest to declare.