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Graft-versus-host disease (GVHD) is a prevalent and potentially lethal complication of hematopoietic stem cell transplantation. Humanized mouse models of xenogeneic GVHD are important tools used to study the human immune response in vivo. Here we used NOD-scid IL-2Rynull mice (NSG) transplanted with human bone marrow stem cells to evaluate the role of immune cell engraftment in the production of acute GVHD. PRO 140, a humanized monoclonal antibody targeting the chemokine receptor, CCR5, was used to evaluate its influence on bone marrow cell engraftment and modulation of acute GVHD. We evaluated the kinetics of engraftment by determining the percentage and absolute numbers of human CD45+ cells and CD3+ T cells from peripheral blood, spleen, and bone marrow in treated and control mice. With a dosing schedule of 2 mg of test or control antibody administered i.p. twice weekly, PRO 140–treated mice showed no signs of GVHD throughout the 70-day study period and gained weight until they were killed at 70 days for flow cytometry analysis. Control mice started losing weight after 25 days, showed classic signs of GVHD (ruffled fur, lethargy, severe hunching), and all were killed by day 54. The percentage and absolute numbers of human CD45+ cells in peripheral blood increased in both groups of mice throughout the 50-day comparison period and was lower in the PRO 140–treated mice at day 50. There was no difference in human CD45+ cells detected in bone marrow from control and PRO 140–treated killed mice. At this time point 76.1% and 68.2% of the hematopoietic cells from peripheral blood and from bone marrow, respectively, were of human lineage and 14.9% and 28%, respectively, were of mouse origin. With a schedule using 10-fold less dose of antibody (.2 mg i.p. twice weekly), PRO 140 still significantly modulated acute GVHD in terms of both weight loss and survival times, but no mice from either control or test group survived. By targeting the CCR5 chemokine receptor, PRO 140 modulated acute GVHD in a dose-response fashion in this xenogeneic mouse model without significantly altering engraftment.

417 Background: In pancreaticobiliary (PB) cancers, there is a paucity of data on predictive and pathophysiologic role of the biliary microbiome. We analyzed bile collected from patients with benign and malignant PB diseases to identify microbiomic signatures associated with malignancy. Methods: We collected bile samples from consenting patients during routine endoscopic retrograde cholangiopancreatography at the Cleveland Clinic, approved by the Institutional Review Board. DNA was extracted from bile specimens using PowerViral RNA/DNA Isolation kit. Bacterial 16S rRNA gene amplification and library construction were performed according to the 16S Metagenomic Sequencing Library Preparation guide from Illumina. Post-sequencing analysis was done using QIIME (Quantitative Insights Into Microbial Ecology), Bioconductor phyloseq, microbiomeSeq and mixMC packages. Results: Of 46 enrolled patients, 32 had PB cancers including pancreatic (N = 25), cholangiocarcinoma (N = 6), and gallbladder (N = 1). The rest (N = 14) had benign PB diseases including acute and chronic pancreatitis, and gallstones. Using multivariate approach in mixMC to classify Operational Taxonomic Units (OTUs), we found a predominance of genera Dicekeya (p = 0.0002), [ Eubacterium] hallii group (p = 0.0007) , Bacteroides (p = 0.00099) , Faecalibacterium (p = 0.007) , Facklamia (p = 0.013) , Peptococcus (p = 0.013) , Bergeyella (p = 0.0024) , Lachnospira (p = 0.026) , and Lactobacillus (p = 0.025) in bile samples from PB cancers as compared to benign PB diseases. Furthermore, bile samples from patients with pancreatic cancer showed an increased abundance of genera Enterobacter, Parabacteroides, Atopobium, Alloprevotella, Prevotella 7, Acinetobacter, Bergeyella, Clostridium sensu stricto, Lactobacillus, and Rothia; and a decreased abundance of genera Tannerella, Peptococcus, Colinsella, Capnocytophaga, Achromobacter, Ruminococcus 2, Bacteroides, Alistipes, Barnesiella,, Lachnoclostridium, Lautropia, Akkermansia, and Christensenellaceae R-7 group as compared to bile samples from patients with cholangiocarcinoma. Conclusions: Distinct microbiome signatures are associated with benign and malignant PB diseases. There is a difference in the relative abundance of OTUs in bile samples between patients with benign PB diseases vs PB cancers, and between pancreatic cancer vs cholangiocarcinoma. Our findings raise the possibility that either these OTUs have a role in carcinogenesis, or that changes in the microenvironment of benign PB diseases differ from PB cancers leading to distinct separation of the OTU clusters. Further studies to explore and validate our findings are needed.

Background Copy-number alterations (CNAs) and gene mutations are hallmarks of cancer genomes, and they are implicated in the development of myeloid neoplasm. However, their relationships have not been fully examined. To address this issue, we have recently developed a novel, next-generation sequencing-based platform for copy-number analysis, which enabled us to detect mutations and CNAs simultaneously. We applied this platform to around 2,000 cases with myeloid neoplasms. Aims We aimed at delineating the landscape of CNAs and their relationships with gene mutations in myeloid neoplasms. Methods We examined 2,101 cases with myeloid neoplasms by whole-exome sequencing (WES) or targeted deep sequencing. Excluding 116 samples showing low qualities of copy-number signals, we performed subsequent analysis on the remaining 1,985 cases with myelodysplastic syndromes (MDS, n = 1,102), myelodysplastic/myeloproliferative neoplasms (MDS/MPN, n = 140), de novo acute myeloid leukemia (de novo AML, n = 448), and secondary AML (sAML, n = 295). In copy-number analysis, total copy numbers and allele-specific copy numbers (ASCNs) were quantified based on sequencing depths and allelic ratios on genome-wide probes. Copy-number signals were corrected for multiple biases (e.g. GC content, ASCN, and fragment length). We also validated the performance of this platform through comparison with SNP-array karyotyping data in 115 de novo AML cases. CNAs longer than 5 Mb were regarded as arm-level CNAs, and those shorter than 5 Mb were regarded as focal CNAs. Results In total, we identified 4,141 CNAs (52.9 % of cases with at least one CNA), and 3,863 mutations (73.9 % of cases with at least one mutation). Most frequent alterations included -7/del(7q) (13.2 %), del(5q) (11.4 %), trisomy 8 (7.2 %), and del(20q) (5.2 %), and mutations of TET2 (12 .3 %), TP53 (11.3 %), ASXL1 (10.1%), and DNMT3A (9.9 %). To evaluate the difference of copy-number landscapes between de novo AML and myelodysplasia (MDS, MDS/MPN, and sAML), we compared the frequencies of CNAs between them. Uni-parental disomy (UPD) of 13q (FLT3) and 11p (WT1), and amplifications of 11q, 13q, and 21q (ERG) were more enriched in de novo AML, while der(1;7), UPD of 11q (CBL), and del(20q) were enriched in myelodysplasia, suggesting differential involvements of CNAs. We next analyzed the correlations between CNA profiles and prognosis in cases with myelodysplasia. Since TP53 status implies a large impact on both patients' prognosis and CNA profiles, we separately analyzed TP53-positive (n = 53) and negative (n = 686) cases with available survival data. In TP53-negative cases, -7/7qLOH (Hazard ratio(HR): 2.28, q < 0.001), and UPD of 11q (CBL) (HR: 2.60, q = 0.0034) significantly correlated with shorter overall survivals (OS), while, in TP53-positive cases, amp(11q), +19, and amp(21q) were marginally associated with shorter OS. To delineate the relationships between CNAs and mutations, we interrogated correlations between both lesions among MDS cases without TP53 alterations (n = 937). A number of significant correlations were detected, such as those between trisomy 8 and del(20q) with U2AF1 mutations (q < 0.05, for each), and monosomy 7 and amp(21q) with mutations of RUNX1 and NRAS (q < 0.01, for each). These correlations were also revealed in clustering analysis based on CNA and mutation profiles, which identified 5 unique clusters: Cluster 1 (n = 171) with trisomy 8, del(20q), and mutations of U2AF1 and ETV6, Cluster 2 (n = 43) with monosomy 7, amp(21q), and mutations of NRAS, SETBP1, and RUNX1, Cluster 3 (n = 19) with amp(1q) and amp(3q), Cluster 4 (n = 127) with those of SF3B1, TET2, and DNMT3A, and Cluster 5 (n = 50) with those of SRSF2, STAG2, ASXL1, and RUNX1. The remaining 527 cases were not assigned into any cluster due to lack of significantly correlated alterations. Finally, the temporal relationships of coexisting alterations were estimated based on their cell fractions; monosomy 7 had significantly greater cell fractions (P = 0.031) and is predicted to precede NRAS mutations, while the cell fractions of U2AF1 mutations tended to be greater than those of trisomy 8 (P = 0.063), suggesting their implications in different stages of disease progression. Conclusion An integrated analysis of CNAs and mutations in >2,000 cases revealed the impacts of CNAs on disease characteristics and provided novel insight into the interplay between CNAs and mutations in the pathogenesis of MDS. Figure Disclosures Atsuta: CHUGAI PHARMACEUTICAL CO., LTD.: Honoraria; Kyowa Kirin Co., Ltd: Honoraria. Kanda:Celgene: Consultancy, Research Funding; Novartis: Research Funding; Shionogi: Consultancy, Honoraria, Research Funding; Nippon-Shinyaku: Research Funding; Taiho: Research Funding; Asahi-Kasei: Research Funding; Bristol-Myers Squibb: Consultancy, Honoraria; Takeda: Consultancy, Honoraria, Research Funding; Eisai: Consultancy, Honoraria, Research Funding; Eisai: Consultancy, Honoraria, Research Funding; Dainippon Sumitomo: Consultancy, Honoraria, Research Funding; Otsuka: Research Funding; Kyowa-Hakko Kirin: Consultancy, Honoraria, Research Funding; Ono: Consultancy, Honoraria, Research Funding; MSD: Research Funding; Chugai: Consultancy, Honoraria, Research Funding; CSL Behring: Research Funding; Taisho-Toyama: Research Funding; Tanabe Mitsubishi: Research Funding; Dainippon Sumitomo: Consultancy, Honoraria, Research Funding; Takeda: Consultancy, Honoraria, Research Funding; Kyowa-Hakko Kirin: Consultancy, Honoraria, Research Funding; Bristol-Myers Squibb: Consultancy, Honoraria; Astellas: Consultancy, Honoraria, Research Funding; Takara-bio: Consultancy, Honoraria; Novartis: Research Funding; Astellas: Consultancy, Honoraria, Research Funding; Sanofi: Research Funding; Pfizer: Research Funding; Asahi-Kasei: Research Funding; Alexion: Consultancy, Honoraria; CSL Behring: Research Funding; Takara-bio: Consultancy, Honoraria; Mochida: Consultancy, Honoraria; Taiho: Research Funding; Celgene: Consultancy, Research Funding; Tanabe Mitsubishi: Research Funding; Taisho-Toyama: Research Funding; Pfizer: Research Funding; Sanofi: Research Funding; Mochida: Consultancy, Honoraria; Alexion: Consultancy, Honoraria; Otsuka: Research Funding. Sekeres:Celgene: Membership on an entity's Board of Directors or advisory committees; Millenium: Membership on an entity's Board of Directors or advisory committees; Syros: Membership on an entity's Board of Directors or advisory committees. Saunthararajah:EpiDestiny: Consultancy, Equity Ownership, Patents & Royalties; Novo Nordisk: Consultancy. Miyazaki:Chugai: Research Funding; Otsuka: Honoraria; Novartis: Honoraria; Nippon-Shinyaku: Honoraria; Dainippon-Sumitomo: Honoraria; Kyowa-Kirin: Honoraria. Usuki:Boehringer-Ingelheim Japan: Other: Received Research ; Daiichi Sankyo: Other: Received Research ; SymBio Pharmaceuticals Limited.,: Other: Received Research ; Novartis: Speakers Bureau; Ono Pharmaceutical: Speakers Bureau; Takeda Pharmaceutica: Speakers Bureau; Chugai Pharmaceutical: Speakers Bureau; Nippon Shinyaku: Speakers Bureau; Mochida Pharmaceutical: Speakers Bureau; MSD K.K.: Speakers Bureau; Celgene Corporation: Other: Received Research , Speakers Bureau; Sumitomo Dainippon Pharma: Other: Received Research , Speakers Bureau; Pfizer Japan: Other: Received Research ; Stellas Pharma: Other: Received Research ; Otsuka: Other: Received Research ; Kyowa Kirin: Other: Received Research ; GlaxoSmithKline K.K.: Other: Received Research ; Sanofi K.K.: Other: Received Research ; Shire Japan: Other: Received Research ; Janssen Pharmaceutical K.K: Other: Received Research . Imada:Bristol-Meyer Squibb K.K.: Honoraria; Celgene K.K.: Honoraria; Chugai Pharmaceutical Co., Ltd.: Honoraria; Kyowa Hakko Kirin Co., Ltd.: Honoraria; Ono Pharmaceutical Co., Ltd.: Honoraria; Otsuka Pharmaceutical Co., Ltd.: Honoraria; Astellas Pharma Inc.: Honoraria; Novartis Pharma K.K.: Honoraria; Takeda Pharmaceutical Co.,LTD.: Honoraria; Nippon Shinyaku Co.,Ltd.: Honoraria. Takaori-Kondo:Kyowa Kirin: Research Funding; Pfizer: Honoraria; Janssen: Honoraria; Chugai: Research Funding; Takeda: Research Funding; Ono: Research Funding; Bristol-Myers Squibb: Honoraria, Research Funding; Novartis: Honoraria; Celgene: Honoraria, Research Funding. Kiguchi:Celltrion, Inc.: Research Funding; Astellas Pharmaceutical Co., Ltd.: Research Funding; Nippon Shinyaku Co., Ltd.: Research Funding; Otsuka Pharmaceutical Co., Ltd.: Research Funding; Kyowa Hakko Kirin Co., Ltd.: Research Funding; MSD CO., Ltd.: Research Funding; Novartis Pharmaceutical Co., Ltd.: Research Funding; Sumitomo Dainippon Pharmaceutical Co., Ltd.: Research Funding; Bristol-Myeres Squibb Co., Ltd.: Research Funding; Janssen Pharmaceutical Co., Ltd.: Research Funding; Celgene Co., Ltd.: Research Funding; SymBio Pharmaceutical Co., Ltd.: Research Funding; Taiho Pharmaceutical Co., Ltd.: Research Funding; Tejin Co., Ltd.: Research Funding; Sanofi K.K., Ltd.: Research Funding. Maciejewski:Alexion: Consultancy; Novartis: Consultancy. Ogawa:Asahi Genomics: Equity Ownership; Qiagen Corporation: Patents & Royalties; Dainippon-Sumitomo Pharmaceutical, Inc.: Research Funding; RegCell Corporation: Equity Ownership; ChordiaTherapeutics, Inc.: Consultancy, Equity Ownership; Kan Research Laboratory, Inc.: Consultancy.

e15744 Background: Recent studies especially in murine models have linked meta-organismal pathways in the gut microbial community to cancers of the pancreas and the biliary tract. However, data on microbiome in the biliary pool in patients to establish models for oncogenesis in the pancreatobiliary (PB) habitat have been limited. We analyzed bile collected from a pilot series of patients to identify microbiome signatures associated with malignancy. Methods: We collected bile samples from patients during routine endoscopic retrograde cholangiopancreatography in this study approved by the Cleveland Clinic Institutional Review Board for Human Subjects’ Protection. Of 10 patients, there were 5 with pancreatic ductal adenocarcinoma (PDA), 3 with cholangiocarcinoma (CC), 1 with ampullary adenocarcinoma, and 1 with gallstone pancreatitis. DNA was extracted from bile specimens using PowerViral RNA/DNA Isolation kit. Bacterial 16S rRNA gene amplification and library construction were performed according to the 16S Metagenomic Sequencing Library Preparation guide from Illumina. Post-sequencing analysis was done using QIIME (Quantitative Insights Into Microbial Ecology) and MICCA (MICrobial Community Analysis). Results: Most reads were from phyla Firmicutes (57.9%) and Proteobacteria (14.9%). One benign specimen (pancreatitis) separated clearly from the rest showing 98.9% of reads from Clostridium sensu stricto (phylum Firmicutes). Analysis of beta diversity showed six samples clustering tightly. Of these, 5 were PDA and 1 was CC. A second cluster included remaining 3 samples, 2 with CC and 1 with PDA; this latter had higher abundance of phyla Fusobacteria (90.6%) and Verrucomicrobia (92.9%). Conclusions: Select bacteria are differentially increased in malignant and benign PB diseases. Furthermore, distinct microbiome signatures may be associated with cancer in the pancreatic and biliary habitats. We intend to evaluate these findings in larger sample sizes and determine associations with clinical outcomes and response to treatment.

Cytogenetic aberrations identified by metaphase cytogenetics (MC) have diagnostic, prognostic, and therapeutic implications in myelodysplastic syndromes (MDS). However, in some MDS patients MC study is unsuccesful. Single nucleotide polymorphism array (SNP-A) based karyotyping could be helpful in these cases. We performed SNP-A in 62 samples from bone marrow or peripheral blood of primary MDS with an unsuccessful MC study. SNP-A analysis enabled the detection of aberrations in 31 (50%) patients. We used the copy number alteration information to apply the International Prognostic Scoring System (IPSS) and we observed differences in survival between the low/intermediate-1 and intermediate-2/high risk patients. We also saw differences in survival between very low/low/intermediate and the high/very high patients when we applied the revised IPSS (IPSS-R). In conclusion, SNP-A can be used successfully in PB samples and the identification of CNA by SNP-A improve the diagnostic and prognostic evaluation of this group of MDS patients.

Recently, recurrent mutations of spliceosomal genes were frequently identified in myeloid malignancies, as well as other types of cancers. One of these spliceosomal genes, U2AF1, was affected by canonical somatic mutations in aggressive type of myeloid malignancies. We hypothesized that U2AF1 mutations causes defects of splicing (missplicing) in specific genes and that such misspliced genes might be important in leukemogenesis. We analyzed RNA deep sequencing to compare splicing patterns of 201 837 exons between the cases with U2AF1 mutations (n = 6) and wild type (n = 14). We identified different alternative splicing patterns in 35 genes comparing cells with mutant and wild-type U2AF1. U2AF1 mutations are associated with abnormal splicing of genes involved in functionally important pathways, such as cell cycle progression and RNA processing. In addition, many of these genes are somatically mutated or deleted in various cancers. Of note is that the alternative splicing patterns associated with U2AF1 mutations were associated with specific sequence signals at the affected splice sites. These novel observations support the hypothesis that U2AF1 mutations play a significant role in myeloid leukemogenesis due to selective missplicing of tumor-associated genes.

Here we report whole-exome sequencing of individuals with various myeloid malignancies and identify recurrent somatic mutations in SETBP1, consistent with a recent report on atypical chronic myeloid leukemia (aCML). Closely positioned somatic SETBP1 mutations encoding changes in Asp868, Ser869, Gly870, Ile871 and Asp880, which match germline mutations in Schinzel-Giedion syndrome (SGS), were detected in 17% of secondary acute myeloid leukemias (sAML) and 15% of chronic myelomonocytic leukemia (CMML) cases. These results from deep sequencing demonstrate a higher mutational detection rate than reported with conventional sequencing methodology. Mutant cases were associated with advanced age and monosomy 7/deletion 7q (-7/del(7q)) constituting poor prognostic factors. Analysis of serially collected samples indicated that SETBP1 mutations were acquired during leukemic evolution. Transduction with mutant Setbp1 led to the immortalization of mouse myeloid progenitors that showed enhanced proliferative capacity compared to cells transduced with wild-type Setbp1. Somatic mutations of SETBP1 seem to cause gain of function, are associated with myeloid leukemic transformation and convey poor prognosis in myelodysplastic syndromes (MDS) and CMML.

Abstract 558 In addition to chromosomal and epigenetic abnormalities, somatic mutations constitute key pathogenic lesions in myeloid neoplasms. Individual somatic mutations or various combinations may be both valuable prognostic markers and targets for new rational therapies. Among them, RAS family genes are ubiquitous oncogenes associated with various cancers. Recurrent canonical mutations in the nucleotide binding domains in NRAS and KRAS result in constitutively activated proteins. In myeloid neoplasms, RAS mutations convey a poor prognosis and are often found in acute myeloid leukemia (AML), myelodysplastic syndromes (MDS) and, rarely, myeloproliferative neoplasms (MPN). We applied whole exome sequencing to paired germline vs. leukemia samples in 65 cases of MDS, 36 MDS/MPN and 32 sAML. We focused our study on the RAS protein superfamily of small GTPases and identified mutations in 3% and 6% of KRAS and NRAS, respectively. Most significantly, we identified somatic recurrent mutations in the F82 residue of Ras-like without CAAX1 (RIT1) gene in 2 patients with chronic myelomonocytic leukemia (CMML) and secondary AML (sAML), respectively. We confirmed the somatic nature of both mutations in sorted CD3+ cells from each patient (pt). RIT1 gene encodes a member of Ras-related GTPases, involved in the p38 MAPK and AKT signaling pathway that mediates cellular survival in response to stress. RIT1 gene amplification has been found in 26% of hepatocellular carcinoma. However, neither amplification nor mutations of this gene have been reported in myeloid malignancies. We thus focused this line of experimentation on this somatic mutation. To establish clinical associations we further studied a cohort of 322 patients with various myeloid malignancies by Sanger sequencing and detected somatic RIT1 mutations in an additional 6 (2%) cases. All mutations were located in exon 5, in the 81 and 82 residues, which encode the switch II domain of this protein, an effector region very close to the GTP-binding site G3, and which is highly conserved among species. Among the 8 mutant cases, 5 (63%) pts had CMML, resulting in a higher frequency of mutations in this subcohort of pts (5 out of 57 CMML, 9%). The other 3 mutations were found in one primary (p)AML (M5b subtype) (1 out of 58 pAML, 2%) and two high-grade MDS, one refractory anemia with excess blasts (RAEB)-2 and one sAML(RAEB-T in the FAB-classification) (2 out of 80, 2.5%). RIT1 mutations were heterozygous in all cases except for one case with trisomy 1 and duplication of the mutant allele. In the cases of WES, we estimated an allelic frequency of ∼35%, consistent with the presence of a heterozygous mutation in ∼70% of sample cells. Because of the large size of the clone and serial samples showing RIT1 mutation since the time of initial diagnosis, it is likely that RIT1 may be of ancestral origin. As RAS-family gene amplifications have been described in cancer, we also studied the presence of amplifications of the RIT1 locus (1q22) by SNP-A. We found 10 cases characterized by a gain involving the RIT1 region (1q21.1-q44): 4 (40%) cases had a diagnosis of CMML, 4 (40%) had myelofibrosis, whereas the remaining patients had MDS (one RAEB-1 and a RA). Quantitative RT-PCR showed RIT1 overexpression in mutants and in patients with 1q amplification (median normalized relative ratio 0,51 and 0,40, respectively) compared to patients with wild type RIT1 and no amplification in 1q (median normalized relative ratio 0,15; P=.039). We theorized that activating RIT1 mutations may constitute a suitable therapeutic target. Because AKT inhibitors can block AKT phosphorylation and therefore reverse the antiapoptotic effect of mutant RIT1, we tested whether AKT inhibitor V (Triciribine) can selectively abrogate the growth of primary cells with RIT1 mutation. In in vitro suspension cultures, a 65% of reduction proliferation was observed with significant effects even at 0.1μM concentrations. In sum, somatic recurrent RIT1 mutations are novel lesions involved in the molecular pathogenesis of myeloid cancers, presumably early in the development of the disease. Moreover, amplifications of RIT1 also lead to overexpression of this Ras-like GTP-ase. Specifically, these abnormalities appear to be more frequent in patients with CMML, but also can be found in other types of MDS. Disclosures: Makishima: Scott Hamilton CARES Initiative: Research Funding. Maciejewski:NIH: Research Funding; Aplastic Anemia&MDS International Foundation: Research Funding.

Chronic lymphoproliferative disorders of natural killer cells (CLPD-NKs) and T-cell large granular lymphocytic leukemias (T-LGLs) are clonal lymphoproliferations arising from either natural killer cells or cytotoxic T lymphocytes (CTLs). We have investigated for distribution and functional significance of mutations in 50 CLPD-NKs and 120 T-LGL patients by direct sequencing, allele-specific PCR, and microarray analysis. STAT3 gene mutations are present in both T and NK diseases: approximately one-third of patients with each type of disorder convey these mutations. Mutations were found in exons 21 and 20, encoding the Src homology 2 domain. Patients with mutations are characterized by symptomatic disease (75%), history of multiple treatments, and a specific pattern of STAT3 activation and gene deregulation, including increased expression of genes activated by STAT3. Many of these features are also found in patients with wild-type STAT3, indicating that other mechanisms of STAT3 activation can be operative in these chronic lymphoproliferative disorders. Treatment with STAT3 inhibitors, both in wild-type and mutant cases, resulted in accelerated apoptosis. STAT3 mutations are frequent in large granular lymphocytes suggesting a similar molecular dysregulation in malignant chronic expansions of NK and CTL origin. STAT3 mutations may distinguish truly malignant lymphoproliferations involving T and NK cells from reactive expansions.

To elucidate differential roles of mutations in myelodysplastic syndromes (MDS), we investigated clonal dynamics using whole-exome and/or targeted sequencing of 699 patients, of whom 122 were analyzed longitudinally. Including the results from previous reports, we assessed a total of 2,250 patients for mutational enrichment patterns. During progression, the number of mutations, their diversity and clone sizes increased, with alterations frequently present in dominant clones with or without their sweeping previous clones. Enriched in secondary acute myeloid leukemia (sAML; in comparison to high-risk MDS), FLT3, PTPN11, WT1, IDH1, NPM1, IDH2 and NRAS mutations (type 1) tended to be newly acquired, and were associated with faster sAML progression and a shorter overall survival time. Significantly enriched in high-risk MDS (in comparison to low-risk MDS), TP53, GATA2, KRAS, RUNX1, STAG2, ASXL1, ZRSR2 and TET2 mutations (type 2) had a weaker impact on sAML progression and overall survival than type-1 mutations. The distinct roles of type-1 and type-2 mutations suggest their potential utility in disease monitoring.

Nonsynonymous TP53 exon 4 single-nucleotide polymorphism (SNP), R72P, is linked to cancer and mutagen susceptibility. R72P associations with specific cancer risk, particularly hematological malignancies, have been conflicting. Myelodysplastic syndrome (MDS) with chromosome 5q deletion is characterized by erythroid hypoplasia arising from lineage-specific p53 accumulation resulting from ribosomal insufficiency. We hypothesized that apoptotically diminished R72P C-allele may influence predisposition to del(5q) MDS. Bone marrow and blood DNA was sequenced from 705 MDS cases (333 del(5q), 372 non-del(5q)) and 157 controls. Genotype distribution did not significantly differ between del(5q) cases (12.6% CC, 38.1% CG, 49.2% GG), non-del(5q) cases (9.7% CC, 44.6% CG, 45.7% GG) and controls (7.6% CC, 37.6% CG, 54.8% GG) (P = 0.13). Allele frequency did not differ between non-del(5q) and del(5q) cases (P = 0.91) but trended towards increased C-allele frequency comparing non-del(5q) (P = 0.08) and del(5q) (P = 0.10) cases with controls. Median lenalidomide response duration increased proportionate to C-allele dosage in del(5q) patients (2.2 (CC), 1.3 (CG) and 0.89 years (GG)). Furthermore, C-allele homozygosity in del(5q) was associated with prolonged overall and progressionfree survival and non-terminal interstitial deletions that excluded 5q34, whereas G-allele homozygozity was associated with inferior outcome and terminal deletions involving 5q34 (P = 0.05). These findings comprise the largest MDS R72P SNP analysis.

Myelodysplastic syndromes (MDS) are a heterogeneous group of chronic myeloid neoplasms, in which disease progression is quite common, eventually terminating in secondary acute myeloid leukemia (sAML). To elucidate differential roles of mutations in MDS progression and sAML evolution, we investigated clonal dynamics of somatic mutations using targeted sequencing of 699 MDS patients, of which 122 were analyzed for longitudinally collected samples. Combining publicly available data, mutational data in a total of 2,250 MDS cases were assessed for their enrichment in specific disease subtypes. All samples were obtained after informed consent. Genotyping data from samples with low- (n=1,207) and high-risk (n=683) MDS as well as sAML (n=360) were available for most prevalently mutated 25 driver genes. In univariate comparison between low- and high-risk MDS, the majority of differentially mutated genes were enriched in high-risk MDS, except for SF3B1, which was more frequently mutated in low-risk MDS. Multivariate analysis was performed using a least absolute shrinkage and selection operator model. As a result, mutations in 7 genes (FLT3, PTPN11, WT1, IDH1, NPM1, IDH2,and NRAS) designated as 'Type-1' mutations, were significantly enriched in sAML compared to high-risk MDS. When comparison was made between high- and low-risk MDS, mutations in 10 genes, including GATA2, NRAS, KRAS, IDH2, TP53, RUNX1, STAG2, ASXL1, ZRSR2, and TET2, were enriched in high-risk MDS. The latter mutations are designated as 'Type-2' mutations, excluding NRAS and IDH2 mutations, which were already assigned to the Type-1 category. To characterize the chronological behavior of Type-1 and Type-2 mutations, we performed longitudinal analyses of 122 cases, of which 90 progressed to sAML. Overall, driver mutations tended to increase their clone sizes between two time points. In accordance with their significant enrichment in sAML, Type-1 mutations were more likely to be newly acquired at the second time points, compared to Type-2 and other mutations (P=0.0001). By contrast, in patients with high-risk MDS at the second time point, Type-2 mutations were more dominant than Type-1 mutations, and most of the Type-2 mutations (88%) increased their clone sizes at the second sampling. Similarly, Type-2 mutations found in high-risk MDS or sAML evolving from low-risk MDS increased their clone sizes more frequently (30 out of 38 mutations (79%)) than Type-2 mutations in stable low-risk MDS without disease progression over time (4 out of 11 (36%)) (P=0.02). These findings suggest that Type-1 and Type-2 mutations might be associated with progression from high-risk MDS to sAML and low- to high-risk MDS, respectively. To further clarify the effects of the different classes of mutations on progression to sAML, 429 patients with MDS were analyzed for progression free survival (or PFS). Patients with Type-1 mutations (Group-I) had a significantly shorter PFS, compared to those who had Type-2 mutations but lacked Type-1 mutations (Group-II) (HR=1.82, 95% CI:1.08−3.05; P=0.025). Nevertheless, PFS in Group-II cases was still significantly shorter than that in other cases (HR=2.46, 95% CI:1.43−4.23; P=0.001). Of note, some Group-II cases subsequently acquired Type-I mutations during progression to sAML. By contrast, SF3B1-mutated patients tended to show slower progression to sAML, unless they carried either of Type-1 or 2 mutations (Group-III). Finally, the effects of these mutations on overall survival (OS) were assessed in a larger cohort of patients with MDS (n=1,347). Group-I cases were shown to have a significantly shorter OS than Group-II cases (HR=1.50, 95% CI:1.20−1.86; P In conclusion, our study has elucidated clonal dynamics associated with MDS progression and sAML evolution. Close monitoring of these sets of distinct mutations in the prospective fashion may help in the prediction of the clinical outcome in MDS. Disclosures Makishima: The Yasuda Medical Foundation: Research Funding. Sekeres:Millenium/Takeda: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees. Meggendorfer:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Ogawa:Kan research institute: Consultancy, Research Funding; Takeda Pharmaceuticals: Consultancy, Research Funding; Sumitomo Dainippon Pharma: Research Funding.

Background Copy number alteration (CNA) is a hallmark of cancer genomes and has been implicated in the development of human cancers, including myeloid neoplasms. We developed a novel, next-generation sequencing-based platform for highly sensitive detection of CNAs with a single exon resolution, which was applied to sequencing data from 1,185 patients to delineate a comprehensive landscape of CNAs in myeloid neoplasms. Materials and Methods We enrolled 1,185 patients with different myeloid neoplasms including myelodysplastic syndromes (n = 607), myelodysplastic/myeloproliferative neoplasms (n = 80), de novo acute myeloid leukemia (AML) (n = 136), secondary AML (sAML) (n = 226), and unknown myeloid malignancies (n = 136). Whole-exome sequencing (WES) was performed on samples from 260 patients, while samples from 925 patients including pre-transplantation peripheral blood samples provided by Japan Marrow Donor Program were subjected to targeted deep sequencing. Eight cases were serially evaluated before and after progression tosAML. RNA baits for targeted deep sequencing were designed to cover 69 driver genes in myeloid neoplasms and 1,158 single-nucleotide polymorphisms (SNPs)for assessment of allelic imbalance. In WES, allelic imbalance was examined using allele frequencies of SNPs within coding regions. Focal CNAs were defined as CNAs whose lengths relative to the chromosomal arms were below 10%. Results To obtain a landscape of CNAs in coding regions, a comprehensive copy number analysis was performed on 260 patients including 136 with de novo AML and 124 with myeloid neoplasms with myelodysplasia, all of whom were studied by WES. A total of 755 CNAs (502 deletions and 253 amplifications) were identified, where 52% of the patients harbored at least one alteration. Using GISTIC 2.0 algorism, we identified 21 significantly altered regions involving known or putative driver genes (Figure 1): losses of 7q22.1 (CUX1), 12p13.2 (ETV6), 13q14 (RB1),17p13.1(TP53), and 17q11.2 (NF1), and gains of 3q26-27 (EVI1), 8q24.21 (MYC), 11q13.5-14.1(PAK1), 11q23.3 (MLL),11q24-25 (ETS1), 13q12.2 (FLT3),21q22.2 (ETS2 and ERG). We next compared the frequencies of CNAs between de novo AML and myeloid neoplasms with myelodysplasia. While chromosomes 7, 12, and 17 were commonly affected, deletions of 13q14 were significantly enriched in myeloid neoplasms with myelodysplasia (Odds ratio [OR]: 5.07, P = 0.040), and amplifications of 11q24-25 (OR: 5.54, P = 0.028), and 21q22.2 (OR: 6.10, P = 0.020) in de novo AML, suggesting a specific role of these events in each disease entity. In addition, serial sampling revealed trisomy8, deletions of 7q and 12p were recurrently acquired during leukemic transformation in patients withmyelodysplasia. Taken together, many driver genes in myeloid neoplasms were frequently targeted by CNAs includingmicrodeletions. Based on these finding, we sought to obtain a more detailed landscape of CNAs in a larger cohort. We combined copy number profiles of patients studied by targeted deep sequencing and those by WES. Of total, 1,691 CNAs (1,096 deletions and 595 amplifications) were detected, where 39% of the cases harbored at least one alteration. Microdeletionsor focal amplifications were frequently found in the significantly altered regions revealed by WES: microdeletionsof ETV6 (n = 10), NF1 (n = 8), CUX1 (n = 5), TP53 (n = 5), and amplifications of FLT3 (n = 7), ETS1 (n = 3), ETS2 (n = 3), and ERG (n = 3), validating the result obtained from a cohort studied by WES. We also identified known driver genes in myeloid neoplasms were recurrently affected with focal CNAs: microdeletions of RUNX1, BCOR, ASXL2, DNMT3A, and ZRSR2, and amplifications of GNAS, RIT1, CSF3R, and BCL11A. Among them, DNMT3A and ASXL2, located within 500 kb in chromosome 2, tended to be co-deleted (3 out of 4 cases). Focal deletions of TP53 were often affected with homozygous deletions or were accompanied by gene mutations, implying bi-allelic inactivation. High amplifications were also observed in regions including ETS1, MLL, FLT3, MYC, and PAK1, which suggest a critical role in the pathogenesis of myeloid malignancy. Conclusion We obtained the landscape of CNAs in myeloid neoplasms based on the sequencing data of 1,185 patients. Collectively, our results indicated that CNAs targeted a specific set genes including well-known drivers of myeloid malignancies, indicating a critical role inleukemogenesis. Disclosures Kanda: Otsuka Pharmaceutical: Honoraria, Research Funding. Sekeres:Celgene: Membership on an entity's Board of Directors or advisory committees; Millenium/Takeda: Membership on an entity's Board of Directors or advisory committees. Makishima:The Yasuda Medical Foundation: Research Funding. Maciejewski:Celgene: Consultancy, Honoraria, Speakers Bureau; Alexion Pharmaceuticals Inc: Consultancy, Honoraria, Speakers Bureau; Apellis Pharmaceuticals Inc: Membership on an entity's Board of Directors or advisory committees. Ogawa:Takeda Pharmaceuticals: Consultancy, Research Funding; Kan research institute: Consultancy, Research Funding; Sumitomo Dainippon Pharma: Research Funding.

Chronic myelomonocytic leukemia is a heterogeneous disease with multifactorial molecular pathogenesis. Various recurrent somatic mutations have been detected alone or in combination in chronic myelomonocytic leukemia. Recently, recurrent mutations in spliceosomal genes have been discovered. We investigated the contribution of U2AF1, SRSF2 and SF3B1 mutations in the pathogenesis of chronic myelomonocytic leukemia and closely related diseases. We genotyped a cohort of patients with chronic myelomonocytic leukemia, secondary acute myeloid leukemia derived from chronic myelomonocytic leukemia and juvenile myelomonocytic leukemia for somatic mutations in U2AF1, SRSF2, SF3B1 and in the other 12 most frequently affected genes in these conditions. Chromosomal abnormalities were assessed by nucleotide polymorphism array-based karyotyping. The presence of molecular lesions was correlated with clinical endpoints. Mutations in SRSF2, U2AF1 and SF3B1 were found in 32%, 13% and 6% of cases of chronic myelomonocytic leukemia, secondary acute myeloid leukemia derived from chronic myelomonocytic leukemia and juvenile myelomonocytic leukemia, respectively. Spliceosomal genes were affected in various combinations with other mutations, including TET2, ASXL1, CBL, EZH2, RAS, IDH1/2, DNMT3A, TP53, UTX and RUNX1. Worse overall survival was associated with mutations in U2AF1 (P=0.047) and DNMT3A (P=0.015). RAS mutations had an impact on overall survival in secondary acute myeloid leukemia (P=0.0456). By comparison, our screening of juvenile myelomonocytic leukemia cases showed mutations in ASXL1 (4%), CBL (10%), and RAS (6%) but not in IDH1/2, TET2, EZH2, DNMT3A or the three spliceosomal genes. SRSF2 and U2AF1 along with TET2 (48%) and ASXL1 (38%) are frequently affected by somatic mutations in chronic myelomonocytic leukemia, quite distinctly from the profile seen in juvenile myelomonocytic leukemia. Our data also suggest that spliceosomal mutations are of ancestral origin.

T-cell large granular lymphocytic leukemia is a rare lymphoproliferative disorder characterized by the expansion of clonal CD3+CD8+ cytotoxic T lymphocytes (CTLs) and often associated with autoimmune disorders and immune-mediated cytopenias.We used next-generation exome sequencing to identify somatic mutations in CTLs from an index patient with large granular lymphocytic leukemia. Targeted resequencing was performed in a well-characterized cohort of 76 patients with this disorder, characterized by clonal T-cell-receptor rearrangements and increased numbers of large granular lymphocytes.Mutations in the signal transducer and activator of transcription 3 gene (STAT3) were found in 31 of 77 patients (40%) with large granular lymphocytic leukemia. Among these 31 patients, recurrent mutational hot spots included Y640F in 13 (17%), D661V in 7 (9%), D661Y in 7 (9%), and N647I in 3 (4%). All mutations were located in exon 21, encoding the Src homology 2 (SH2) domain, which mediates the dimerization and activation of STAT protein. The amino acid changes resulted in a more hydrophobic protein surface and were associated with phosphorylation of STAT3 and its localization in the nucleus. In vitro functional studies showed that the Y640F and D661V mutations increased the transcriptional activity of STAT3. In the affected patients, downstream target genes of the STAT3 pathway (IFNGR2, BCL2L1, and JAK2) were up-regulated. Patients with STAT3 mutations presented more often with neutropenia and rheumatoid arthritis than did patients without these mutations.The SH2 dimerization and activation domain of STAT3 is frequently mutated in patients with large granular lymphocytic leukemia; these findings suggest that aberrant STAT3 signaling underlies the pathogenesis of this disease. (Funded by the Academy of Finland and others.).

Myelodysplastic syndromes (MDSs) are chronic and often progressive myeloid neoplasms associated with remarkable heterogeneity in the histomorphology and clinical course. Various somatic mutations are involved in the pathogenesis of MDS. Recently, mutations in a gene encoding a spliceosomal protein, SF3B1, were discovered in a distinct form of MDS with ring sideroblasts. Whole exome sequencing of 15 patients with myeloid neoplasms was performed, and somatic mutations in spliceosomal genes were identified. Sanger sequencing of 310 patients was performed to assess phenotype/genotype associations. To determine the functional effect of spliceosomal mutations, we evaluated pre-mRNA splicing profiles by RNA deep sequencing. We identified additional somatic mutations in spliceosomal genes, including SF3B1, U2AF1, and SRSF2. These mutations alter pre-mRNA splicing patterns. SF3B1 mutations are prevalent in low-risk MDS with ring sideroblasts, whereas U2AF1 and SRSF2 mutations are frequent in chronic myelomonocytic leukemia and advanced forms of MDS. SF3B1 mutations are associated with a favorable prognosis, whereas U2AF1 and SRSF2 mutations are predictive for shorter survival. Mutations affecting spliceosomal genes that result in defective splicing are a new leukemogenic pathway. Spliceosomal genes are probably tumor suppressors, and their mutations may constitute diagnostic biomarkers that could potentially serve as therapeutic targets.

Background While lenalidomide (LEN) shows high efficacy in myelodysplastic syndromes (MDS) with del[5q], responses can be also seen in patients presenting without del[5q]. We hypothesized that improved detection of chromosomal abnormalities with new karyotyping tools may better predict response to LEN. Design and methods We have studied clinical, molecular and cytogenetic features of 42 patients with MDS, myeloproliferative neoplasms (MPN), MDS/MPN overlap syndromes and secondary acute myeloid leukemia (sAML) without del[5q] by metaphase cytogenetics (MC) who underwent therapy with LEN. Results Fluorescence in situ hybridization (FISH) or single nucleotide polymorphism array (SNP-A)-based karyotyping marginally increased the diagnostic yield over MC, detecting 2/42 (4.8%) additional cases with del[5q], one of whom were responded to LEN. Responses were more often observed in patients with a normal karyotype by MC (60% vs abnormal MC; 17%, p = .08) and those with gain of chromosome 8 material by either of all 3 karyotyping methods (83% vs all other chromosomal abnormalities; 44% p = .11). However, 5 out of those 6 patients received combined LEN/AZA therapy and it may also suggest those with gain of chromosome 8 material respond well to AZA. The addition of FISH or SNP-A did not improve the predictive value of normal cytogenetics by MC. Mutational analysis of TET2, UTX, CBL, EZH2, ASXL1, TP53, RAS, IDH1/2, and DNMT-3A was performed on 21 of 41 patients, and revealed 13 mutations in 11 patients, but did not show any molecular markers of responsiveness to LEN. Conclusions Normal karyotype and gain of chromosome 8 material was predictive of response to LEN in non-del[5q] patients with myeloid malignancies.

The DNA hypomethylating drug decitabine maintains normal hematopoietic stem cell (HSC) self-renewal but induces terminal differentiation in acute myeloid leukemia (AML) cells. The basis for these contrasting cell fates, and for selective CpG hypomethylation by decitabine, is poorly understood. Promoter CpGs, with methylation measured by microarray, were classified by the direction of methylation change with normal myeloid maturation. In AML cells, the methylation pattern at maturation-responsive CpGs suggested at least partial maturation. Consistent with partial maturation, in gene expression analyses, AML cells expressed high levels of the key lineage-specifying factor CEBPA, but relatively low levels of the key late-differentiation driver CEBPE. In methylation analysis by mass spectrometry, CEBPE promoter CpGs that are usually hypomethylated during granulocyte maturation were significantly hypermethylated in AML cells. Decitabine-induced hypomethylation was greatest at these and other promoter CpGs that are usually hypomethylated with myeloid maturation, accompanied by cellular differentiation of AML cells. In contrast, decitabine-treated normal HSCs retained immature morphology, and methylation significantly decreased at CpGs that are less methylated in immature cells. High expression of lineage-specifying factor and aberrant epigenetic repression of some key late-differentiation driver genes distinguishes AML cells from normal HSCs, and could explain the contrasting differentiation and methylation responses to decitabine. © 2012 Macmillan Publishers Limited All rights reserved. Fil: Negrotto, Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Cleveland Clinic; Estados Unidos Fil: Ng, K .P.. Cleveland Clinic; Estados Unidos Fil: Jankowska, A. M.. Cleveland Clinic; Estados Unidos Fil: Bodo, J.. Cleveland Clinic; Estados Unidos Fil: Gopalan, B.. Cleveland Clinic; Estados Unidos Fil: Guinta, K.. Cleveland Clinic; Estados Unidos Fil: Mulloy, J.C.. Cincinnati Children’s Hospital; Estados Unidos Fil: Hsi, E.. Cleveland Clinic; Estados Unidos Fil: MacIejewski, J.. Cleveland Clinic; Estados Unidos Fil: Saunthararajah, Y.. Cleveland Clinic; Estados Unidos

Systematic application of single-nucleotide polymorphism arrays (SNP-As) as a karyotyping tool led to the realization that segmental somatic uniparental disomy (UPD) is a common defect in many cases of myelodysplastic syndrome (MDS), myeloproliferative neoplasms (MPNs), MDS/MPN and acute myeloid leukemia (AML).1 Discovery of UPD9p paved the way for identification of the JAK2V617F mutation in MPN. Since then, through application of SNP-A, several new mutations have been identified in the homozygous configuration in the malignant cells of patients with hematological malignancies. These include mutations in CBL2, 3 and TET2,4 for example. Similarly, SNP-A analysis demonstrated that MPL5 or TP536 mutations can occur in homozygous configurations. Assays of JAK2V617F mutant allele burden consequent to UPD are increasingly being utilized clinically because of diagnostic and prognostic relevance. Based on these observations, it can be postulated that areas of somatic UPD may identify regions that harbor mutations in the regions affected by the copy number neutral loss of heterozygosity/UPD.7 If found, somatic UPD most often spans large areas of the affected chromosome, thus making identification of mutated target genes quite challenging.

MDS and related disorders, including MDS/MPN and sAML that evolved from these conditions constitute disease continuum characterized by a wide spectrum of molecular lesions which often overlap. Here, we defined general mutational spectrum and clonal architecture in a large cohort (n=718) of MDS studied by whole exome sequencing (WES) and target deep sequencing. Within this cohort 97 cases were studied at multiple time points to clarify the clinical impact of clonal dynamics on phenotype commitment or outcomes. All samples were obtained after informed consent, according to protocols approved by the respective ethics boards of the participating institutions. When mean and maximum variant allele frequency (VAF) for whole mutations were at one time-point evaluated in disease phenotypes, significantly higher averaged values suggested their larger clones in sAML and CMML compared to MDS. Clustering analysis of multiple mutational events by Pyclone software discriminated the cases with multiple mutational clones (positive heterogeneity) and those with a single expansion of MDS clone (no heterogeneity detected). Over 80% of low-risk MDS and all the sAML harbored multiple clusters of mutations. These results suggest that intra-tumor heterogeneity of MDS is most likely due to various sizes of clonal and subclonal mutations, likely impacting clinical behavior. To delineate clonal dynamics in MDS, we assessed mutational burden and their temporal changes in serially collected samples (n=97). Among these, Pyclone analysis was applied to exome sequencing at two time points (n=11 pairs). All cases showed various mutational clusters with individual expansions and declines, including initially present, newly acquired or disappearing during clinical course. Initial subclones were identified at disease presentation in 55% of cases, of which in 86% the subclones expanded to occupy whole MDS population with clonal sweep. New subclones acquired during clinical course were identified in 91%, in which 60% cases harbored clonal sweep. Disappearing clones were observed in 55% of cases. Next, we applied clustering analysis on clonal size of driver mutations evaluated at multiple time points (n=97 cases) to categorize the most frequently mutated genes into 3 subtypes. Mutational burden of PTPN11 most frequently increased and were associated with leukemic evolution (an example of type I gene). Similarly, CBL, NRAS, STAG2, RUNX1, and IDH1 were categorized into the type I genes, demonstrating increased clonal size resulting in the evolutions into high-risk phenotypes. Although JAK2 mutations were related to the stable clinical course when the mutational burden decreased, cases with highly expanded JAK2 mutations resulted in leukemic evolution (occasional evolution or expansions; type II gene). DNMT3A, SRSF2, TP53, U2AF1, and ASXL1 mutations were also categorized into such type II consequences with occasional progression. The last category (type III) included clonal/founder genes EZH2, TET2, SF3B1 and PRPF8, demonstrating random shifts of clonal size and lack of association with leukemic evolution. The proposed hierarchical categorization correlates with clinical parameters. Cases with the increasing burden of type I gene mutations showed most significant increases in myeloblasts. Overall survival measured from second sampling time points in the cases with increasing type I mutations was significantly shorter in the whole cohort (HR=2.05, 95%CI; 1.14-3.79, P=0.016) and in the cases solely with IPSS INT-1 (HR=2.37, 95%CI; 1.01-5.97, P=0.048). Subcohorts classified according to the presence or absence of increasing type I mutations did not differ with regard to the IPSS categories. In contrast, increased mutational burden of type II and III genes did not correlated with any of the clinical parameters examined, even though some gene mutations including TP53, EZH2, and U2AF1 represented poor prognostic factors at disease presentation. In conclusion, this work demonstrates that detailed understanding of clonal dynamics allows for new insights into clinical significance of somatic mutations, made possible only by serial sample sequencing at multiple time points. Increasing clonal burden of extracted genes associated with predictive prognostic impact should be prospectively validated in more uniform and larger cohort of MDS. Disclosures Sekeres: TetraLogic: Membership on an entity's Board of Directors or advisory committees; Celgene Corporation: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees. Shih:Novartis: Research Funding.

Somatic mutations constitute key pathogenetic elements in MDS. Unbiased whole exome sequencing (WES) and deep NGS led to discovery of new somatic mutations and also to the recognition of i) tremendous diversity of mutations and their combinations; ii) individual intra-tumor heterogeneity and clonal hierarchy. Chromosomal lesions further increase the complexity of molecular defects. While in MDS molecular defects are acquired in order, observations made in AML highlight the importance of ancestral events; e.g., t(8;21), inv16 or t(15;17) and other lesions that are used as the basis for nosological sub-classification. Thus, it is the identity of individual ancestral events or their classes rather than the spectrum of secondary events or the distribution of mutations, that will allow for molecular, functionally-relevant and diagnostically useful classification within MDS. This would explain why only a few somatic mutations have been found to be prognostically important, as their position in the clonal hierarchy has not been accounted for. With this in mind, we applied WES (N=206) and targeted deep NGS (N=836) and studied 100 samples serially with analyses focused on ancestral events. Globally, through WES we identified and validated 2386 mutational events in 1458 genes. Of these, 112 genes were mutated at significant frequencies (q Using cross-sectional analyses, the highest mean VAF could be interpreted as consistent with the ancestral nature of the mutations, as seen for instance in a proportion of TET2 and SF3B1 mutant cases. In contrast, the lowest mean VAF indicated secondary events, as occur in NPM1 and RAS pathway mutations. Similar conclusions were made based on cross-sectional analyses showing a similar distribution of ancestral but not secondary events in MDS and sAML. All gene mutations were categorized into those that are predominantly ancestral and those that are facultatively secondary. The most frequent founder mutations were identified (TET2, DNMT3A, SF3B1, ASXL1, TP53, U2AF1, RUNX1, SRSF2) and used to sub-classify approximately 80% of patients, with the remainder containing more infrequent ancestral mutations. While in a combined fashion (as both founder and secondary events) many of these mutations were not predictive of prognosis, they gained relevance when only cases affected by ancestral mutations were used for prognostication. Thus some of the mutations, when present as secondary events may not be predictive. Founding mutations may determine subsequent clinical and molecular features. While other frequently affected genes, SF3B1 or ASXL1, are not associated with a significant increase in the number of concomitant mutations, cases with TET2 mutations showed significantly more frequent mutations per case than those with wild-type TET2 (14.6 vs. 9.1; p=0.001). Moreover, ancestral TET2 mutations were associated with concomitant mutations due to high C-to-T transitions, possibly because reduced 5-hydroxymethylcytosine might create the specific mutator milieu. Most important is the association not of any type, but of ancestral mutations with certain pathomorphologic features and outcomes. Founding TET2 mutations are associated with MPN/MDS while secondary TET2 mutations are present in MDS. Ancestral DNMT3A mutations determine a rapid progression to AML, whereas subclonal DNMT3A mutations are also found in high-risk MDS. RAS pathway mutations are ancestral in CMML and also secondarily positive in the late stage of MDS (sAML). Specific ancestral events may determine subsequent mutational events, and while both types of mutation may affect the clinical phenotype, the initial events are less diverse and more subtype-specific. In conclusion, WES clarified the distinct landscape and ordering of the somatic mutational spectrum in MDS. Disclosures No relevant conflicts of interest to declare.

MDS typically affects older adults, and hereditary factors have been considered less contributory to disease pathogenesis. Moreover, their impact is obscured by the complexity of the clinical presentation and history. Similarly, familial MDS and pediatric MDS is rare and likely distinct from adult MDS occurring in younger adults. Younger MDS patients (pts), excluding those who present with treatment-related disease, may represent a distinct subtype of MDS characterized by a specific molecular pattern of lesions. We compared two groups of MDS pts focusing on pathological diagnosis at presentation, family history of solid malignancies and blood disorders (Leukemia and MDS) in first and second degree relatives, cytogenetic abnormalities and somatic mutations. Our analysis of 1030 MDS pts included MDS, MDS/myeloproliferative neoplasm (MPN) and secondary acute myeloid leukemia (sAML) pts. Overall the median age at presentation of this population was 71years (range 14-100); we classified the younger subset as those falling into the lower 8thpercentile of age to identify. Accordingly, the younger population was characterized by age less than 50 years (range 14-49; median age 41), and the older population age ≥ 50years (range 50-100; median age 75). Treatment-related MDS was excluded. Younger MDS pts more frequently presented with higher-risk disease compared to the older population (46% vs. 31%; P=.004). There was no significant difference between the two groups with regard to family history of cancers (40 vs. 47%; P=.21) and blood disorders (10 vs. 6%; P= .1). When we compared cytogenetic abnormalities between these patient subsets, there was no difference in detection of rate of abnormal cytogenetics (53% vs. 52%; P=.5) or complex karyotype (23 vs. 25%; P=.86). However, del 20q was more common in the older subset (19 vs. 6%; P=.03). We then investigated somatic mutational patterns using new generation deep sequencing for the 60 most commonly encountered MDS mutations (defined in the 200 MDS exome cohort presented in other abstract from our group). Data were available for 26 younger pts and 179 older pts. By analyzing comprehensive mutational spectrum, the average number of somatic mutational events (mean; 2.4/case) was significantly higher in the older subgroup compared to the younger (1.8/case; P In sum, 8% of MDS pts present at a younger age in our cohort. MDS in younger pts presents with more advanced disease and is less commonly affected by del20q- and TET2 mutations, consistent with less common myeloproliferative features in this population. Disclosures: Makishima: AA & MDS international foundation: Research Funding; Scott Hamilton CARES grant: Research Funding.

Hypomethylating agents decitabine and azacitidine are standard treatments for MDS. In their use, one hopes to rectify cytopenias and prolong survival by retarding further disease progression. However, individual treatment responses vary from complete remissions (CR) to complete refractoriness. In general, at least months of therapy is needed prior to assessing response. Thus, patients may need to be subjected to prolonged exposure to ineffective therapy, suffering toxicities without clinical benefit, while alternative and potentially more effective treatments are delayed. Currently, there are no reliable phenotypic or mutational markers for predicting response to hypomethylating agents. Once whole exome sequencing (WES) became available for more routine analysis, we theorized that somatic mutational patterns may help identify patients who would most benefit from these drugs, thereby maximizing response rate by rational patient selection. To pursue this hypothesis, we screened a cohort of 168 patients with MDS who received either azacitidine or decitabine for the presence of somatic mutations. Only those who received sufficient therapy, i.e., completed at least 4 cycles, were selected for outcome analysis. WES and targeted deep NGS for a subset of 60 genes most frequently affected by somatic mutations in MDS (as determined in a set of 200 exome MDS project, see abstract from our group) was applied to 94 evaluable patients. Median age was 68 years (range, 26-85), 34% were female, and MDS subtypes were as follows: RA/RCUD/RARS 7%, RCMD 20%, RAEB-1/2 32%, MDS/MPN & CMML-1/2 21%, and sAML 16%. Response was assessed using IWG 2006 criteria at 4 and 7 months after therapy initiation. Overall response was 34%; rate of CR (including marrow/cytogenetic CR) was 22%, any HI 7%, SD 19%, and no response 35%. The cohort was then dichotomized into “responders” (N=64) and “non-responders” (N=69) with responders classified as those achieving CR/PR or any HI. Baseline patient characteristics were similar between both groups, including average age at treatment initiation, sex, disease subtypes, proportion of abnormal/complex karyotypes, and presence of common cytogenetic aberrations. Overall, the most frequently mutated genes include: TET2 (12%), IDH1/IDH2 (5%), SRSF2 (11%), ASXL1 (28%), SF3B1 (13%), RUNX1 (11%), EZH2/EED/SUZ12 (11%), SETBP1 (6%), CBL (7%), and PPFIA2 (10%). For some analyses we also divided mutations into functional gene families; e.g., DNMT family (DNMT1, DNMT3A, DNMT3B), PRC2 family (EZH2, EED, SUZ12, JARID2, RBBP4, PHF1), IDH family (IDH1, IDH2), CBL family (CBL, CBLB), RAS family (NRAS, KRAS, HRAS, NF1, NF2, RIT1, PTPN11), and among others. The most common molecular abnormalities in responders included the presence of complex karyotype (19% vs. 26% in refractory), del7q/-7 (18% vs. 22%), del5q (19% vs. 15%), and mutations in DNMT3 (25% vs. 22%), ASXL1 (25% vs. 32%), and others. Similarly, the most common defects found in refractory included also the U2AF1/2 family of genes (16% vs. 7% in responders). When compared and selected by the lowest p value, the top mutations in terms of predicting response were SRSF2 (OR 2.4), cohesin (5.1), ATM (OR 5.6) and PHF6 (OR 4.22). Mutations predicting non-response include RAS (OR .3), U2AF1/2 (OR 0.4) and LUC7L defects (OR .53). To generate better predictors, we have combined mutations in “either/or” fashion. For instance, the presence of either SRSF2 and cohesin (p=.0318) or cohesin and PHF6 mutations (p=.02) will be considered predictors of response and the presence of either or RAS/U2AF1(p=.019) and cohesin/ATM (p=.008) and SRSF2 (p=.006) predictors of refractoriness. In sum, mutational patterns may be helpful in identifying patients who may benefit from hypomethylating therapies. Identification of the most predictive genes could guide development of molecular marker-based selection of patients for hypomethylating agent therapy, but will require ongoing analysis and additional prospective testing for validation Disclosures: Makishima: AA & MDS international foundation: Research Funding; Scott Hamilton CARES grant: Research Funding. Maciejewski:NIH: Research Funding; Aplastic anemia&MDS International Foundation: Research Funding.

Germ line mutations in growth factor independent-1 (GFI1) have been described in a small subset of patients (pts) with severe congenital neutropenia. Subsequently, the GFI136N polymorphism, present in 3-5% of controls, has been found overrepresented (11%) in pts with primary (p) acute myeloid leukemia (AML), conveying 1.6 fold risk of development of AML. Mutant GFI136S and N variants lack affinity to HOXA9 (overrepresented in corresponding AML cases), shows increased proliferative potential in vitro and accelerates RAS-driven myeloproliferative neoplasm (MPN) disease in mice. Whole exome next generation (WE NGS) technology facilitates comprehensive screens for the presence of both somatic and germ line genetic alteration. In this study, we used NGS to search for germline variants of the GFI1 gene. We screened 140 pts (mean age 66.8 years, range 44-85) with MDS and related disorders (MDS/MPN and secondary (s) AML) for the presence of GFI1 variants. We found non-synonymous variants in 11 cases (8%), including the previously described pathogenic p.S36N (n=8), p.P107A (n=2), or p.L400F (n=1), while the corresponding frequencies for these alterations were .04 and .001, .002 in the general population. This frequency appears comparable or higher to those previously reported for pAML, but our screen of the TCGA AML cohort, perhaps due to very low coverage for this gene, did not reveal any GFI1 polymorphisms. We next focused on the clinical features of altered GFI1 carriers. A significant proportion of GFI1 cases were younger (age In sum, our results demonstrate that potentially pathogenic GFI1 mutations are present in increased frequency in younger pts with MDS and thus may constitute a new predisposing factor for MDS and related myeloid neoplasms. Disclosures: Makishima: AA & MDS international foundation: Research Funding; Scott Hamilton CARES grant: Research Funding. Maciejewski:NIH: Research Funding; Aplastic anemia&MDS International Foundation: Research Funding.

Chromosomal aberrations and somatic mutations constitute key elements of the pathogenesis of myelodysplastic syndromes (MDS), a clonal hematologic malignancy characterized by cytopenias, a dysplastic bone marrow and propensity to clonal evolution. Next generation sequencing (NGS) enables definition of somatic mutational patterns and clonal architecture as a discovery platform, and for clinical applications. We systematically applied NGS to 707 cases of MDS and MDS-related disorders. 205 cases (low-risk MDS: N=78, high-risk MDS: N=42, MDS/MPN: N=48 and sAML: N=37) were tested by whole exome sequencing (WES). For validation in an additional 502 patients (low-risk MDS: N=192, high-risk MDS: N=104, MDS/MPN: N=111 and sAML: N=95), targeted deep NGS was applied for 60 index genes which were most commonly affected in the cohort analyzed by WES. For NGS data analysis a statistical pipeline was developed to focus on: i) identification of the most relevant somatic mutations, and ii) minimization of false positive results. We studied serial samples from 21 exemplary informative patients. We also compared somatic mutational patterns to those seen in primary AML TCGA cohort (N=201). Given the size of the cohort, there was, for example, a 87% chance of seeing mutations at a frequency of 1% and a 98% of seeing those with a frequency of 2%. While focusing on the most common events, we observed 1117 somatic mutations in 199 genes. The 88 genes mutated mutated in >1% of cases with MDS carried 388 mutations in MDS+sAML (2.5/case), 128 in MDS/MPN (2.7/case) and 398 in pAML (2.0/case). The average number of mutations per case increased during progression (2.2 in lower-risk, 2.8 in higher-risk MDS, 3.4 in sAML). In MDS, the 30 most frequently affected genes were present at least once in 70% of patients. The 30 most frequently mutated genes in MDS/MPN were mutated in 82% of patients. Individual mutations were also sub-grouped according to their function. When we compared three MDS subcategories (lower-risk, higher-risk MDS and sAML) in a cross-sectional view, RTK family, RAS family, IDH family and cohesin family mutations were more frequently detected in the sAML group than in the MDS group. In contrast, the frequency of the DNMT family, TET2 and ASXL family gene mutations did not increase in frequency in the sAML cohort. In addition to better definition of mutational patterns of known genes, we have also defined new mutations, including in the RNA helicase family and the BRCC3pathway. Clonal architecture analysis indicates that mutations of TET2, DNMT3A, ASXL1, and U2AF1 most likely represent ancestral/originator events, while those of the IDH family, RTK family and cohesin family are typical secondary events. Establishment of mutational patterns may improve the precision of morphologically-based diagnosis. The comparison between MDS-related diseases (MDS+sAML) and pAML revealed a notably different mutational pattern suggestive of a distinct molecular derivation of these two disease groups. While RTK, IDH family and NPM1 mutations were more frequently observed in the pAML cohort, mutations of SF3B1 and SRSF2, were more common in MDS+sAML. With regard to the connections between individual mutation combinations, RTK mutations were strongly associated with DNMT, but not with RAS family mutations in the pAML cohort, while the mutual association between TET2 and PRC2 family, cohesin family and RUNX1were encountered in the MDS+sAML cohort. Individual mutations may have prognostic significance, including having an impact on survival, either within the entire cohort or within specific subgroups. In the combined MDS cohort, TP53 family mutations were associated with a poor prognosis (HR; 3.65, 95%CI; 1.90-7.01, P In conclusion, our study continues to indicate the power of NGS in the molecular analysis of MDS. MDS and related disorders show a great deal of pathogenetic molecular overlap, consistent with their morphologic and clinical pictures, but also distinct molecular differences in mutational patterns. Some of the specific mutations are pathognomonic for specific subtypes while some may convey a prognostic rather than discriminatory value. Disclosures: Makishima: Scott Hamilton CARES grant: Research Funding; AA & MDS international foundation: Research Funding. Polprasert:MDS foundation: Research Funding.

Abstract 2 MDS and other chronic myeloid malignancies such as MDS/MPN are characterized by a frequent progression to secondary AML (sAML), a likely multistep process of acquisition of genetic abnormalities. Genes involved in congenital genetic cancer susceptibility syndromes are often targets of somatic mutations in various tumors. For instance, germ-line mutations of SETBP1 are associated with Schinzel-Giedion syndrome (SGS), which is characterized by skeletal malformations, mental retardation and frequent neuroepithelial tumors. While SETBP1 overexpression in myeloid malignancies links to poor prognosis, somatic mutations of SETBP1 were not previously identified in leukemias. When we performed whole exome sequencing of 20 cases with myeloid malignancies, in addition to detecting previously described lesions, such as TET2, CBL and ASXL1, we identified a somatic SETBP1 mutation (D868N) in 2 cases with RAEB. Analysis of DNA from CD3+ cells from these patients confirmed its somatic nature. Sanger sequencing was applied to all coding exons in an additional 48 cases, leading to detection of 2 additional somatic mutations (G870S and I871T) in 2 patients with CMML and sAML, respectively. These findings prompted us to further expand our screening cohort: targeted SETBP1 sequencing was performed in a total of 734 patients (283 with MDS, 106 with sAML, 167 with MDS/MPN, 138 MPN and 146 with primary AML): 52 mutations were detected in 52 patients (7.1%); D868N, G870S and I871T alterations were more frequently observed (N=27, N=16 and N=5, respectively), while D868Y, S869N, D880E and D880N were less prevalent. These mutations, of which 92% (48 out of 52) were identical to those in the SGS germ line, were detected in 15% with CMML (24/156), 15% with sAML (16/106) and 7% CML blast phase (2/28). Clinically, mutant cases were associated with higher age (p=.014), deletion of chromosome 7q (p=.0005) and shorter median survival (28 vs. 13 months, p To directly test whether SETBP1 mutations represent gain-of-function, we performed retroviral transduction of murine Setbp1 engineered with two of the somatic mutations, D868N and I871T, and evaluated the ability of the mutants to immortalize normal murine myeloid progenitors. With a low viral titer of 1 x105 cfu, both Setbp1 mutants caused efficient immortalization of myeloid progenitors, similar to overexpressed WT Setbp1. In addition, cells immortalized with mutant Setbp1 proliferated faster than cells with WT Setbp1. These data suggest that mutations of SETBP1 in our study represent gain-of-function in leukemias. The in vitro immortalization effect of overexpressed WT Setbp1 was associated with and dependent on Hoxa9 and Hoxa10 overexpression. We performed quantitative RT-PCR and western blot experiments to evaluate expression of these genes in our mutant cases. Relative HOXA9 and HOXA10 mRNA expression values were higher in all mutant cases (N=7) than median of those in WT cases (N=4). Also, both HOXA9 and HOXA10 proteins were detected in all cases with SETBP1 mutations, suggesting that HOXA9 and HOXA10 induction is consistently associated with SETBP1 mutations similar to observations in forced expression of WT Setbp1. Moreover, in agreement with findings in primary cells showing that SETBP1 mutations or high SETBP1 expression share a common genetic association with RUNX1 mutations, Runx1 expression was reduced after in vitro immortalization of normal bone marrow cells by forced Setbp1 overexpression and two Runx1 promoter sequences were amplified after ChIP performed with antibody specific for exogenous Setbp1 protein. Moreover, Setbp1 shRNA knockdown resulted in enhanced Runx1 transcription consistent with the negative regulation of this gene by Setbp1. These results indicate that SETBP1 is associated with decreased activity of RUNX1 due to hypomorphic mutations or by direct down-modulation WT RUNX1 expression bypassing the need for mutations. In sum, somatic recurrent SETBP1 mutations are lead to gain of function and are associated with molecular pathogenesis of myeloid leukemic transformation of various primary myeloid subentities. Disclosures: Makishima: Scott Hamilton CARES Initiative: Research Funding. Maciejewski:NIH: Research Funding; Aplastic Anemia&MDS International Foundation: Research Funding.

Abstract 1405 Genes involved in congenital genetic cancer susceptibility syndromes are also targets of somatic mutations in various tumors. Examples include WT1, NF1, CBL, TP53 and MLL2 affected both in germ line as well as somatic mutations present in malignant disorders. To apply this approach to investigation of pathogenic mutations in myeloid malignancies, we selected 183 congenital disorders in which germline mutations of disease specific genes are reported to be pathogenic. Their main clinical presentations are skeletal abnormalities (N=54 disorders), skin abnormality (N=24), mental retardation (N=17) and hematological disorders (N=12). In total, we searched for mutations in 204 genes associated with these congenital disorders. We analyzed whole exome of various myeloid malignancies, including 60 cases with myelodysplastic syndromes (MDS), 29 MDS/MPN, 5 with MPN and 122 with acute myeloid leukemia (AML) and found somatic mutations in 62 genes, which also mutated in germ line in various congenital syndromes. Of those, the most frequently mutated genes were TP53 (25 cases) and WT1 (16 cases), associated with germline mutation of Li-Fraumeni syndrome and Wilms tumor, respectively. Some somatic mutations, for example, NF1 (R1276Q) and PTPN11 (D61N), were exactly the same as observed in corresponding congenital disorders (Neurofibromatosis or Noonan syndrome). One of the novel findings is that somatic SET binding protein 1 (SETBP1) mutations (D868N, G870S and I871T) were commonly observed in sAML and CMML, and were identical to germline mutations in Schinzel-Giedion syndrome (see designated abstract). We found recurrent somatic SETBP1 mutations in 15% of each CMML and sAML. Moreover, multiple genes pathogenic in Usher syndrome (congenital hearing and vision loss, complicated by vasoproliferative retinal tumor), were somatically mutated in various myeloid neoplasms. Out of 9 genes which are causative for this syndrome, 15 mutations of 6 genes (MYO7A, USH1C, CDH23, PCDH15, USH2A, and GPR98) were observed in 13 cases, including 2 frameshift and 13 missense mutations. These genes coordinate with each other to form a functional network. CDH23 and PCDH15 are cadherins and act as cell adhesion molecules. MYO7A are actin-based motor molecules with a variety of functions. USH1C serves as an anchor and codes for a scaffolding protein to form a complex with all the other proteins. Through the PDZ binding site, USH1C forms a complex with CDH23, which was the most frequently mutated gene in this family (1 frame shift and 3 misssense mutations). CDH23 mutations were observed in 2 cases with primary AML, sAML and MDS. Specifically, a somatic missense mutation G2771S of CDH23 in a secondary AML case was identical to germline of Usher syndrome. The second most frequently mutated gene, GPR98, is located in 5q14.3 locus; a small hemizygous clone found in del5q of an MDS case. In a serial sample analysis, this mutation increased to become the larger main clone during AML evolution. Moreover, in this case, an additional CDH23 mutation was acquired in the course of leukemic expansion. In such cases with Usher syndrome gene mutations, U2AF1, ZRSR2, EZH2, IDH2 and ETV6 mutations were also observed, suggesting pathogenic cooperation with these well-known tumor suppressor genes and oncogenes. Disclosures: Maciejewski: NIH: Research Funding; Aplastic Anemia&MDS International Foundation: Research Funding. Makishima:Scott Hamilton CARES Initiative: Research Funding.

Abstract 310 CMML is characterized by monocytic proliferation, cytomorphologic dysplasia, and frequent progression to AML. Heterogeneity in or subtlety of presentation can make diagnosis challenging. Recent advances in molecular technology set the stage for systematic study of genetic and genomic lesions associated with CMML. Initially, RAS and RUNX1 mutations were identified in CMML; subsequently, mutations in TET2, CBL, ASXL1 and EZH2 have been discovered. Most recently, recurrent mutations in various genes of the spliceosomal machinery have been added, with SRSF2 likely the most common mutation in this condition. We hypothesized that more precise analysis of molecular lesions in CMML may allow for better categorization of this condition according to molecular pathogenesis and may provide clues to target therapy of this rather refractory condition. We identified 136 patients with CMML or secondary AML (sAML) with antecedent CMML: 87 CMML-1, 20 CMML-2 and 29 post-CMML sAML. The original cohort has been expanded by an additional 53 patients since first reported. The mean follow up period was 16 months (range, 0–114). Abnormal cytogenetics were found in 50% of the cohort by both metaphase and SNP-array-based karyotyping. In a representative subset of 27 patients, we have applied whole genome sequencing (WES) for which paired tumor/germ line DNA was used. To minimize false positives and focus on the most prevalent/relevant somatic events, we implemented a rational bioanalytic filtering approach and results were aligned using Burrows-Wheeler Aligner and variants detected using the GATK pipeline (Best Practice Variant Detection from Broad Institute). We focused on somatic defects with a frequency of >5% of the cohort. For the most commonly affected genes, results were validated using an expanded panel of 18 genes in 72 additional patients and, thus, for the most relevant genes a cohort of 95 patients was studied. The most frequently mutated genes were TET2 (48%), SRSF2 (35%), ASXL1 (17%) and RUNX1 (17%), whereas CBL (13%), EZH2 (13%), UTX (8%) and U2AF1 (8%), SETPB1 (10%), and RIT1 (9%) were less frequent. We also found TP53 and RUNX1 mutations in 5% and 16% of patients, respectively. A JAK2 V617F mutation was present in one case of seemingly typical CMML. BCOR and STAG2 mutations were found in 13% and 9% of patients, respectively; KRAS/NRAS mutations were in 10%. Spliceosomal gene mutations seem to be mutually exclusive, but were frequently associated with other non-spliceosomal gene mutations examined. Within the cohort of 28 SRSF2 mutant cases, 15 had coexisting TET2 mutations, 22 had ASXL1 mutations, 7 had RUNX1 and 5 had CBL mutations. Among 10 U2AF1 mutant cases, 3, 5 and 2 had TET2, ASXL1, and RUNX1 mutations, respectively. SETBP1 mutations were present in 34% of CMML-1/2 and frequently associated with RUNX1, SRSF2, CBL (approximately 2% each) and ASXL1 (4%) mutations. Cohesin mutations were less frequent (10%) because RAD21 and SMC mutations were absent. Mutations of PTPN11 and NF1 were less frequent in adult CMML than those reported in JMML. We also identified several less-recurrent gene mutations that likely modify pathogenesis or clinical outcomes of specific cases. Serial studies performed on 6 cases showed insight into the clonal architecture, producing a series of putative ancestral and secondary events, including uniparental disomy and acquisition of KRAS/NRAS or SETPB1 mutations. Association between mutational status and overall survival (OS) was assessed using Kaplan-Meier statistics. While all permutations were tested, we highlight here only significant positive and relevant negative results. In the whole cohort, presence of CBL mutations conferred worse OS (p=.018; HR 2.44, 95%CI 1.18–4.69). Median OS was 16 months for CMML-1, 6 months for CMML-2, and 14-months for sAML. In subgroup analyses, CBL mutations were also significant worse prognostic factor in CMML-1 cohort (p=.037; HR 3.23, 95%CI 1.07–8.04). In sum, WES provides intricate information on the molecular pathogenesis of CMML and the wide mutational spectrum correlates with the clinical diversity. Expert-based analysis of the genomic data may be supplanted by unsupervised and unbiased approaches which would cluster patients based on molecular similarities. Disclosures: Maciejewski: NIH: Research Funding; Aplastic Anemia&MDS International Foundation: Research Funding. Makishima:Scott Hamilton CARES Initiative: Research Funding.

Abstract 307 Whole-exome (WES) sequencing revealed tremendous mutational heterogeneity in leukemia. While WES can be applied for discovery, it also has potential as a diagnostic tool that can overcome the shortcomings of current methods. We theorized that, in addition to mutation discovery, systematic application of WES in MDS may reveal distinct mutational patterns allowing for new molecular classification. We performed WES in 116 paired exomes, including MDS (n=57), MDS/MPN (n=36), and sAML (n=23). We also included comparative analysis with pAML (N=202; TCGA), and other publicly available data for a total of 333 exomes; 10 patients were studied serially. Paired DNA (marrow/CD3+ cells) was subjected to WES, sequence-aligned by BW Aligner, and variants detected via GATK pipeline (Broad Institute). We used defined criteria to minimize false-positives: P5% prevalence, and not found in ex/internal SNP databases. This narrowed the spectrum to 645 mutations (54 genes) for analysis with clinical/phenotypic correlations. Mutations were isolated or grouped by pathway, e.g., PRC2, cohesin complex, plexins and dyneins, etc. In MDS, examples of prevalent mutations include SF3B1 (14%), DNMT3A (11%) and U2AF1/2 (9%). In MDS/MPN: TET2 (36%), SRSF2 (22%) and ASXL1 (19%) and SETBP1 (6%); in sAML: NRAS/RAS (16%), RUNX1 (16%) and cohesin mutations (12%), in contrast to pAML with mutational spectrum dominated by FLT3, DNMT3A, NMP1 or SMC3/1A (cohesin complex). The exome panel did not cover 20% patients, suggesting that their pathogenesis may be related to less recurrent events (613 candidates: 2nd screening phase). When mutational spectrum of sAML vs pAML were compared, mutants of SF3B1 (7 vs 1%, P=.04), BCOR (7 vs 1%, P=.04), CDH11/23 (13 vs. 1%, P=.003), FMN2 (7 vs. 1%, P=.04), PPFIA2 (7% vs 0%, P=.01), SPTAN1 (7% vs 0%, P=.01) and VPS8 (7 vs 0%, P=.017) were more frequent in sAML while DNMT3A and NPM1 were less common. Analysis of MDS/MPN revealed mutations in PRC2 (2 vs 11%, P=.05), SRSF2 (5 vs. 22%, P=.010) and TET2 (3 vs. 33%, P After analyzing survival impact of individual mutations, functional groups, cytogenetic category and clinical parameters, we found TP53, ETV6, PRPF8, FMN2, UMODL1, KIT, GATA2, complex karyotype and chr. 5 anomalies had a prognostic impact on OS. However, in multivariate analyses, the first variable to stratify our cohort was, as expected, the diagnosis subtype (HR 2.2, P In sum, mutational spectrum of myeloid neoplasms can be assessed with WES. The pattern of frequency and concurrence in each diagnostic subtype differs substantially, a feature that can be exploited diagnostically. Despite heterogeneity, mutations and their combinations can be found to categorize patients and serve as prognostic markers. Analysis of additional cases is ongoing and will be presented at the meeting. Disclosures: Makishima: Scott Hamilton CARES Initiative: Research Funding. Maciejewski:NIH: Research Funding; Aplastic Anemia&MDS International Foundation: Research Funding.

Abstract 1333 While immune mechanisms are involved in the pathogenesis of idiopathic aplastic anemia (AA), identification of heritable predisposition/susceptibility traits has been difficult due to the impact of exogenous factors and the low prevalence of AA. The seemingly sporadic and likely complex and heterogeneous traits leading to AA are not easily amenable to genetic studies. With the advent of whole genome scanning (WGS) technologies such as single nucleotide polymorphism arrays (SNP-A), large scale investigations in various disorders have been conducted. A systems level understanding of a particular disease may allow for the identification of candidate genetic variants as prognostic and diagnostic biomarkers. Previous studies utilized arrays with mostly tagging SNPs and thereby the identification of causative polymorphisms was only indirectly possible through the narrowing of LD intervals. We have applied a custom cancer chip (Illumina) containing 211,155 SNP probes designed for non-synonymous SNPs, allowing for a more direct discovery of pathogenic genes with the aim of identifying low prevalence genetic variants that contribute to the development, risk and therapy responsiveness in idiopathic AA. Our study involved 116 cases used for discovery and 120 cases to be used for confirmatory studies, as well as a cohort of 1964 controls to improve the power of detection. After exclusion of SNPs with a GenTrain score of 0.8) to a total of 7445 loci. Remarkably, informative LD blocks were identified, represented by multiple markers pointing to the presence of informative polymorphisms in the corresponding regions. A total of 3 SNPs were prioritized for final investigation based on the frequency differential between patients/controls. Of great interest was rs2544773 located in MYT1L represented directly by a singular marker. The frequency of the heterozygous variant among patients was 41.9% vs. 6.5% in controls and 15.0% vs. 0.4% for the minor homozygous variant (p Comparison of AA patients with healthy individuals has been a primary focus of GWAS. However, we have also compared subgroups defined by clinical criteria. We subdivided patients based on responsiveness to immunosuppressive therapy. CEBPZ was represented by rs3213746 through LD with rs12469082 (p In sum, our study represents novel, whole genome approach using custom designed, high density cancer microarray that unravels new gene targets responsible for disease susceptibility as well as response to immunosuppressive therapy. Disclosures: No relevant conflicts of interest to declare.

Abstract 457 Ring sideroblasts (RS) are abnormal nucleated erythroblasts characterized by iron granules in mitochondrial cristae. RS are seen in acquired and congenital sideroblastic anemia. Dysfunction in mitochondrial metabolism has been implicated in the pathogenesis of RS. However, the true mechanism leading to RS formation remains elusive. Clonal sideroblastic anemias are usually acquired in the context of MDS: 15% or more RS in the bone marrow (BM) with appropriate morphologic and cytogenetic criteria in MDS is best classified as RARS, but varying quantities of RS ( Disclosures: No relevant conflicts of interest to declare.

Abstract 4137 Relapse remains the most common cause of treatment failure in allogeneic hematopoietic stem cell transplantation (AlloHCT) for AML. Several risk factors (i.e. older age, persistent disease at transplant, adverse cytogenetics, secondary AML, non-myeloablative conditioning regimen) have been identified as predictors for post-transplant AML recurrence. In addition, the adverse prognostic influence of specific mutations (DNMT3, ASXL1, IDH1/2, RUNX1, TET2, TP53 etc.) has been identified in both de novo and secondary AML treated with standard chemotherapy regimens. The impact of these mutations on clinical outcomes following AlloSCT, however, remains largely unexplored. Consequently, we conducted this study to investigate the prognostic role of molecular lesions including metaphase (MC) and SNP array (SNP-A) cytogenetic defects and somatic mutations in patients undergoing AlloHCT. A total of 186 patients were identified who received myeloablative AlloHCT for AML (2000–2010) and had pre-transplant diagnostic leukemic sample available for testing. We performed SNP-A karyotyping and sequencing for RUNX1, DNMT3, TP53, ASXL1, CBL, IDH1/2, NPM1, FLT3ITD and TET2 gene mutations and correlated the results with clinical outcomes following AlloHCT. SNP-A based karyotyping helped to upstage the cytogenetics by inclusion of previously undetected cryptic abnormalities.Cox proportional hazards analysis was used to identify prognostic factors for relapse, relapse free (RFS) and overall survival (OS). Analysis was based on 103 patients (55%) who had data on cytogenetics. Of these 103 patients, 42 (41%) had disease relapse following transplantation and 58 (56%) died within the median follow up of 39 months (range, 8–133) following their myeloablative AlloSCT. The frequencies of mutations were estimated; for example, FLT3, NPM1, DNMT3, ASXL1, IDH1/2, CBL, RUNX1 and TP53 were detected in 18%, 13%, 14%, 9%, 9%, 4%, 2% and 2% of the cases, respectively. Overall, mutations were present in 35% of AML cases, and were exclusive to those with intermediate or favorable risk cytogenetics. Various combinations were encountered, however in those with 2 concomitant mutations, NPM1 was present in all cases. In patients with intermediate risk cytogenetics (n=83) and those with mutational abnormalities the leukemia relapse rate was 40% and 38%, respectively. In particular, among patients harboring NPM1 mutation relapses occurred in those who were positive for either DNMT3 or FLT3ITD. Lower rate of relapse (25%) was observed in patients with ASLX1 and IDH1/2 mutations. In one case of aggressiveTP53 mutation the patient was alive and leukemia free 3 years after her AlloHCT. In multivariable analysis, complex cytogenetics was an independent predictor for inferior RFS (HR=1.97, 95% CI, 1.04–3.7) and OS (HR=1.96, 95% CI, 1.04–3.7).Older age at transplant (per 10 yr increase, HR=1.24, 95% CI, 1.01–1.5) was associated with poorer OS, whereas higher comorbidity score (HR=1.86, 95% CI, 1.04–3.3) was associated with poorer RFS. There was no significant difference in post-transplant outcomes between patients in intermediate risk cytogenetics with detected genetic mutations (excluding isolated NPM1) and those with no detectable mutations. Our preliminary results suggest that myeloablative AlloHCT could minimize the prognostic impact of adverse molecular markers in AML. These mutations potentially serve as important biomarkers in determining the management of AML. Further studies designed to determine their precise role are planned. Disclosures: No relevant conflicts of interest to declare.

Abstract 2411 One of the most serious complications of aplastic anemia (AA) is the clonal evolution to myelodysplastic syndrome (MDS). Monosomy 7 (del[7]) is the most common chromosomal aberration encountered in this setting, but it can also occur in primary MDS along with deletion 7q (del[7q]). In our whole cohort of AA, we detected del[7] in 24 cases of clonal evolution; however, unlike in MDS no cases of del[7q] were observed. In contrast, in MDS or myelodysplastic/myeloproliferative neoplasms, del[7]/[7q] were present in 12% and 11%, respectively. Based on an initial observation of an index AA case with a mutation of CBL, we speculated that certain molecular events such as point mutations can promote or are at least associated with the evolution of del[7]. Given the distinct distribution of del[7] and del[7q] in primary and secondary MDS (derived from AA), we stipulate that the associated mutational pattern will be distinct. This may be due to different driving mechanisms, such as immune escape or a growth factor-rich milieu in AA. Pursuant to this theory, we performed a screen for CBL, RUNX1, TET2, UTX, EZH2, DNMT3A, ASXL1 and IDH family mutations in patients who developed del[7] after AA (N=24). 14 cases were adults and 10 were pediatric cases. In addition, we analyzed 15 del[7], 13 del[7q] and 10 UPD[7q] abnormalities in patients with MDS without antecedent AA. We identified 3 CBL (13%), 5 RUNX1 (20%), 1 TET2 and 1 DNMT3A mutation in patients with del[7] after AA; all CBL mutations are observed in adult cases of AA (21%). However, 0, 1, and 2 CBL mutations were found in primary MDS with del[7], del[7q] and UPD[7q], respectively. In contrast, RUNX1 mutations were seen in both AA sub-groups (14% and 30% in adults and children, respectively). Also, no differences were seen with regard to the distribution of RUNX1 mutations in either post-AA MDS with del[7] or primary MDS with del[7], del[7q] and UPD[7q]. Most significantly, ASXL1 was found to be the most frequently mutated gene in the cohort without AA (37%), although no mutations were seen in patients with del[7] after AA. Additionally, UTX and EZH2, both involved in the trimethylation of histone H3 lysine 27, were found to be mutated only in cases of MDS with UPD[7q] and del[7q], but no mutations were seen in primary and AA-derived MDS with del[7]. When studied serially, none of the tested mutations was seen in the initial AA phase, but the mutated clone increased gradually during clonal evolution of del[7]. We also investigated the presence of additional chromosomal abnormalities using single nucleotide polymorphism array (SNP-A)-based karyotyping in the cases with del[7] after AA. In addition to del[7], 22 gains, 20 losses and 4 regions of somatic uniparental disomy (UPD) were identified. These abnormalities, including microdeletions, were found in 50% and 60% of adult and pediatric cases, respectively. Recurrent lesions were detected on chromosome 6, 8 and 21. A microdeletion on chromosome X involved the tumor-associated gene PHF6 in a male case. In another patient, trisomy 21 was accompanied by a RUNX1 mutation. Regions of UPD included 6p resulted in loss of heterozygosity of MHC class I and 11q was associated with homozygous CBL mutations in 2 cases. In sum, our analysis supports the theory that distinct mechanisms of molecular progression during MDS evolution may be operative in AA and primary MDS. Moreover, del[7], del[7q] and UPD[7q] have distinct molecular profiles with frequent TET2 mutations in del[7q] and UPD[7q]. ASXL1 mutations appear to be most ubiquitous promoting event in MDS with LOH [7/7q], suggestive of their “type II' nature. In contrast, other mutations such as those in CBL may be selected for e.g., through cytokine-rich milieu and activation of CBL-regulated receptor tyrosine kinases. Disclosures: No relevant conflicts of interest to declare.

Abstract 3566 MDS patients (pts) are destined to either progress to more aggressive disease or die of MDS-related complications. The International Prognostic Scoring System (IPSS) and other systems assess the survival and risk of evolution to acute myelogenous leukemia (AML), based in part on specific cytogenetic abnormalities. However, heterogeneity still exists even within cytogenetic groups, in part due to cryptic lesions, making predictions imperfect. In this respect, we and others have demonstrated that single nucleotide polymorphism array (SNP-A) karyotyping may improve the diagnostic yield, and that previously cryptic lesions can improve prognostic resolution of cytogenetic testing when compared to metaphase cytogenetics (MC) alone. Despite the recent identification of a variety of somatic mutations in MDS, their therapeutic value is unproven, and because of conflicting findings as to the risk for many mutations, they have not been routinely introduced into diagnostic algorithms. Mutational events may constitute suitable biomarkers that could strengthen current prognostic schemes. In addition, malignant progression is associated with acquisition of new molecular defects, which may impact our understanding of the molecular pathogenesis of MDS and allow for distinction of ancestral from facilitating defects. We hypothesized that serial cytogenetic testing for a comprehensive spectrum of mutations and cytogenetic defects would reveal which molecular event is associated with progression. We have analyzed a cohort of 76 MDS pts, 38 of whom experienced progression to AML (median age=68.5, IPSS = 0.5) matched to 38 pts (median age=69, IPSS =0.5) who did not experience progression. In addition to MC, we compared these groups for the presence of selected mutations, including TP53, RUNX1, TET2, ASXL1, DNMT3A, IDH1/2, NPM1, CBL and EZH2. The progressor group (PG) consisted of 20 (53%) low and intermediate-1 risk patients; the non-progressor group (NPG) had 22 (62%). In 60% of PG and 49% NPG at presentation, normal cytogenetics were present, while 16% and 14% had poor-risk cytogenetics, respectively. In addition, in 13% of PG and 11% of NPG, del7/7q was present. CBL, TP53, NPM1, ASXL1, IDH1, IDH2, RUNX1, DNMT3A, TET2 and EZH2 mutations were detected in (for PG vs. NPG): 0 (0/33) vs. 9% (3/35) p=1; 0 (0/29) vs. 5% (1/20) p=.4; 0 (0/33) vs N/A, 20% (6/30) vs. 18% (6/34) p=1; 9%(3/32) vs. 0 (0/39) p=.08; 0 (0/25) vs 0 (0/36) p=1; 0% (0/26) vs. 16% (1/6) p=.18; 7% (2/27) vs. 11% (4/37) p=1; 19% (4/21) vs. 37% (13/35) p=.23; and 5% (1/19) vs. 6% (2/32) p=1, respectively. We conclude that these pt groups had similar rates of mutations. We subsequently compared the cytogenetic and mutational status between initial presentation and at AML progression in the PG group. Progression was associated with occurrence of new cytogenetic lesions in 41% (14/34) while it remains stable in 53% (18/34) of pts. The most common new cytogenetics defects associated with evolution included trisomy 8, monosomy 7/del7q and monosomy 18. In 1, 2, and 1 pts, progression was associated with acquisition of CBL, TP53, and RUNX1 mutations, respectively. In contrast in 5, 3, 2 and 4 pts, ASXL1, IDH1, DNMT3A and TET2 mutations were present already at presentation. New mutations were detected upon leukemic evolution in 10/14 patients with abnormal MC and 3/14 with normal MC. We conclude that ASXL1 and TET2 (and perhaps IDH1 and DNMT3A) constitute early events while acquisition of TP53, CBL and possibly RUNX1 were events leading to progressive, advanced disease. Disclosures: Afable: Alexion: Speakers Bureau. Sekeres:Celgene Corporation: Honoraria, Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees. Maciejewski:Celgene: Speakers Bureau; Alexion: Speakers Bureau; Celgene: Research Funding; Eisai: Research Funding; NIH: Research Funding; AA & MDS International Foundation: Research Funding.

Abstract 1402 Chronic myelomonocytic leukemia (CMML) is characterized by monocytic proliferation, cytomorphologic dysplasia and frequent progression to acute myelogeneous leukemia (AML). The molecular basis of CMML is poorly defined, although somatic mutations in a number of genes have recently been identified in a proportion of patients (epigenetic regulatory genes, spliceosomal genes, apoptosis genes, growth signal transducers and others). We performed a comprehensive analysis of molecular lesions, including somatic mutations detected by sequencing and chromosomal abnormalities investigated by metaphase and SNP-array karyotyping. We have selected a cohort of 72 patients (36 CMML1, 16 CMML2 and 20 sAML evolved from CMML). Our mutational screen performed in stages (as new mutations were discovered by our and other groups) and currently reveals mutations in UTX in 8%, DNMT3A in 9%, CBL in 14%, IDH1/2 in 4%, KRAS in 2.7%, NRAS in 4.1%, JAK2 in 1%, TET2 in 48%, ASXL1 in 43%, EZH2 in 5.5%, RUNX1 37%. Based on the discovery of various spliceosomal mutations in myeloid malignancies, novel mutations were also found in CMML, in U2AF1 in 12%, SF3B1 in 14%, SFRS19 in 6 % of cases tested. Chromosomal defects were detected in 60% of patients. In particular, a high frequency of somatic uniparental disomy (sUPD) were identified 71% of patients with abnormal cytogenetics, including UPD1p (N=3), UPD7q (N=8), UPD4q (N=6), UPD2p (N=2), UPD17q (N=2), UPD11q (N=5), UPDX (N=1), UPD21q (N=2). Some of the detected mutations were homozygous through their association with sUPD as for example for 3 EZH2, 1 UTX, 6 TET2, 2 DNMT3A, 5 CBL, 1 NRAS, 1 U2AF1 mutations. Furthermore, UPD17p implies that a P53 mutation is also present in this case as previously LOH17p was shown to be invariably associated with P53 mutations. Similarly, 2 cases of UPD17q imply that homozygous mutation of SRSF2, which is one of the Serine/arginine-rich splicing factor, may be present in this location and the mutation analysis is ongoing. In over 90% of >1 mutation was found but many patients harbored multiple mutations with frequent combinations of TET2/CBL or TET2/ASXL1 as well as RUNX1 and U2AF1 serving as examples. There was an accumulation of mutations from sAML, CMML2 and CMML1 suggesting stepwise accumulation of lesions. In serial studies, some of the mutations were present at the inception (e.g., TET2, ASXL1 and DNMT3A) in some cases originally heterozygous mutations were also while other can occur in the course of disease (e.g. CBL). RAS and DNMT3A mutations were associated with a higher blasts count. In sum, combined analysis of molecular lesions in CMML reveals that similar phenotype may be a result of diverse mutations associated with seemingly unrelated pathways and that clinical phenotype may be a result of a combination of mutations which accumulate as the disease progresses. Survival analyses will require large cohorts to account for various confounding factors including the presence of multiple chromosomal abnormalities and mutations in one patient, however currently EZH2, DNMT3 and CBL mutations appear to convey less favorable prognosis. Disclosures: No relevant conflicts of interest to declare.

*401 Distribution and Significance of EZH2 Mutations in MDS and Related Myeloid Malignancies Hideki Makishima, Anna Jankowska, Hadrian Szpurka, Alan List, Michael McDevitt, Kathryn uinta, Mehdi A. Keddache, Christine O’Keefe, Mikkael A. Sekeres, Jaroslaw Maciejewski Department of Translational Hematology and Oncology Research, Cleveland Clinic, Department of Hematologic Malignancies, Lee H Moffitt Cancer Center, Department of Medicine, Division of Hematology, Johns Hopkins University School of Medicine

Abstract 297 Loss of heterozygosity (LOH) involving chromosome-7 is one of the most common unbalanced chromosomal defects found in chronic and acute myeloid malignancies. Recent application of single nucleotide polymorphism arrays (SNP-A) led to realization that recurrent areas of LOH may be not only due to deletion of the whole chromosome-7, its long arm but due to copy-neutral LOH, most often involving 7q. We hypothesized that deletions and uniparental disomy (UPD) involving long arm of chromosome-7 may be associated with pathogenic hemizygous or homozygous mutations, respectively. Such mutations may affect tumor suppressor genes and likely contribute to/drive malignant evolution in myeloid disorders. We identified a large number of patients with lesions of chromosome-7 (monosomy-7, del(7q), and UPD(7q)), including 38 patients with microdeletions 7q. After unsuccessful targeted Sanger sequencing of large numbers of genes on chromosome-7 we set up to apply the next generation sequencing (NGS) of the exome libraries generated from patients with LOH7. Exome chromosome-7 libraries were enriched for the content of coding sequences using the SureSelect capture synthetic biotinylated RNA probes, tiling all the coding regions from chromosome-7. For NGS exome sequencing we selected 6 cases of monosomy-7 (2 sAML, 1 MDS, 1 chronic myelomonocytic leukemia (CMML), 1 juvenile myelomonocytic leukemia (JMML), and 1 aplastic anemia (AA)), 2 cases of del(7q) with MDS, 3 cases of UPD(7q) (2 MDS and 1 MDS/MPN) and also studied paired germline samples when possible. We treated monosomy-7 and del(7q) as one class and analyzed them together. Cases with UPD(7q) were analyzed separately. Averaged sequencing depth was 79. Each monosomy-7 sample had 3788, 3792, 5306, 4013, 5237, 4016 potential alterations (average; 4359/sample), and each del(7q) sample had 5431, 4521 observations (average; 4976/sample). After exclusion of observations outside of affected regions del(7q), we eliminated previously reported SNPs and non-coding lesions and selected 658 observations of which 422 were nonsynonymous. For further analysis, the alteration leading to stop codons were chosen as tier 1 candidates (N=16). After elimination of false positives due to the accumulation of reading errors at specific locations were discarded, 3 candidates were left and verified by Sanger sequencing. All of 3 were confirmed as new SNPs. After elimination of false positives, the alteration present in multiple samples were designated as tier 2 group (N=101). All of these sequence changes were shown to be new SNPs; 2 were not confirmed by traditional sequencing. Mutations for which the non-reference base occurred greater than 50% were designated tier 3 candidates (N=73), of which 25 candidates have been already checked by resequencing. To date, we have identified 2 somatic point mutations confirmed by Sanger sequencing, including NRCAM1Q1040K and LMTK2A1147T and each identified in different monosomy-7 samples. Screening of 30 monosomy-7 or del(7q) samples showed that observed mutations were not recurrent. The similar stepwise analytic approach was applied to 3 cases of UPD(7q) (average; 4312 observations per sample). After exclusion of reported SNPs and synonymous alterations, we selected a total of 147 alterations. The number was further reduced to 5 potential pathogenic changes after elimination of false positive NGS artifacts. By verification with Sanger sequencing, recurrent EZH2 homozygous mutations (both were R690H) were confirmed in 2 cases with UPD7q. Then we sequenced whole the exons in additional 12 cases of UPD(7q) were sequenced yielding 2 EZH2 mutations. In addition, EZH2 mutations were identified in 2 cases of microdeletion 7q36.1 and 4 cases without LOH7q occurring in heterozygous constellation. No mutations of EZH2 were found in monosomy-7 or del(7q) sequenced (N=28). In conclusion, to date, using NGS strategy, we have identified 3 new mutations including NRCAM1Q1040K, LMTK2A1147T, and recurrently occurring mutation of EZH2 (EZH2R690H). Several additional candidate mutations are currently screened. Disclosures: Maciejewski: Eisai: Research Funding; Celgene: Research Funding.

Abstract 607 Using single nucleotide polymorphism arrays (SNP-A) as a karyotyping tool led to the recognition that segmental somatic uniparental disomy (UPD) is a common and important defect in myelodysplastic syndromes (MDS) and related conditions. Homozygous mutations associated with UPD have been found. Additionally, SNP-A-detected submicroscopic deletions have proven helpful in narrowing the search for mutant genes to shared regions of loss of heterozygosity (LOH). Mapping of such microdeletions was instrumental in the identification of TET2 and CBL mutations, frequently found in a homozygous constellation within UPD of the corresponding chromosomal regions. UPD7q is one of the most frequent areas of UPD present in MDS, MDS/MPN and sAML. We hypothesized that this region may be associated with the presence of pathogenic mutations in a homozygous configuration. We utilized two strategies: i) because of the large size of the area commonly affected by UPD7, we applied next generation sequencing (NGS) for the identification of affected genes, and ii) we systematically sequenced genes contained in the overlapping deleted regions. In total, 15 patients with UPD7q were identified. Exome libraries were generated from 2 cases with UPD7q and subjected to sequencing. In one, a missense C to T mutation was found at nt148137376 of EZH2 (100% of sequences), resulting in R690H. The somatic origin of this homozygous mutation was confirmed by sequencing of DNA from a skin biopsy. Simultaneously, we identified 2 patients with overlapping microdeletion involving 7q36.1. The minimally affected area involved 2 genes: CUL1 and EZH2. Sequenced all exons of both genes revealed no mutations in CUL1. However, a mutation in EZH2 exon 19 was identified in proximity to the mutation detected through NGS. The mutation involved position Ile715 producing a frame shift. We detected EZH2 mutations in 10/351 patients (7% of MDS/MPN, 2% of MDS and 0.9% of AML). We found 8 different EZH2 mutations present in 4/15 (27%) of cases with UPD7q, 2/30 (7%) patients with deletion 7q and 4/306 (1%) without LOH. Of note is that both hemizygous mutations were found in patients with microdeletions and none of the patients with large del(7q) or monosomy 7 harbored EZH2 mutation. There were 8 missense and 2 frame shift mutations, located in the SET domain of the EZH2 gene. Diagnoses included 3 cases of refractory cytopenia with multilineage dysplasia, while 5 had myelomonocytoid malignancies, and one each with MDS/MPN unclassifiable and atypical chronic myeloid leukemia (aCML). Overall, EZH2 mutations were detected in 4/53 (8%) cases of CMML, consistent with the high prevalence of somatic UPD7 in this disease. Interestingly, no EZH2 mutant case had a chromosome 7 abnormality by metaphase cytogenetics, but SNP-A karyotyping detected cryptic LOH7q in 6/10 patients with EZH2 mutations. EZH2 is a polycomb associated gene encoding a methyltransferase targeting H3K27, thereby producing a repressive mark. Loss of function or hypomorphic mutations of EZH2 would thus be predicted to result in abrogation of inhibitory chromatin marks and chromatin decompaction, conducive to expression of oncogenes. Immunofluorescence and western blot showed that EZH2 mutations in myeloid malignancies lead to decreased methylation of H3K27 and thereby are functionally relevant. Expression analysis of EZH2 did not show significantly decreased expression in MDS or haploinsuffciency in patients with del7/7q. In a patient with aCML and UPD7q, homozygous R690H EZH2 mutation was detected and trimethylated H3K27 was abrogated while H3K9 methylation appeared normal, consistent with functional impairment of the SET domain. Interestingly, an EZH2 mutation was associated with heterozygous TET2 S733fsX21 and heterozygous ASXL1 W538X mutations, suggesting multiple genes associated with epigenetic regulation may be mutated and act synergistically in malignant evolution. These triple mutant cells ultimately formed lethal tumors when injected to NOD SCID gamma mice. In summary, our investigations demonstrate EZH2 mutations in patients with myeloid malignancies frequently associated with UPD7q, or 7q36.1 microdeletion, but not monosomy 7 and del(7q). These findings suggest that an increasing possibility that mutations in the polycomb gene family represent a new class of molecular lesions conveying a clonal epigenetic instability phenotype and can constitute leukemogenic events. Disclosures: No relevant conflicts of interest to declare.

Abstract 3374 Metaphase spreads have an established value in the routine diagnostic workup of myeloid malignancies and bone marrow failure disorders. In myelodysplastic syndrome (MDS) abnormal karyotypes play a large role in scoring systems and may greatly impact prognosis, or even predict responsiveness to certain therapies. In aplastic anemia (AA) cytogenetic abnormalities detected by metaphase karyotyping may rule out hypoplastic MDS. In myeloproliferative neoplasia (MPN), an abnormal karyotype may distinguish between reactive or malignant proliferation. Due to technical problems, including specimen quality, viability, hypocellularity or a failure of growth, this routine test may fail to yield conclusive results in some patients. With the advent of SNP-A karyotyping, which only requires extracted DNA, non-informative cases can be resolved. As a cytogenetic test, single nucleotide polymorphism array (SNP-A) analysis can provide an opportunity to improve risk assessment and selection of proper treatment modalities. The advantages of SNP-A include excellent resolution, detection of copy neutral loss of heterozygosity (also known as uniparental disomy or UPD), and perhaps most importantly, the ability to test archived DNA samples, rather than actively dividing cells. However, unlike metaphase cytogenetics, this technology cannot detect subsets of abnormal populations or certain classes of genomic rearrangements, such as balanced translocation, inversion or ring chromosomes. In this study, we examined the prognosis and disease characterization for patients with non-informative cytogenetics (N=144) collected over the last 8 years. SNP-A-based karyotyping has been performed for a representative subset of these patients (N=60) to assess whether this technique could provide clinically relevant information. These patients included patients with MDS (N=20), AA (N=20), AML (N=12) and MDS/MPN (N=3). Bone marrow obtained following induction chemotherapy was excluded. We have detected 27 somatic microdeletions and 33 microduplications ( Based on these criteria, SNP-A analysis revealed an abnormal karyotype in 14 (23%) patients; 3 with AA and 11 with myeloid disorders. The most common recurrent abnormalities included deletion 5q (N=5) and del7/7q (N=3) but other lesions including13q-, del20, +8p were also seen. Of note we have also detected somatic UPD (regions >25Mb) in 2 cases, including 22q11.23qter and 14q12-q22.1. In 4/60 (7%) a complex karyotype was detected, while 10 had sole lesions (>10Mb). In presumed AA patients, we have identified 2 patients with monosomy 7, prompting a change of diagnosis to MDS and thereby altering their clinical management. In MDS, when cytogenetic prognostic groupings were applied in previously unscored patients, 10/20 had IPSS scores of 3 or greater. The presence of chromosomal abnormalities detected by SNP-At indictated the presence of advanced risk disease and thereby contributed into poorer survival as predicted by IPSS. Disclosures: No relevant conflicts of interest to declare.

Abstract 4016 Lenalidomide (LEN) is effective in patients with myelodysplastic syndromes (MDS) and the del(5q) cytogenetic abnormality, and has activity in a proportion of patients without this chromosomal defect. To date, no clinically actionable biomarkers, other than the presence of del(5q) detected by metaphase cytogenetics, have been identified to predict response to LEN. The diagnostic yield of metaphase cytogenetics can be enhanced by application of fluorescence in situ hybridization (FISH) for targeted chromosomal lesions including del(5q), as this technique is more sensitive. Similarly, single nucleotide polymorphism array (SNP-A)-based karyotyping, due to its superb resolution, allows for detection of previously cryptic unbalanced chromosomal defects. Both techniques can be preformed on interphase cells and thereby do not require cell division. We hypothesized that application of these technologies may allow for better identification of putative responders to LEN in patients with MDS without del(5q); we stipulated that i) we may detect previously unrecognized cases of del(5q) and that ii) more precise analysis of the karyotypes may allow for recognition of other chromosomal markers of response or refractoriness to LEN. In patients with MDS (N=82), MDS/myeloproliferative neoplasm (MPN) (N=13), acute myeloid leukemia (AML) (N=23), and MPN (N=4), the detection rate of del(5q) increased only marginally with use of additional techniques, from 24% (metaphase cytogenetics (MC) + FISH), to 25% (MC + SNP-A), 25% (FISH + SNP-A) and 26% (all 3 methods). Within this cohort, we then analyzed by FISH and SNP-A karyotype a subset of 42 patients with myeloid malignancies without del(5q) by MC who received LEN. This cohort included 33 MDS (RA, N=5; RARS, N=12; RARS-T, N=1; RCMD, N=1; RAEB1, N=4; RAEB2, N=6; MDS-U, N=4), 6 MDS/MPN and MPN patients (CMML1, N=1; CMML2, N=3, IMF; N=2) and 3 secondary AML. By MC, 32 (76%) showed normal karyotype, 1 (2.4%) no growth and 9 (21%) abnormal karyotype other than del(5q). The overall response rate (ORR) (2006 International Working Group criteria) was 44%, including 3 CR, 3 PR and 8 HI. Previously cryptic del(5q) was detected in an additional 1/18 patient by both SNP-A and FISH (secondary AML with normal metaphase cytogenetics), but this case was refractory to LEN. Del(5q) was also revealed by FISH in 1 patient with unsuccessful MC, but, due to the small size of the clone (8%), SNP-A did not detect this lesion. This patient had a sustained PR with transfusion independence. In 28 patients who received LEN for more than 3 months, the ORR to LEN in patients with normal metaphase cytogenetics was 62%, and 17% for those with chromosomal aberrations (p=.08); the addition of SNP-A did not improve the predictive value of normal cytogenetics. We also analyzed 10 patients without del(5q) by MC who received combination therapy with azacitidine (AZA) and LEN, for whom the ORR was 80% (7 CR, 1 PR). By metaphase cytogenetics, 7/10 patients had a normal karyogram and a response of 86%, compared to 3 patients with chromosomal lesions, 1 of whom responded. Similar to the results in LEN alone, inclusion of defects detected by SNP-A or FISH did not allow for better separation of responders based on normal cytogenetics by MC. Six out of 38 LEN-treated patients had a gain of chromosome 8 material by FISH or SNP-A. 4 out of 6 patients had CR (all of them received combination therapy of AZA and LEN), 1 out of 6 had HI, and 1 with complex karyotype had NR (ORR was 83%), while ORR in patients with other chromosomal abnormalities by FISH or SNP-A was 18%. In conclusion, FISH and SNP-A, when added to routine metaphase cytogenetics, marginally increased the diagnostic yield leading to detection of only 2/42 additional cases with del(5q). In our cohort, the non-del(5q) patients with normal karyotype and those with trisomy 8 or microduplication on chromosome 8 were associated with a favorable response to LEN. Disclosures: Sekeres: Celgene: Consultancy, Honoraria, Research Funding. List:Celgene: Research Funding. Maciejewski:Celgene: Research Funding.

Abstract 612 Background: Chromosome 5q deletion (del5q) is the most common cytogenetic abnormality in myelodysplastic syndrome (MDS). Although haplodeficiency of several genes may contribute to the disease phenotype, allelic deletion of the ribosomal protein S14 (RPS14) gene is a key effector of the hypoplastic anemia. Disruption of ribosome assembly arising from RPS14 deletion leads to nucleolar stress that triggers p53 activation. In a murine model of the human 5q- syndrome, TP53 inactivation was alone sufficient to rescue the hematologic phenotype, indicating that the molecular pathogenesis of del(5q) MDS is p53-dependent. The tumor suppressor TP53 gene is a key regulator of stem cell homeostasis and senescence. A well described single nucleotide polymorphism (SNP) located at codon 72 in the proline-rich, pro-apoptotic domain of TP53 has been linked to cancer and mutagen susceptibility, and treatment outcome. Substitution of a cytosine (‘C’ allele) for the more common guanine (‘G’ allele) results in translation of a proline rather than arginine residue at position 72, with diminished apoptotic potential. Given the pathogenetic role of p53 in del(5q) MDS, we hypothesized that homozygosity for the ‘C’ allele may be associated with disease predisposition. Methods: Bone marrow and blood samples were investigated from 118 del(5q) MDS patients, 102 non-del(5q) MDS patients, and 98 healthy controls. Genomic DNA was extracted and codon 72 of the TP53 gene was amplified by PCR. Forward and reverse Sanger sequencing was performed to determine genotype. Relationship to disease specific features at diagnosis including cytogenetic risk category, IPSS score, blast percentage, and age were investigated as well as the relationship to response to lenalidomide and AML transformation using SAS software (Version 9.2, SAS Institute Inc., Cary, NC, USA). Results: Genotype distribution significantly differed between del(5q) MDS patients (18% CC, 47% CG, and 35% GG), non-del(5q) MDS patients (9% CC, 58% CG, and 33% GG),and healthy controls (7% CC, 43% CG, and 50% GG) (p=0.01). The frequency of the homozygous CC genotype was >2x greater in del(5q) MDS (18%) compared to both non-del(5q) MDS (9%) and healthy controls (7%) (p=0.05). There was no significant frequency difference between non-del(5q) and healthy controls. Del(5q) MDS patients were >6 times more likely to carry the CC genotype vs. GG when compared to healthy controls [odds ratio (OR)=6.71, 95% CI: 1.56 to 28.86], whereas non-del(5q) patients were >3 times more likely to carry the CC genotype vs. GG when compared to healthy controls (OR=3.87, 95% CI: 0.66 to 22.71). The corresponding ‘C’ allele frequency was significantly greater among del(5q) MDS patients (41.7%) compared to healthy controls (28.6%) (p=0.006), and approached significance in non-del(5q) patients (37.8%) versus controls (p=0.06). There was no association between TP53 R72P genotype and cytogenetic risk group in either del(5q) (p=0.67) or non-del(5q) MDS patients (p= 0.60), IPSS (del5q, p=0.29; non-del5q, p=0.89), or response to lenalidomide (del5q, p=0.57; non-del5q p=0.89). Mean age at diagnosis was significantly (p=0.04) lower in del(5q) MDS (67.4 years; SD=11.1 years) compared to non-del(5q) MDS patients (70.8 years; SD=9.1years), although significant differences in age according to TP53 R72P genotype were not apparent in either MDS cytogenetic group (del5q, p=0.99; non-del5q, p=0.89). Conclusion: Our findings indicate that the TP53 R72P homozygous CC genotype occurs with significantly greater frequency in del(5q) MDS compared to both non-del(5q) MDS patients and healthy controls, suggesting that this polymorphism may play a key role in the pathogenesis of and predisposition to del(5q) MDS. Disclosures: Kurtin: Celgene: Honoraria. Maciejewski:Celgene: Research Funding; Eisai: Research Funding; Alexion: Consultancy. Nevill:Celgene: Honoraria. Karsan:Celgene: Research Funding. List:Celgene: Research Funding.