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IF 15.132 (2017); International audience; The introduction of novel agents has led to major improvements in clinical outcomes for patients with multiple myeloma. To shorten evaluation times for new treatments, health agencies are currently examining minimal residual disease (MRD) as a surrogate end point in clinical trials. We assessed the prognostic value of MRD, measured during maintenance therapy by next-generation sequencing (NGS). MRD negativity was defined as the absence of tumor plasma cell within 1 000 000 bone marrow cells (

A CpG-stimulated autologous tumor cell vaccine for patients with MCL is safe and feasible and induces detectable antitumor T cell immune responses. Patients who received the CpG-MCL vaccination demonstrated freedom from MRD at 1 yr after ASCT that surpassed previously reported rates., Here, we report on the results of a phase I/II trial (NCT00490529) for patients with mantle cell lymphoma who, having achieved remission after immunochemotherapy, were vaccinated with irradiated, CpG-activated tumor cells. Subsequently, vaccine-primed lymphocytes were collected and reinfused after a standard autologous stem cell transplantation (ASCT). The primary endpoint was detection of minimal residual disease (MRD) within 1 yr after ASCT at the previously validated threshold of ≥1 malignant cell per 10,000 leukocyte equivalents. Of 45 evaluable patients, 40 (89%) were found to be MRD negative, and the MRD-positive patients experienced early subsequent relapse. The vaccination induced antitumor CD8 T cell immune responses in 40% of patients, and these were associated with favorable clinical outcomes. Patients with high tumor PD-L1 expression after in vitro exposure to CpG had inferior outcomes. Vaccination with CpG-stimulated autologous tumor cells followed by the adoptive transfer of vaccine-primed lymphocytes after ASCT is feasible and safe.

Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. However, the personalized identification and validation of neoantigens remains a major challenge. Here we discover neoantigens in human mantle-cell lymphomas by using an integrated genomic and proteomic strategy that interrogates tumour antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients. Remarkably, all discovered neoantigenic peptides were exclusively derived from the lymphoma immunoglobulin heavy- or light-chain variable regions. Although we identified MHC presentation of private polymorphic germline alleles, no mutated peptides were recovered from non-immunoglobulin somatically mutated genes. Somatic mutations within the immunoglobulin variable region were almost exclusively presented by MHC class II. We isolated circulating CD4+ T cells specific for immunoglobulin-derived neoantigens and found these cells could mediate killing of autologous lymphoma cells. These results demonstrate that an integrative approach combining MHC isolation, peptide identification, and exome sequencing is an effective platform to uncover tumour neoantigens. Application of this strategy to human lymphoma implicates immunoglobulin neoantigens as targets for lymphoma immunotherapy.

Recent advances in next-generation sequencing (NGS) have enabled the quantitation of circulating tumour DNA (ctDNA) encoding the clonal rearranged V(D)J immunoglobulin locus. We aimed to evaluate the clonal heterogeneity of follicular lymphoma (FL) in the tumour and the plasma at diagnosis and to assess the prognostic value of the ctDNA level. Plasma samples at diagnosis were available for 34 patients registered in the PRIMA trial (NCT00140582). One tumour clonotype or more could be detected for 29 (85%) and 25 (74%) patients, respectively, in the tumour or plasma samples. In 18 patients, several subclones were detected in the tumour (2 to 71 subclones/cases) and/or in the plasma (2 to 20 subclones/cases). In more than half of the cases, the distribution of subclones differed between the tumour and plasma samples, reflecting high clonal heterogeneity and diversity in lymphoma subclone dissemination. In multivariate analysis, a high level of ctDNA was the only independent factor associated with patients’ progression-free survival (HR 4, IC 95 (1.1-37), p=.039). In conclusion, an NGS-based immunosequencing method reveals the marked clonal heterogeneity of follicular lymphoma in patients with FL, and quantification of ctDNA at diagnosis represents a potential powerful prognostic biomarker that needs to be investigated in larger cohorts.

Next-generation sequencing (NGS)-based circulating tumour DNA (ctDNA) detection is a promising monitoring tool for lymphoid malignancies. We evaluated whether the presence of ctDNA was associated with outcome after allogeneic haematopoietic stem cell transplantation (HSCT) in lymphoma patients. We studied 88 patients drawn from a phase 3 clinical trial of reduced-intensity conditioning HSCT in lymphoma. Conventional restaging and collection of peripheral blood samples occurred at pre-specified time points before and after HSCT and were assayed for ctDNA by sequencing of the immunoglobulin or T-cell receptor genes. Tumour clonotypes were identified in 87% of patients with adequate tumour samples. Sixteen of 19 (84%) patients with disease progression after HSCT had detectable ctDNA prior to progression at a median of 3·7 months prior to relapse/progression. Patients with detectable ctDNA 3 months after HSCT had inferior progression-free survival (PFS) (2-year PFS 58% vs. 84% in ctDNA-negative patients, P = 0·033). In multivariate models, detectable ctDNA was associated with increased risk of progression/death (Hazard ratio 3·9, P = 0·003) and increased risk of relapse/progression (Hazard ratio 10·8, P = 0·0006). Detectable ctDNA is associated with an increased risk of relapse/progression, but further validation studies are necessary to confirm these findings and determine the clinical utility of NGS-based minimal residual disease monitoring in lymphoma patients after HSCT.

Recent studies have shown limited utility of routine surveillance imaging for diffuse large B-cell lymphoma (DLBCL) patients achieving remission. Detection of molecular disease by immunoglobulin high-throughput sequencing (Ig-HTS) from peripheral blood provides an alternate strategy for surveillance. We prospectively evaluated the utility of Ig-HTS within 311 blood and 105 tumor samples from 75 patients with DLBCL, comparing Ig-HTS from the cellular (circulating leukocytes) and acellular (plasma cell-free DNA) compartments of peripheral blood to clinical outcomes and (18)fluoro-deoxyglucose positron emission tomography combined with computed tomography (PET/CT; n = 173). Clonotypic immunoglobulin rearrangements were detected in 83% of patients with adequate tumor samples to enable subsequent monitoring in peripheral blood. Molecular disease measured from plasma, compared with circulating leukocytes, was more abundant and better correlated with radiographic disease burden. Before treatment, molecular disease was detected in the plasma of 82% of patients compared with 71% in circulating cells (P = .68). However, molecular disease was detected significantly more frequently in the plasma at time of relapse (100% vs 30%; P = .001). Detection of molecular disease in the plasma often preceded PET/CT detection of relapse in patients initially achieving remission. During surveillance time points before relapse, plasma Ig-HTS demonstrated improved specificity (100% vs 56%, P < .0001) and similar sensitivity (31% vs 55%, P = .4) compared with PET/CT. Given its high specificity, Ig-HTS from plasma has potential clinical utility for surveillance after complete remission.

Patients with HIV are at increased risk for developing B-cell lymphomas likely due in part to chronic antigen stimulation leading to clonal immunoglobulin (Ig) gene rearrangements. Clonal Ig DNA has been identified in the plasma in patients with lymphomas. However, next-generation sequencing (NGS)-based identification of circulating Ig clonotypes has not been well-characterized, particularly in HIV-related lymphomas. The AIDS Malignancies Consortium (AMC) enrolled 51 untreated patients with HIV-related B-cell lymphomas and analyzed paired tumor and plasma specimens for Ig clonotypes using an NGS-based approach (AMC064, NCT00981097). Lymphoma-specific clonotypes (>5% frequency) were identified in 83% (33/40) of the tumor specimens. Results from paired tumor and plasma specimens showed identical circulating clonotypes in the plasma from 97% (32/33) of patients. High International Prognostic Index (IPI) scores of 3–4 among patients with diffuse large B-cell lymphoma correlated with higher lymphoma molecules/million diploid genomes in the plasma compared with lower IPI scores of 0–2, median 77335 vs. 6876, p = 0.005. Further prospective studies are merited to determine whether plasma clonal Ig DNA has prognostic significance as a biomarker in HIV-related lymphomas and if the presence of lower frequency detection (≤ 5%) may have similar implications.

While immune checkpoint blockade elicits efficacious responses in many patients with cancer, it also produces a diverse and unpredictable number of immune-related adverse events (IRAE). Mechanisms driving IRAEs are generally unknown. Because CTLA-4 blockade leads to proliferation of circulating T cells, we examined in this study whether ipilimumab treatment leads to clonal expansion of tissue-reactive T cells. Rather than narrowing the T-cell repertoire to a limited number of clones, ipilimumab induced greater diversification in the T-cell repertoire in IRAE patients compared with patients without IRAEs. Specifically, ipilimumab triggered increases in the numbers of clonotypes, including newly detected clones and a decline in overall T-cell clonality. Initial broadening in the repertoire occurred within 2 weeks of treatment, preceding IRAE onset. IRAE patients exhibited greater diversity of CD4+ and CD8+ T cells, but showed no differences in regulatory T-cell numbers relative to patients without IRAEs. Prostate-specific antigen responses to ipilimumab were also associated with increased T-cell diversity. Our results show how rapid diversification in the immune repertoire immediately after checkpoint blockade can be both detrimental and beneficial for patients with cancer. Cancer Res; 77(6); 1322–30. ©2016 AACR.

Quantification of minimal residual disease (MRD) following allogeneic hematopoietic cell transplantation (allo-HCT) predicts post-transplant relapse in patients with chronic lymphocytic leukemia (CLL). We utilized an MRD-quantification method that amplifies immunoglobulin heavy chain (IGH) loci using consensus V and J segment primers followed by high-throughput sequencing (HTS), enabling quantification with a detection limit of one CLL cell per million mononuclear cells. Using this IGH-HTS approach, we analyzed MRD patterns in over 400 samples from 40 CLL patients who underwent reduced-intensity allo-HCT. Nine patients relapsed within 12 months post-HCT. Of the 31 patients in remission at 12 months post-HCT, disease-free survival was 86% in patients with MRD10(-4) and 20% in those with MRD ≥10(-4) (relapse hazard ratio (HR) 9.0; 95% confidence interval (CI) 2.5-32; P0.0001), with median follow-up of 36 months. Additionally, MRD predicted relapse at other time points, including 9, 18 and 24 months post-HCT. MRD doubling time12 months with disease burden ≥10(-5) was associated with relapse within 12 months of MRD assessment in 50% of patients, and within 24 months in 90% of patients. This IGH-HTS method may facilitate routine MRD quantification in clinical trials.

Since the incorporation of tyrosine kinase inhibitors into the treatment of Philadelphia chromosome–positive (Ph+) acute lymphoblastic leukemia (ALL), the notion that all patients with "high-risk" ALL uniformly require allogeneic (allo) hematopoietic cell transplantation (HCT) has received increasing scrutiny. Although multiple studies have shown superiority of alloHCT over autologous (auto) hematopoietic cell transplantation for high-risk patients, these findings may be explained, in part, by contamination of the peripheral blood progenitor cell (PBPC) leukapheresis product by residual leukemic cells in patients undergoing autoHCT. We retrospectively evaluated minimal residual disease (MRD) using next-generation sequencing (NGS) in the PBPC leukapheresis product of 32 ALL patients who underwent autoHCT. Twenty-eight patients (88%) had diagnostic samples with quantifiable immunoreceptor rearrangements to follow for MRD. Twelve (38%) patients had Ph+ B-ALL, 12 (38%) had Philadelphia chromosome–negative (Ph−) B-ALL, and 4 (14%) had T cell ALL. With a median follow-up of 41 months (range, 3 to 217), median relapse-free survival (RFS) and overall survival for the entire cohort were 3.2 and 4.2 years, respectively; at 5 years after transplantation, 42% of patients remain alive and relapse free. Using MRD detection at a threshold of ≥ 1 × 10−6, median RFS for patients with detectable MRD was 6.5 months and was not reached for patients without detectable disease (P = .0005). In multivariate analysis, the only factor significantly associated with relapse was the presence of MRD ≥1 × 10−6 (odds ratio, 23.8; confidence interval, 1.8 to 312.9; P = .0158). Our findings suggest that NGS for MRD detection can predict long-term RFS in patients undergoing autoHCT for high-risk ALL.

Objective Ankylosing spondylitis (AS), a chronic inflammatory disorder, has a notable association with HLA–B27. One hypothesis suggests that a common antigen that binds to HLA–B27 is important for AS disease pathogenesis. This study was undertaken to determine sequences and motifs that are shared among HLA–B27–positive AS patients, using T cell repertoire next-generation sequencing. Methods To identify motifs enriched among B27-positive AS patients, we performed T cell receptor β (TCRβ) repertoire sequencing on samples from 191 B27-positive AS patients, 43 B27-negative AS patients, and 227 controls, and we obtained >77 million TCRβ clonotype sequences. First, we assessed whether any of 50 previously published sequences were enriched in B27-positive AS patients. We then used training and test cohorts to identify discovered motifs that were enriched in B27-positive AS patients versus controls. Results Six previously published and 11 discovered motifs were enriched in the B27-positive AS samples as compared to controls. After combining motifs related by sequence, we identified a total of 15 independent motifs. Both the full set of 15 motifs and a set of 6 published motifs were enriched in the B27-positive AS patients as compared to B27-positive healthy individuals (P = 0.049 and P = 0.001, respectively). Using an independent cohort, we validated that at least some of these motifs were associated with AS, and not simply with B27-positive status. Conclusion We identified TCRβ motifs that are enriched in B27-positive AS patients as compared to B27-positive healthy controls. This suggests that a common antigen, presented by HLA–B27 and detected by CD8+ T cells, may be associated with AS disease pathogenesis.

Monitoring antigen-specific T cells is critical for the study of immune responses and development of biomarkers and immunotherapeutics. We developed a novel multiplex assay that combines conventional immune monitoring techniques and immune receptor repertoire sequencing to enable identification of T cells specific to large numbers of antigens simultaneously. We multiplexed 30 different antigens and identified 427 antigen-specific clonotypes from 5 individuals with frequencies as low as 1 per million T cells. The clonotypes identified were validated several ways including repeatability, concordance with published clonotypes, and high correlation with ELISPOT. Applying this technology we have shown that the vast majority of shared antigen-specific clonotypes identified in different individuals display the same specificity. We also showed that shared antigen-specific clonotypes are simpler sequences and are present at higher frequencies compared to non-shared clonotypes specific to the same antigen. In conclusion this technology enables sensitive and quantitative monitoring of T cells specific for hundreds or thousands of antigens simultaneously allowing the study of T cell responses with an unprecedented resolution and scale.

Presentation of novel antigenic peptides (neoantigens) that distinguish malignant from normal cells by major histocompatibility complexes (MHC) can serve as potent substrates for specific anti-tumor immune responses. We sought to identify mantle cell lymphoma (MCL) neoantigens by taking an integrated genomic and proteomic strategy that interrogates antigen peptides presented by MHC-class I and class II. Peptides bound to MHC were purified via immunoprecipitation followed by identification using mass spectrometry. Mass spectra were searched against patient-specific proteome databases generated by whole exome sequencing and targeted immunoglobulin gene sequencing. This approach was applied to systematically characterize over 36,000 immunopeptides from 17 patients’ tumor specimens. Interestingly, 52 neoantigenic peptides were derived from the lymphoma immunoglobulin (Ig) heavy or light chain variable regions. Although we identified MHC presentation of private germline polymorphic alleles, no mutated peptides were recovered from non-Ig somatically mutated genes. Furthermore, somatic mutations within the immunoglobulin variable region were almost exclusively presented by MHC-II. T-cells specific for Ig-derived neoantigens were found in two patients. Following ex vivo activation and expansion, the T-cells were remarkably able to mediate killing of autologous lymphoma cells. These results demonstrate that combining MHC isolation, peptide identification and exome sequencing is an effective platform to uncover tumor neoantigens. Application of this strategy to MCL implicates immunoglobulin neoantigens as targets for lymphoma immunotherapy.

Cytotoxic T lymphocyte–associated antigen-4 (CTLA-4) blockade can promote antitumor T cell immunity and clinical responses. The mechanism by which anti–CTLA-4 antibodies induces antitumor responses is controversial. To determine the effects of CTLA-4 blockade on the T cell repertoire, we used next-generation deep sequencing to measure the frequency of individual rearranged T cell receptor β (TCRβ) genes, thereby characterizing the diversity of rearrangements, known as T cell clonotypes. CTLA-4 blockade in patients with metastatic castration-resistant prostate cancer and metastatic melanoma resulted in both expansion and loss of T cell clonotypes, consistent with a global turnover of the T cell repertoire. Overall, this treatment increased TCR diversity as reflected in the number of unique TCR clonotypes. The repertoire of clonotypes continued to evolve over subsequent months of treatment. Whereas the number of clonotypes that increased with treatment was not associated with clinical outcome, improved overall survival was associated with maintenance of high-frequency clones at baseline. In contrast, the highest-frequency clonotypes fell with treatment in patients with short overall survival. Stably maintained clonotypes included T cells having high-avidity TCR such as virus-reactive T cells. Together, these results suggest that CTLA-4 blockade induces T cell repertoire evolution and diversification. Moreover, improved clinical outcomes are associated with less clonotype loss, consistent with the maintenance of high-frequency TCR clonotypes during treatment. These clones may represent the presence of preexisting high-avidity T cells that may be relevant in the antitumor response.

We assessed the prognostic value of minimal residual disease (MRD) detection in multiple myeloma(MM) patients using a sequencing-based platform in bone marrow samples from 133 MM patients in at least very good partial response (VGPR) after front-line therapy. Deep sequencing was carried out in patients in whom a high-frequency myeloma clone was identified and MRD was assessed using the IGH-VDJH, IGH-DJH, and IGK assays. The results were contrasted with those of multiparametric flow cytometry (MFC) and allelespecific oligonucleotide polymerase chain reaction (ASO-PCR). The applicability of deep sequencing was 91%. Concordance between sequencing and MFC and ASO-PCR was 83% and 85%, respectively. Patients who were MRD- by sequencing had a significantly longer time to tumor progression (TTP) (median 80 vs 31 months; P, This research project was supported by grants PS09/01370, PS09/1450, PI12/01761, and PI12/023121 from the Fondo de Investigaciones Sanitarias; RD12/10 Red de Cáncer (Cancer Network of Excellence) from the Instituto de Salud Carlos III, Spain, and from the Fondo de Investigaciones Sanitarias, Asociación Española Contra el Cáncer (AECC, GCB120981SAN) and the CRIS foundation. This study was supported in part by research funding from Sequenta, Inc. (F.P., L.W., M.M., M.F.).

Neoantigens arising through somatic mutations are increasingly recognized as key tumor antigens driving clinical immune responses. We sought to identify human lymphoma neoantigens through a genomic and proteomic characterization of peptide ligands of major histocompatibility complex class I (MHC-I) and class II (MHC-II) of a cohort of patients with untreated mantle cell lymphoma. Peptide identification was performed through analysis of MHC-I and MHC-II peptide ligands using liquid chromatography and tandem mass spectrometry (LC/MS-MS), and augmented by generating patient-specific proteome databases through tumor:normal whole exome sequencing and targeted immunoglobulin gene sequencing in 17 patients. A total of 66 neoantigen peptides from 9 patients were found to be presented by MHC, and surprisingly all neoantigenic peptides were derived from either the lymphoma immunoglobulin heavy or light chain genes. There was no detectable MHC presentation of hundreds of candidate somatic neoantigenic peptides from other genes despite widespread antigen presentation of the proteome including proteins encoded by germline heterozygous single nucleotide polymorphisms. Clonotypic lymphoma immunoglobulin sequences were among the most commonly presented proteins by both MHC-I and MHC-II, yet MHC-I presentation of variable regions was nearly absent and included only a single neoantigen derived from IGVH. In contrast, the variable region was frequently presented by MHC-II and included neoantigen peptides created through somatic hypermutation or VDJ recombination. Autologous circulating T-cells specific for immunoglobulin-derived neoantigens could be detected using MHC-II tetramers and their frequency dynamically changed with vaccination and therapy. These findings suggest that immunoglobulin derived neoantigens are frequently presented by lymphoma, and represent potential targets for CD4, but not CD8, T-cell mediated therapies. Figure. MHC-I and MHC-II presentation of lymphoma immunoglobulin. (A) MHC-I (left) and MHC-II (right) presented peptides derived from patients' immunoglobulin were mapped to the immunoglobulin domains. Peptides recovered from all seventeen patients are mapped to a schematic of the IgM molecule with a heat map indicating the number of recovered peptides covering each position. (B) Expanded view of the immunoglobulin heavy chain variable region. The heatmap represents the total number of MHC-presented peptides that span that position, including non-neoantigens for MHC-I (above) and MHC-II (below). Neoantigen peptides created by either somatic hypermutation or VDJ rearrangement are mapped above or below the heat map. Red, positions within the recovered peptides which are altered from germline variable genes thus creating neoantigens. Boxes, peptides derived from a single patient. Figure. MHC-I and MHC-II presentation of lymphoma immunoglobulin. (A) MHC-I (left) and MHC-II (right) presented peptides derived from patients' immunoglobulin were mapped to the immunoglobulin domains. Peptides recovered from all seventeen patients are mapped to a schematic of the IgM molecule with a heat map indicating the number of recovered peptides covering each position. (B) Expanded view of the immunoglobulin heavy chain variable region. The heatmap represents the total number of MHC-presented peptides that span that position, including non-neoantigens for MHC-I (above) and MHC-II (below). Neoantigen peptides created by either somatic hypermutation or VDJ rearrangement are mapped above or below the heat map. Red, positions within the recovered peptides which are altered from germline variable genes thus creating neoantigens. Boxes, peptides derived from a single patient. Disclosures Newman: Roche: Consultancy. Carlton:Adaptive Biotechnologies: Employment, Equity Ownership. Moorhead:Adaptive Biotechnologies: Employment. Faham:Adaptive Biotechnologies Corp: Employment.

Background The assessment of residual tumor cells persisting after therapy, or minimal residual disease (MRD), is a central component of accurate disease prognosis in acute lymphoblastic leukemia (ALL) (Pui et al, JCO 2011). MRD assessment has recently been shown to be useful for monitoring disease before and after stem cell transplantation and during salvage therapy for early detection of an imminent relapse (Bruggemann et al., SemOncol 2012). Allele-specific oligonucleotide (ASO)-PCR can be used to assess MRD; however, this technique requires preparation of clonotype-specific primers for each individual which is laborious and time-consuming. We recently demonstrated the utility of sequencing-based MRD assessment in lymphoid malignancies (Faham et al., Blood 2012). This quantitative approach, termed the LymphoSIGHT™ platform, relies on amplification and sequencing of immunoglobulin and T-cell receptor gene segments using consensus primers and can address some of the limitations associated with traditional MRD detection techniques. This sequencing platform has a sensitivity to detect one cancer cell per million leukocytes in peripheral blood and bone marrow samples. In this retrospective study, we evaluated the ability of the sequencing and ASO-PCR methods to detect MRD prior to clinical relapse in 17 patients with childhood ALL. Methods Using the sequencing assay, we analyzed bone marrow and/or peripheral blood samples collected at the diagnostic and relapse time points from 17 childhood ALL patients. Diagnostic and relapse samples were assessed for clonal rearrangements of immunoglobulin (IGH-VDJ, IGH-DJ, IGK) and T cell receptor (TRB, TRD, TRG) genes. Following identification of leukemia specific clonotype(s), we measured the corresponding MRD levels in 66 follow-up samples that were collected prior to clinical relapse. We analyzed the time from MRD positivity to clinical relapse for each patient using the sequencing and ASO-PCR methods. Results Sequencing detected the presence of a high-frequency clonal rearrangement of at least one receptor (“calibrating receptor”) in all the 17 childhood ALL patients; all patients had at least 2 calibrating receptors at diagnosis and/or relapse, 15 patients had at least 3 calibrating receptors, and 6 patients had 4 or more. The IGH-VDJ and TRG assays were the most frequent gene rearrangement: at least one IGH-VDJ and/or TRG clonal rearrangement was detected in 13 ALL patients. TRD was the third most informative receptor, with clonal rearrangements being detected in 11 patients. In the majority of patients, most leukemic clones identified at diagnosis were also present at high levels in the relapse sample. We analyzed the time from MRD positivity to clinical relapse in the patient cohort. In 2 patients (Figure 1, Patients G and P), we observed MRD positivity by sequencing 16 and 6.5 months prior to relapse, respectively. ASO-PCR also detected MRD positivity in Patient P at the 6.5 month time point. In 6 patients there was a sample collected within 1-3 months prior to relapse, and sequencing detected MRD in 4 of these patients (67%, Figure 1 Patients B, A, R, I), while ASO-PCR detected MRD in 2 of the 6 patients (33%, Figure 1 Patients B, R). Conclusions The clinical value of monitoring MRD by ASO-PCR for assessment of treatment response and outcome has been established in multiple lymphoid malignancies. This preliminary study provides further support for the sequencing-based MRD monitoring in ALL patients. This new approach offers improvements over ASO-PCR in the ability to monitor multiple clonal sequences and in the sensitivity to detect the leukemic cell. Thus, the sequencing method represents a new potential approach for MRD monitoring. However a larger number of patients must be analyzed to support its clinical application. Disclosures: Faham: Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity’s Board of Directors or advisory committees. Pepin:Sequenta, Inc.: Employment, Equity Ownership. Carlton:Sequenta, Inc.: Employment, Equity Ownership.

The persistence of minimal residual disease (MRD) during therapy is the strongest adverse prognostic factor in acute lymphoblastic leukemia (ALL). We developed a high-throughput sequencing method that universally amplifies antigen-receptor gene segments and identifies all clonal gene rearrangements (ie, leukemia-specific sequences) at diagnosis, allowing monitoring of disease progression and clonal evolution during therapy. In the present study, the assay specifically detected 1 leukemic cell among greater than 1 million leukocytes in spike-in experiments. We compared this method with the gold-standard MRD assays multiparameter flow cytometry and allele-specific oligonucleotide polymerase chain reaction (ASO-PCR) using diagnostic and follow-up samples from 106 patients with ALL. Sequencing detected MRD in all 28 samples shown to be positive by flow cytometry and in 35 of the 36 shown to be positive by ASO-PCR and revealed MRD in 10 and 3 additional samples that were negative by flow cytometry and ASO-PCR, respectively. We conclude that this new method allows monitoring of treatment response in ALL and other lymphoid malignancies with great sensitivity and precision. The www.clinicaltrials.gov identifier number for the Total XV study is NCT00137111.

The ability to distinguish clonal B-cell populations based on the sequence of their rearranged immunoglobulin heavy chain (IgH) locus is an important tool for diagnosing B-cell neoplasms and monitoring treatment response. Leukemic precursor B cells may continue to undergo recombination of the IgH gene after malignant transformation; however, the magnitude of evolution at the IgH locus is currently unknown. We used next-generation sequencing to characterize the repertoire of IgH sequences in diagnostic samples of 51 children with B precursor acute lymphoblastic leukemia (B-ALL). We identified clonal IgH rearrangements in 43 of 51 (84%) cases and found that the number of evolved IgH sequences per patient ranged dramatically from 0 to 4024. We demonstrate that the evolved IgH sequences are not the result of amplification artifacts and are unique to leukemic precursor B cells. In addition, the evolution often follows an allelic exclusion pattern, where only 1 of 2 rearranged IgH loci exhibit ongoing recombination. Thus, precursor B-cell leukemias maintain evolution at the IgH locus at levels that were previously underappreciated. This finding sheds light on the mechanisms associated with leukemic clonal evolution and may fundamentally change approaches for monitoring minimal residual disease burden.

Immune checkpoint inhibitors can induce clinical responses to a broad range of tumor types by presumably enhancing T cell responses against the tumor. These treatments are also associated with certain side effects that are also thought to be immune mediated (termed immune-related adverse events, or IRAEs). The mechanism by which IRAEs occur, and biomarkers that may predict IRAE development, are unknown. In prior work (Cha et al. Sci Transl Med 2014), we demonstrated that treating metastatic cancer patients with checkpoint inhibitors blocking CTLA-4 can lead to T cell repertoire diversification. However, we found that prolonged survival was not associated with the induction of high frequency clonotypes, but rather the maintenance of a pre-existing T cell response. Here, we examined whether treatment-induced TCR diversification is related to another clinical outcome: the development of IRAEs. We find that IRAEs are specifically associated with a more diverse T cell repertoire and with an increase in the number of T cell clonotypes, including the generation of de novo clones. This broadening of the circulating T cell repertoire occurred early with treatment, preceding the development of IRAEs. While IRAE patients demonstrate markedly greater diversity in their CD4+ T cells, they demonstrate a greater degree of change in clonal frequencies in their CD8+ T cells after ipilimumab, which may have key implications in the pathogenic mechanism of IRAE development. Finally, clinical response to checkpoint blockade is also associated with increased diversity. These results indicate that immune repertoire diversity following immune checkpoint inhibition can be both detrimental and beneficial to patients with metastatic cancer. Citation Format: David Y. Oh, Jason Cham, Li Zhang, Grant Fong, Mark Klinger, Malek Faham, Lawrence Fong. T cell repertoire diversification is associated with immune related toxicities following immune checkpoint inhibition in metastatic cancer patients. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4362.

Monitoring antigen-specific T cells is critical for the study of immune responses and development of biomarkers and immunotherapeutics. We previously developed and validated a novel multiplex assay (MIRA, or Multiplexed Identification of T cell Receptor Antigen specificity) that combines conventional immune monitoring techniques and TCR repertoire sequencing to assess T cell specificity to large numbers of query antigens. MIRA is a sensitive assay enabling detection of antigen-specific TCR clonotypes well below the limit of detection of conventional immune monitoring assays including flow cytometry and ELISPOT. Here we report the results from a scaled-up version of the assay using 270 different query peptide antigens (159 self- and 111 pathogen-derived). We identified >500 TCR clonotypes at frequencies as low as 1 per million T cells that were specific to 41 query antigens from 6 healthy HLA-A*02-positive individuals. Most of the antigen-specific TCRs identified recognized one of 27 different peptides derived from a variety of pathogens including CMV, EBV, Flu, Rotavirus, HSV, mTB, WNV and HIV. A subset of antigen-specific TCRs recognized one of 14 different peptides derived from self including MART1, RCC, BCL-2, MAGE, STEAP1, KLK4, CAMEL and MOG. These data support the notion that escape and survival of self antigen-specific T cells occurs without causing overt autoimmunity in healthy individuals. We show here that MIRA can be used to assess TCR specificities to hundreds of query antigens simultaneously. The assay is highly scalable and can be easily modified to accommodate thousands of additional query antigens. This technology may be used to monitor T cell specificity to antigens relevant to infection, autoimmunity and cancer.

Introduction: Aggressive induction chemotherapy followed by autologous stem cell transplant (ASCT) is effective for younger patients with mantle cell lymphoma (MCL). Among patients undergoing ASCT, cytarabine-based induction regimen induced higher rates of MRD-negativity compared to R-CHOP (Hermine et al, ASH 2012), and achievement of MRD-negative status was predictive of good outcome. R-bendamustine (RB) has superior efficacy compared to R-CHOP (Rummel et al, Lancet 2013; Flinn et al, Blood 2014) but, there are no data regarding its impact on MRD. S1106 (SWOG) was conducted to compare R-HyperCVAD/MTX/ARAC (RH) or RB to identify the better induction regimen followed by ASCT. We report the result of MRD analysis and updated 2 year PFS/OS. Method: S1106 was a US intergroup (SWOG/ECOG/CALGB), randomized phase II trial. The primary objective was to estimate 2 year PFS, with secondary objectives to assess response rates, OS, toxicities, and MRD status. Inclusion criteria were: untreated stage III, IV or bulky stage II MCL, Cyclin D1 +, age > 18 < 65, and adequate organ function. Randomization was stratified by MIPI. Patients received either 4 cycles of RH or 6 cycles of RB, followed by ASCT. MRD was assessed at baseline and post induction. Genomic tumor DNA was extracted from FFPE tissue or bone marrow aspirate mononuclear cells. PCR amplification of IGH-VDJ, IGH-DJ, and IGK regions was performed followed by high-throughput sequencing to determine the tumor clonotype(s) (Adaptive Biotechnologies). DNA from peripheral blood mononuclear cells (PBMC) and plasma was amplified and sequenced to determine lymphoma molecules per million diploid genomes. Results: A total of 53 patients were accrued out of planned 160. This study was closed prematurely based on predetermined criteria of stem cell mobilization failures on the RH arm. Table 1 shows patient characteristics. The ORR was 94% in RH vs. 83% in RB. The CR rates were 35% (RH) and 40% (RB). Only 4/17 patients on RH and 21/35 patients in RB underwent ASCT; the rest could not complete study (Table 1). RH induced significantly more grade 3/4 heme toxicities as compared to RB (Table 1). The median follow up was 29 months in RH and 26 months in RB. The estimated 2 year PFS was 81% (Fig 1) and OS was 87% for both arms. 27 patients consented to the optional MRD assessment, with 12 paired serial samples (baseline and post induction). 10 were in RB and 2 were in RH. Both patients in RH were MRD positive at baseline and achieved MRD negative status. 1/10 patient in RB was MRD negative at baseline and remained negative throughout treatment. 8/9 patients in RB with baseline MRD-positivity converted to MRD-negative status by the end of induction, and 3/8 did not go to ASCT. Three additional patients were missing baseline samples but were MRD negative at the end of RB. Overall, the estimated 2 year PFS was 100% for all 13 patients who achieved MRD negative status at the end of RB. Conclusions: RH is not an ideal platform for future transplant trials in MCL due to stem cell mobilization failures. RB achieved a 2 year PFS of 81%, higher than the planned target of 75%. It also achieved an 89% MRD negative rate on all the paired samples tested. Low CR on RB could be due to lack of mandatory PET. All patients with MRD negative status remain in remission, with some not having undergone ASCT. Premature closure of the study limited the sample size and the precision of PFS estimates and MRD. However, this analysis suggests that RB can achieve a deep remission and could be a platform for future trials in MCL. | | RH (n=17) | RB (n=35) | | -------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Age | 59 (44-66) | 57 (33-64) | | Male (p=0.003) Female | 9 8 | 32 3 | | Performance status 0 1 | 11 6 | 26 9 | | Disease Stage III IV | 1 16 | 3 32 | | B sx Yes No | 6 11 | 10 25 | | BM involvement Positive Negative | 14 3 | 31 4 | | Extranodal involvement Yes No | 15 2 | 32 3 | | KI 67 30% | 20% 60% 20% | 14% 66% 20% | | MIPI Score Intermediate/High Risk Low Risk | 6 11 | 13 22 | | Grade 3/4 Hematological toxicities (Induction only) | Anemia 56% Neutropenia 63% Febrile neutropenia 31% Thrombocytopenia 69% | Anemia 8.6% Neutropenia 34% Febrile neutropenia 14% Thrombocytopenia 17% | | Reasons for early off treatment or not going to ASCT | Failure to collect stem cell 5 Thrombocytopenia 4 Pancytopenia 1 Others 2 | Patient choice 4 Progressive disease 2 Failure to collect stem cell 1 Allergy 1 Seizure 1 Insurance denial 1 Others 3 | Table 1. ![Figure 1.][1] Figure 1. Disclosures Chen: genentech: Consultancy, Speakers Bureau; Seattle Genetics: Consultancy, Research Funding, Speakers Bureau; Merck: Consultancy, Research Funding; Millennium: Consultancy, Research Funding, Speakers Bureau. Forman: Mustang Therapeutics: Research Funding. Cashen: Celgene: Speakers Bureau. Blum: cephalon: Research Funding; Pharmacyclics: Research Funding; Janssen: Research Funding; Celgene: Research Funding. Fenske: Pharmacyclics: Honoraria; Millennium/Takeda: Research Funding; Seattle Genetics: Honoraria; Celgene: Honoraria. Cheson: Celgene: Consultancy, Research Funding; Spectrum: Consultancy; Astellas: Consultancy; Gilead: Consultancy, Research Funding; Roche/Genentech: Consultancy, Research Funding; MedImmune: Research Funding; Ascenta: Research Funding; Pharmacyclics: Consultancy, Research Funding; AstraZeneca: Consultancy; Teva: Research Funding. Smith: Pharmacyclics: Consultancy; Celgene: Consultancy. Faham: adaptive biotech: Employment, Other: stockholders. Wilkins: adaptive biotech: Employment. Leonard: teva: Consultancy; genentech: Consultancy. Kahl: Genentech: Consultancy; AbbVie: Research Funding; Teva: Consultancy. [1]: pending:yes

Introduction Achieving complete remission (CR) improves survival outcomes in multiple myeloma (MM). Applying more sensitive flow-cytometry or PCR based minimal residual disease (MRD) testing further improves prognostication and MRD negativity confers better outcomes among CR patients. In our Total Therapy (TT) trials, gene expression profiling based risk (GEP) identifies 15% patients with high risk (HR) MM whose clinical course is characterized by early relapsing disease and prognosis has remained grim despite advances in therapy. Of interest is whether high-risk (HR) patients fail to achieve MRD negativity leading to relapse. We have determined response rates across the total therapy (TT) trials and in this study we report the impact of molecular negativity by MRD assessment in patients who have achieved at least very good partial response (VGPR) or CR at 4-8 months and 12-24 months, respectively, after enrollment in TT3b-TT5 from 2005-2009. We use next-generation sequencing (NGS)-based MRD assessment (Adaptive Biotechnologies) which is sensitive to 1 MM cell in 106 normal cells. Furthermore, we evaluate MRD status in long term relapse-free survivors (>6 years) to determine the importance of MRD status in prolonged remission. Materials and methods Study subjects include 591 patients enrolled in TT3b-TT5 to determine VGPR/nCR/CR by EBMT/IMWG criteria and to analyze PFS and OS of HR and SR patients defined by our GEP model. For MRD testing, we identified 102 patients from the TT3b-TT6 protocols that achieved at least VGPR and had bone marrow (BM) sample available at 4-8 months and 12-24 months after enrollment. Of these 102 patients, 14 patients had HR disease and 88 had SR. Six of 14 HR patients already had clinical relapse between 12-24 months, but were included to determine MRD at 4-8 months. Of all 102 patients, 51 are currently still in CR 6-9 years after protocol enrollment and most recent flow-cytometric MRD status was evaluated. NGS-based MRD Assessment: Genomic DNA was amplified using locus-specific primer sets for immunoglobulin heavy-chain complete (IGH-VDJH) and incomplete (IGH-VDH) as well as for immunoglobulin κ locus (IGκ). The amplified products were subjected to sequencing and clonal gene rearrangements were analyzed. Final MRD measurement was calculated at a sensitivity level of 1 cancer cell per 1 million cell equivalents. Flow Cytometry based MRD assessment: Erythrocyte-lysed BM samples were immunophenotyped by use of 8-color (CD138/CD38/CD19/CD45/CD27/CD81/CD56/CD20) staining technique. Myelomatous Plasmacells (PCs) were separated from healthy PCs by different phenotype expression and MRD was deemed negative when no myelomatous PCs were detectable at a sensitivity of Results Response by EBMT/IMWG criteria across our TT3b-TT5 (n=591) protocols showed no significant difference between HR and SR patients by year 1 of enrollment. In the SR group (n=502) 74.9%-77.9% of patients achieve at least nCR/VGPR and 40.3%-50.4% CR. For the HR patients (n=89) the results are similar with 75%-77.9% achieving at least VGPR and 50%-50.4% CR. However, the majority of HR patients start relapsing after one year of enrollment with a relapse rate of 59% for HR at 3 years compared to only 19% for SR at the same time point, indicating that MRD positive disease likely exists at 12-24 months for those patients with relapse. NGS-based MRD assessment will answer this question and data will be available by December 2015. Fifty one patients of the initial 102 patient group continue to be in complete remission to date >6 years after enrollment. Of these, 47 are MRD negative at a MRD level of 10-4. Conclusions Using conventional response methods, there is no difference between HR and SR MM at 1 year after initiation of treatment. However clinical outcome for HR disease is very poor and characterized by early relapsing disease, indicating that MRD persists even when patients have achieved CR. Sequencing is the most sensitive method for MRD detection and will be used in the present study to evaluate the importance of sequential MRD testing in HR and SR disease. We show that the majority of patients achieving long term remission at 6-8 years are MRD negative indicating the importance of molecular response for long term success. Disclosures Schinke: University of Arkansas for Medical Sciences: Employment. Mitchell:Cancer Research and Biostatistics: Employment. Faham:adaptive biotech: Employment, Other: stockholders. Patel:University of Arkansas for Medical Sciences: Employment. Thanendrarajan:University of Arkansas for Medical Sciences: Employment. Mohan:University of Arkansas for Medical Sciences: Employment. Mathur:University of Arkansas for Medical Sciences: Employment. Matin:University of Arkansas for Medical Sciences: Employment. Radhakrishnan:University of Arkansas for Medical Sciences: Employment. Stephens:University of Arkansas for Medical Sciences: Employment. van Rhee:University of Arkansa for Medical Sciences: Employment. Zangari:Novartis: Research Funding; Millennium: Research Funding; University of Arkansas for Medical Sciences: Employment; Onyx: Research Funding. Jethava:University of Arkansas for Medical Sciences: Employment. Petty:University of Arkansas for Medical Sciences: Employment. Alapat:University of Arkansas for Medical Sciences: Employment. Johnson:University of Arkansas for Medical Sciences: Employment. Epstein:University of Arkansas for Medical Sciences: Employment. Barlogie:University of Arkansas for Medical Sciences: Employment. Davies:Celgene: Consultancy; Onyx: Consultancy; Janssen: Consultancy; Millenium: Consultancy; University of Arkansas for Medical Sciences: Employment. Heuck:Millenium: Other: Advisory Board; Celgene: Consultancy; Janssen: Other: Advisory Board; Foundation Medicine: Honoraria; University of Arkansas for Medical Sciences: Employment. Hoering:Cancer Research and Biostatistics: Employment. Weinhold:University of Arkansas for Medical Sciences: Employment; Janssen Cilag: Other: Advisory Board. Morgan:Weismann Institute: Honoraria; MMRF: Honoraria; CancerNet: Honoraria; University of Arkansas for Medical Sciences: Employment; Bristol Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees.

Introduction: Immunoglobulin (Ig) gene rearrangement is a hallmark of early B-cell development. Multiple myeloma (MM), a malignancy of plasma cells, typically have mutated Ig sequences but are thought to be stable throughout the course of the disease. We previously observed that multiple Ig sequences related by somatic hypermutation (SHM) may be present in some MM patients at diagnosis. Here we provide an expanded observation and investigate whether there is ongoing evolution in Ig sequences over the course of the disease. Methods: 550 MM patientsenrolled in IFM/DFCI study were included in this analysis. The next-generation sequencing (NGS)-based immunosequencing platform was used to detect evidence of oligoclonality at the Ig heavy chain loci. Using universal primer sets, we amplified IGH variable, diversity, and joining gene segments from DNA and/or RNA isolated from purified CD138+ MM cells collected at the time of diagnosis. Amplified products were sequenced and analyzed (Faham et al., Blood 2012). MM-specific clonotypes were identified for each patient based on their high frequency (5%) within the B-cell repertoire in the diagnostic (dx) sample. The highest frequency MM clonotype in a dx sample is termed the Òindex clonotype.Ó DNA and/or RNA isolated from dx AND post-treatment bone marrow samples were assessed for evidence of evolved MM clonotypes. A clonotype was considered ÒevolvedÓ based on CDR3 sequence homology to the dx Òindex clonotype.Ó Results: We identified Ig clones in 340 RNA samples and 311 DNA samples from the IFM/DFCI cohort.We first looked at V segment usage in these MM clones comparedto a database of ~30 million Ig VDJ sequences derived from normal B cells. The frequencies for 6 V segments were found to be significantly different from this dataset compared to the database.We then looked for cases with evidence that Myeloma cells have two unrelated origins. We found 9/550 (1.6%) cases which had evidence of unrelated clones as evident by having three IgH or two functional sequences. We then considered cases where we find two IgH sequences that are related to each other by SHM. 128/340 (37.6%) of RNA dx samples showed evidence of evolved clones via SHM, with 69/128 (53.9%) having 3 or more related clones, while 15/311 patients (4.8%) showed evidence of evolved clones related to the index clone via SHM in DNA samples from diagnosis. Of note, the majority of RNA evolved clones were found at low frequency ( Conclusions: We observed multiple evolved clonotypes in a substantial percentage of dx MM samples (37.6%). The presence of multiple clonotypes related by SHM indicates that this mechanism remains active after myeloma development in at least a portion of the cells. We also found marked changes in the relative frequency of the MM clonotypes in post-treatment samples and emergence of new Ig clones which may not be due to selective advantage of the newly acquired mutations in the Ig gene, but rather some other ongoing genomic mutation process. Thus, these evolved myeloma clonotypes may be useful as surrogate markers for other oncogenic mutations providing resistance to therapy. Figure 1. Evolution of related clones in the post-maintenance time point. Below are the sequences of two related clones, with one base difference bolded and underlined. Figure 1. Evolution of related clones in the post-maintenance time point. Below are the sequences of two related clones, with one base difference bolded and underlined. Disclosures Richardson: Novartis: Membership on an entity's Board of Directors or advisory committees; Celgene Corporation: Membership on an entity's Board of Directors or advisory committees; Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees, Research Funding; Gentium S.p.A.: Membership on an entity's Board of Directors or advisory committees, Research Funding; Millennium Takeda: Membership on an entity's Board of Directors or advisory committees. Attal:celgene: Membership on an entity's Board of Directors or advisory committees; jansen: Honoraria. Anderson:Celgene Corporation: Consultancy; Millennium: Consultancy; BMS: Consultancy; Gilead: Consultancy; acetylon pharmaceuticals: Equity Ownership; Oncocorp: Equity Ownership. Faham:Adaptive Biotechnologies Corp.: Employment, Other: Stockholder. Avet-Loiseau:BMS: Membership on an entity's Board of Directors or advisory committees; jansen: Membership on an entity's Board of Directors or advisory committees; celgene: Membership on an entity's Board of Directors or advisory committees; jansen: Membership on an entity's Board of Directors or advisory committees; millenium: Membership on an entity's Board of Directors or advisory committees; onyx: Membership on an entity's Board of Directors or advisory committees; millenium: Membership on an entity's Board of Directors or advisory committees; onyx: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees.

Introduction MCL has a poor prognosis. In eligible patients, intensifying frontline, CHOP-like regimens (e.g., cytarabine) as well as high-dose chemotherapy and autologous stem cell transplant (HDT/ASCT) consolidation in first remission have improved progression free survival (PFS) but less so, overall (OS). Preclinical animal models show benefits of adding tumor-specific T-cells to ASCT. CpG (PF-3512676) is a toll-like receptor 9 (TLR9) agonist and an effective vaccine adjuvant that induces costimulatory molecule expression on both antigen-presenting and MCL cells. This phase I/II clinical trial (NCT00490529) adds autologous T-cell transfer, harvested from patients after vaccination with CpG-activated autologous MCL cells - a maneuver termed immunotransplant. This is a planned interim analysis for safety and efficacy triggered by the first 20 patients reaching 1 year post ASCT. Methods Prior to therapy, subjects' tumor cells are collected by biopsy or apheresis and patient-specific vaccine is created by incubating fresh tumor cells with CpG (3 mcg/mL PF-3512676, 72-hr culture), then irradiated and cryopreserved. Patients receive induction chemoimmunotherapy of physician's choice. Patients achieving at least partial response (PR) then receive 3 subcutaneous autologous tumor vaccinations (1 x 108 cells/dose) mixed with CpG (18 mg) every 4-7 days. Primed T-cells (≥ 1 x 1010 CD3 cells) were collected by apheresis 2-4 weeks following vaccine 3 and a rituximab (375 mg/m2) B-cell purge. After standard HDT/ASCT (conditioning = BCNU, cyclophosphamide, etoposide), primed T-cells and a 4th vaccination are given on day+1. A 5th CpG-MCL vaccination followed 3 months post ASCT. The primary endpoint of this study is freedom from minimal residual disease (MRD) at 1 year post ASCT, measured by presence of patient-specific, malignant B-cell VDJ sequence in peripheral blood (ClonoSeq™, analyzed at a sensitivity of ≥ 1 clone/10,000 leukocytes) -an endpoint previously shown to be highly prognostic. Secondary endpoints include PFS, OS, and immune response to vaccine. 59, transplant-eligible, MCL patients are targeted for accrual in this 2-stage design. Results In this interim analysis of 24 patients accrued, 20 have surpassed 1 year post ASCT. All patients had Stage IV disease. Median values included (range): follow-up 43.5 months (11.5-60.1), age 60 years (47-70), and MIPI score 5.9 (5.1-7.8). Vaccine was made from biopsy alone (n=12), apheresis alone (n=9), or both (n=1). Frontline therapy included R-CHOP (n=7), R-hyperCVAD (n=14), alternating R-CHOP/R-DHAP (n=2), and R-EPOCH (n=1). 19 patients achieved complete response while another 3 had PR. All responding patients were vaccinated, able to yield sufficient T-cells for adoptive transfer, and proceeded through standard HDT/ASCT. At 1-year post ASCT, freedom from MRD was 90.5% (n=21). 2 patients did not reach 1-year post ASCT. One died from an ASCT complication (metapneumovirus) while the other relapsed 6 months following ASCT (included in MRD analysis). The most common toxicity due to CpG-MCL vaccine was erythematous rash at injection site (90.9%, n=20, each grade 1). No serious adverse events were seen related to vaccines or adoptive T-cell transfer. All patients had successful hematopoietic recovery, but two were delayed and received backup stem cell infusions with eventual recovery. Though median PFS and OS have not been reached, 3-year PFS and OS at interim analysis are 54.5% and 63.6%, respectively (intention to treat). In this data set, higher expression of co-stimulatory molecules (such as CD40, CD80, and CD86) on a subject's MCL in response to CpG was associated with freedom from MRD (p =0.02). Post-ASCT, higher peripheral T-cell granzyme and perforin response to ex vivo re-challenge with autologous MCL cells was also associated with freedom from MRD (p =0.01). Conclusions The addition of CpG-activated, whole MCL vaccination and autologous, adoptive T-cell transfer to standard therapy appears both feasible and safe. At interim analysis, the 1-year freedom from MRD surpasses rates previously reported in other studies and warrants further investigation. To date, 46 patients have either completed and/or are continuing to undergo study treatment and the study remains open to accrual for patients newly diagnosed with MCL. Disclosures Miklos: Pharmacyclics: Research Funding. Rezvani:Pharmacyclics: Research Funding. Faham:Adaptive Biotechnologies: Employment. Levy:Immune Design: Research Funding; Dynavax: Research Funding.

Introduction: High dose chemotherapy followed by autologous stem cell transplantation (ASCT) cures a subset of patients with chemosensitive relapsed or refractory (rel/ref) diffuse large B-cell lymphoma (DLBCL). Several factors associated with post-ASCT outcome have been identified, including pre-ASCT PET status, but better biomarkers are needed in order to optimally select candidates for the procedure. In other lymphoma subtypes with defining chromosomal translocations, PCR detection of pre- and post-ASCT minimal residual disease (MRD) in peripheral blood and of tumor contamination in the stem cell product is associated with inferior outcome. Until recently, MRD detection in DLBCL was limited by the rarity of detectable circulating disease using conventional techniques. The immunosequencing platform (Adaptive Biotechnologies, Corp.) is a next-generation-sequencing (NGS)-based MRD assay that detects small amounts of circulating tumor DNA (CTD) in patients with lymphoid malignancies. The assay detects CTD at diagnosis in most DLBCL patients and CTD levels track with response to induction therapy (Armand, 2013). Persistence of CTD or recurrence of CTD after completion of therapy is highly associated with DLBCL relapse (Kurtz, 2015; Roschewski, 2015). We evaluated whether CTD in autologous stem cell grafts was predictive of outcome in patients with rel/ref DLBCL undergoing ASCT. Methods: We retrospectively studied patients with rel/ref DLBCL, including transformed indolent lymphoma (TIL), who had paired archival tumor and autologous stem cell specimens and underwent ASCT at Brigham and Women's Hospital/Dana-Farber Cancer Institute from 2003-2013. Genomic tumor DNA was extracted from archival formalin-fixed paraffin-embedded (FFPE) tissue and analyzed using the NGS-based MRD assay. PCR amplification of IGH-VDJ, IGH-DJ,and IGK regions using universal consensus primers was performed followed by NGS to determine the tumor clonotype(s), defined as having a frequency > 5% in the tumor specimen. DNA from all available autologous peripheral blood or bone marrow stem cell specimens from each patient was amplified using universal consensus primers and sequenced to determine the level of CTD, defined as the number of lymphoma molecules per diploid genome. Results: We identified 98 eligible patients with rel/ref DLBCL/TIL. The median age was 60 (range 22-77) years; 63% were male; 65% had DLBCL, 29% had TIL, and 5% had primary mediastinal DLBCL; the median number of prior lines of therapy was 2 (range 2-5); all had received prior rituximab; 38% had primary refractory disease; 60% were in complete remission at ASCT; 96% received CBV conditioning. Median follow-up was 56 (range 19-123) months. The 4y progression-free survival (PFS) and overall survival (OS) in the entire cohort were 46% and 64%, respectively. Among 83 patients (85%) with sufficient DNA for clonotype determination, a clonotype was identified in 59 (71%). CTD data was complete in 53 patients (52 received peripheral blood stem cells (PBSC) and 1 received bone marrow). Eight patients (15%) had detectable CTD (CTD+) in the stem cell autografts (all PBSC) and 6/8 relapsed after ASCT. One CTD+ patient had early non-relapse mortality less than 1 month after ASCT and was never restaged. Seven of 8 CTD+ patients had TIL histology, 5 of whom relapsed (4 with aggressive lymphoma). The 4y PFS and OS in CTD+ v CTD- patients were 13% v 48% (p=0.01), and 38% v 67% (p=0.013), respectively [Figure 1]. In multivariable models including CTD status and pre-ASCT characteristics, CTD+ was the only factor associated with OS (HR 3.1, p=0.018), but was not significantly associated with PFS. Discussion: In patients with rel/ref DLBCL undergoing ASCT, the presence of CTD in the autologous stem cell graft is associated with inferior survival. CTD detection in the autograft may be more common in patients with TIL. In studies evaluating CTD detection in DLBCL, the plasma compartment has been more sensitive for detecting CTD than mononuclear cells. The use of concentrated cell specimens in this study may have decreased the sensitivity of the assay. Nevertheless, if the present findings are confirmed in a larger population, CTD detection may permit the identification of a subgroup of patients with a particularly poor outcome after ASCT, for whom alternative approaches could be considered. Figure 1. Overall (A) and Progression-Free (B) Survival in CTD+ vs CTD- Patients Figure 1. Overall (A) and Progression-Free (B) Survival in CTD+ vs CTD- Patients Figure 2. Figure 2. Disclosures Herrera: Sequenta, Inc.: Research Funding; Pharmacyclics: Research Funding; Genentech: Research Funding. Kong:Adaptive Biotechnologies, Corp.: Employment, Other: Stockholder. Davids:Genentech: Other: ad board; Pharmacyclics: Consultancy; Janssen: Consultancy. Rodig:Perkin Elmer: Membership on an entity's Board of Directors or advisory committees; Bristol Myers Squibb: Research Funding. Faham:Adaptive Biotechnologies Corp.: Employment, Other: Stockholder. Armand:BMS: Research Funding; Infinity: Consultancy, Research Funding; Merck: Consultancy, Research Funding; Sequenta, Inc.: Research Funding.

Background: Recent advances in next-generation sequencing (NGS) techniques enable the quantitation of circulating tumor DNA (ctDNA) encoding the clonal rearranged V(D)J immunoglobulin (IG) receptor gene sequence. The aims of this study were 1) To evaluate the clonal heterogeneity of follicular lymphoma (FL) and its variations between tumor and plasma at diagnosis in patients (pts) included in PRIMA trial, and 2) To assess the prognostic value of the level of ctDNA at diagnosis on PFS (median follow up of 6 years). Methods: Using the NGS-based immunosequencing method (Adaptive Biotechnologies, South San Francisco, CA), the lymphoma clonotype was first established in the tumor biopsy using locus-specific primer sets for IGH-V, IGH-D and IGK rearrangements. Clonotypes regarded as originating from the lymphoma clone were present at a frequency greater than 5%. The lymphoma-derived sequences identified in the biopsy sample were then used as targets to assess the presence of ctDNA in plasma samples. The quantity and frequency of the ctDNA in plasma is calculated relative to the total number of reads in the sample and defined as lymphoma clonotype molecules per million diploid genomes. For 34 FL pts from the PRIMA trial, both tumor biopsy and plasma samples at diagnosis were available. Results: One tumor clonotype or more could be detected in 29 pts (85%) in the tumor diagnostic sample (DNA isolated from fresh frozen tissue). Indeed, with the IGH-V assay, between 1 to 3 different clonotypes were identified in 23 pts. With the IGH-D assay, 1 clonotype was detected in 2 pts. With the IGK assay, 1 to 2 different clonotypes were detected in 17 pts. The tumor clonotypes were detected in diagnostic plasma samples in 25 out of the 29 pts (83%). Moreover, in 14 pts we detected clones in the plasma samples that are related (with point mutations in the V(D)J sequence) to the highest frequency index clone identified in the tumor sample. In half of the cases, we observed a different repartition of the subclonal populations between tumor and plasma samples at diagnosis: for these cases the highest frequency clone in the tumor was not the highest frequency clone in the plasma. Among the 24 pts with an IGH clonotype (IGH-V or IGH-D assay), ctDNA could be detected in 19 cases. We could not find a correlation between peripheral blood dissemination and the presence of a stereotyped sequence or an N-glycosylation motif within the CDR3 region of IGH clonotypes. Interestingly, in one case, two different related clones were detected at high frequency in tumor sample and the putative parental clone, not detected in the tumor sample, was detected in plasma sample as the highest frequency clone. The level of ctDNA ranged from 0 to 345,000/million diploid genomes in the 29 plasma samples (median 39,720). The presence of ctDNA was correlated with bone marrow involvement (p=.005), but not with FLIPI score, LDH level, anemia, bulky disease, presence of circulating lymphoma cells (detected by morphology or flow examination), Ann Arbor stage or β2microglobulin level. The absolute level of ctDNA in diagnostic samples did not correlate with any of the clinical characteristics. We assessed the prognostic value of the level of ctDNA at diagnosis. Pts (14/29) with higher levels of ctDNA at diagnosis (>40,000/million diploid genomes) had shorter PFS than patients with lower levels of ctDNA (median 15.7 m vs NR, p=.027, Fig 1). In an exploratory multivariate Cox regression model including FLIPI score, bulky disease and β2-microglobuline level, high ctDNA level was the only factor significantly associated with a worse PFS (HR 4.2, p=.039). In the observation arm, pts with high ctDNA levels had a median PFS of only 11.6 months vs NR (p=.01). Whereas in the maintenance arm, the prognostic value of elevated ctDNA levels was erased (p=.6). Conclusion: Using the NGS-based immunosequencing method, we were able to show a variation in clonal heterogeneity between tumor biopsy and plasma samples obtained at diagnosis. The poor prognostic value of elevated ctDNA levels in plasma at diagnosis appeared higher than other clinical parameters in a multivariate cox regression model. These findings need to be validated in larger cohorts. Figure 1. PFS according to the level of circulating tumor DNA Figure 1. PFS according to the level of circulating tumor DNA Disclosures Carlton: Adaptive Biotechnologies Corp.: Employment, Equity Ownership. Faham:adaptive biotech: Employment, Other: stockholders. Salles:Roche: Honoraria, Research Funding.

Introduction: Chronic lymphocytic leukemia (CLL) cells typically carry one or more clonally rearranged immunoglobulin (Ig) genes. The specific sequence of an Ig rearrangement, or clonotype, can serve as a marker of minimal residual disease (MRD) in blood or bone marrow samples. The clonoSEQ assay (Adaptive Biotechnologies Corp) employs a next-generation sequencing (NGS) based MRD quantification method that uses consensus primers to amplify and then sequence the entire repertoire of Ig genes in a clinical sample. Each Ig clonotype, including the one marking a patient's CLL, can then be individually quantified with high precision. We previously demonstrated the utility of this NGS approach for predicting relapse-free survival in a single-institution cohort of CLL patients undergoing reduced-intensity allogeneic hematopoietic cell transplantation (RIC alloHCT). In this landmark analysis, we now assess the prognostic utility of molecular MRD quantification one year following RIC alloHCT in a multi-institution cohort. Methods: We retrospectively evaluated the outcomes and MRD status of patients surviving without relapse to one year after RIC alloHCT for CLL. Patients were assessable for MRD based on availability of a tumor specimen from which to determine the CLL-associated Ig heavy chain (IgH) clonotypes and a cryopreserved peripheral blood mononuclear cell (PBMC) aliquot obtained one year post-HCT. Forty-six patients underwent conditioning with total lymphoid irradiation and anti-thymocyte globulin (TLI/ATG) and 56 were conditioned with fludarabine and busulfan (Flu/Bu) regimens. Clonal IgH rearrangements were identified by NGS-based IgH profiling in CLL-bearing blood or marrow samples obtained prior to HCT and these clonotypes were quantified in the IgH repertoire of PBMC samples from one year (+/- 90 days) post-HCT. Results: One hundred two patients were assessable for outcomes beyond the one year post-HCT landmark. Amongst 97 patients with a diagnostic sample available, the IgH clonotype calibration rate was 90%. Five archived diagnostic samples yielded insufficient DNA to proceed with clonotype identification. 87/102 (85%) patients had paired tumor and one year PBMC samples suitable for MRD quantification. Patients receiving TLI/ATG or Flu/Bu conditioning had similar clinical characteristics. Median relapse-free survival (RFS) from the one year landmark was 4.7 years with TLI/ATG and 6.8 years with Flu/Bu (p=0.08; Figure 1A), and overall survival was not significantly different (Figure 1B). Acute GVHD (grades 2-4) occurred in 15.6% with TLI/ATG and 37.5% with Flu/Bu. Chronic GVHD occurred in 53% and 77%, respectively, with less extensive grade chronic GVHD using TLI/ATG (39%) compared with Flu/Bu (73%). Amongst patients alive and in remission one year after RIC alloHCT, peripheral blood MRD Conclusions: In this non-randomized retrospective analysis of outcomes after RIC alloHCT for high-risk CLL, use of TLI/ATG or Flu/Bu conditioning regimens were associated with similar RFS, though a trend toward earlier relapse with TLI/ATG is observed. Flu/Bu was associated with substantially higher rates of acute and chronic GVHD and higher rates of death in remission. Irrespective of conditioning regimen used, molecular MRD quantification at one year post-HCT provides strong positive and negative predictive value for subsequent relapse. Identification of MRD positive patients at risk for relapse may permit the implementation of post-HCT immune modulation or maintenance treatment to reduce relapse risk for those in need, but spare MRD negative patients from the potential for additional toxicity. Figure 1. Relapse-free (A) and overall (B) survival in high-risk CLL patients undergoing RIC alloHCT following TLI/ATG or Flu/Bu conditioning. At one year after RIC alloHCT, peripheral blood MRD ≥10-6 strongly predicts increased risk of relapse (p Disclosures Logan: Pharmacyclics: Consultancy; Amgen: Consultancy; Jazz Pharmaceuticals: Consultancy. Herrera:Genentech: Research Funding; Sequenta, Inc.: Research Funding; Pharmacyclics: Research Funding. Rezvani:Pharmacyclics: Research Funding. Kong:Adaptive Biotechnologies Corp: Employment, Equity Ownership. Faham:Adaptive Biotechnologies Corp.: Employment, Other: Stockholder. Miklos:Pharmacyclics: Research Funding.

Background: Autologous stem cell transplantation (ASCT) in conjunction with therapeutic drugs such as bortezomib, thalidomide, and lenalidomide can dramatically improve response rates and the prognosis of patients with multiple myeloma (MM). However, most patients with MM are considered to be incurable, and relapse owing to minimal residual disease (MRD) is the main cause of death among these patients. Here we utilized a next-generation sequencing (NGS) approach for MRD assessment, which offers at least 1 to 2 logs greater sensitivity (10-6) compared to allele-specific oligonucleotide PCR (ASO-PCR) and flow cytometry, respectively (Faham et al Blood 2012). Previous studies have shown that NGS-based MRD assessment 90 days post-ASCT has prognostic value (Martinez-Lopez et al Blood 2014). In this study, we compared the prognostic value of MRD assessment in autografts and bone marrow (BM) samples from MM patients in the ASCT setting. Methods: One hundred and twenty-three Japanese patients with newly diagnosed MM who received various induction regimens prior to ASCT were retrospectively analyzed. All patients received ASCT and were followed between June 15, 2004 and April 25, 2015. All patients had achieved a partial response (PR) or better after ASCT. Analyzed samples included: (1) BM slides from 96 MM patients at diagnosis, (2) fresh/frozen BM cells from 27 MM patients at diagnosis, (3) autografts and/or (4) post-ASCT BM cells obtained at the time of best response based on serum and urine tests. IGH-based ASO-PCR was performed as described previously (Methods Mol Biol 2009). NGS-based MRD assessment was performed using the immunosequencing platform (Adaptive Biotechnologies, South San Francisco, CA) (Martinez-Lopez et al Blood 2014). Results: We compared MRD results in 51 samples assessed by ASO-PCR and NGS. We observed a high correlation between NGS and ASO-PCR results at MRD levels of 10-5 or higher (r=0.86, P Conclusions: In this study, we show the prognostic value of NGS-based MRD assessment in autografts of patients with MM. The NGS platform has improved sensitivity compared with ASO-qPCR in detecting MRD in autografts. Importantly, this retrospective study suggests that therapeutic intervention based on NGS-based MRD positivity has a significant effect on patient outcome in the post-ASCT setting. Disclosures Zheng: Adaptive Biotechnologies Corp.: Employment, Equity Ownership. Moorhead:Adaptive Biotechnologies Corp.: Employment, Equity Ownership. Faham:Adaptive Biotechnologies Corp.: Employment, Other: Stockholder.

Background Although multiple studies have shown superiority of allogeneic hematopoietic cell transplantation (alloHCT) over autologous hematopoietic cell transplantation (autoHCT) for patients with "high-risk" acute lymphoblastic leukemia (ALL), these findings may be explained, in part, by contamination of the peripheral blood progenitor cell (PBPC) leukapheresis product by residual leukemic cells in patients undergoing autoHCT. Methods We retrospectively evaluated minimal residual disease (MRD) via next-generation sequencing (NGS) (Adaptive Biotechnologies, S. San Francisco, CA) in the PBPC leukapheresis products from 32 ALL patients who underwent autoHCT. All patients had "high-risk" ALL, as defined by B-lineage disease with WBC at diagnosis >30,000/uL; high-risk cytogenetics including t(9;22), t(4;11), other 11q23 abnormalities, or monosomy 7; or primary refractory disease. Peripheral hematopoietic cell mobilization consisted of cytarabine 2000mg/m2 IV every 12 hours (16,000mg/m2 cumulative) concurrent with etoposide 40mg/kg cumulative by continuous IV infusion over 4 days. The autoHCT conditioning consisted of 1320cGy total body irradiation (TBI) given in 11 fractions from day -8 to -5, etoposide 60mg/kg IV on day -4, and cyclophosphamide 100mg/kg IV on day -2. Tyrosine kinase inhibitors (TKI) were allowed for patients with Philadelphia chromosome-positive (Ph+) B-ALL. Seven patients (22%) participated in a multi-institutional trial in which the PBPC graft underwent ex vivo complement-mediatedpurging using monoclonal antibodies against CD9/CD10/CD19/CD20 for patients with B-lineage disease, or against CD2/CD3/CD4/CD5/CD8 for patients with T-lineage disease. Kaplan-Meier curves were generated using GraphPad Prism (GraphPad Software, La Jolla, CA) and statistical differences assessed via Log-Rank and Wilcoxon analyses, with a p-value of Results Twenty-eight patients (88%) had diagnostic bone marrow samples with quantifiable immunoglobulin or T cell receptor (Ig/TCR) gene rearrangements suitable for MRD quantification in the PBPC collections. Twelve (38%) patients had Ph+ B-ALL, 12 (38%) had Ph-neg B-ALL, and 4 (14%) had T-cell ALL. The majority of patients were male, in first complete remission, and autografted between 2000-2009, with a median age at autoHCT of 32 (range 19-55). With a median follow-up of 41 months (range 3-217), median relapse-free survival (RFS) and overall survival (OS) for the entire cohort are 3.2 and 4.2 years, respectively. At 5 years post-autoHCT, 42% of patients remain alive and relapse-free. Of the 28 diagnostic bone marrow specimens, 21 (75%) had rearrangements in more than 1 immunoreceptor locus (Figure 1A). A total of 73 rearrangements were identified across all patients. Clonal Ig heavy chain (IGH) sequences with complete VDJ rearrangement were the most commonly identified rearrangement, present in 17 of 28 patients (61%) and representing 30 of the 73 (41%) total rearrangements. When stratified by graft MRD burden, the median RFS for patients with MRD detectable at a level ≥10-6 (n=13) was 6.5 months, and has not been reached for patients without detectable MRD above this threshold (n=15; p=0.0005; Figure 1B). Ex vivo antibody-based purging failed to eradicate leukemia cells from the PBPC collections of 3 patients with detectable MRD who received a purged graft (Figure 1C), all of whom ultimately relapsed. Of the Ph+ cohort, 6 (50%) had detectable MRD in the PBPC graft. Two (33%) of these patients were not treated with a TKI; 1 relapsed at 4 months post-autoHCT and the other died from non-relapse mortality. Of the 4 Ph+ patients with detectable MRD who received a TKI, 2 (50%) remain long-term relapse-free survivors. Of the 6 patients without MRD who were treated with a post-autoHCT TKI, 5 (83%) remain relapse-free. Conclusion We demonstrate that the NGS-based immunosequencing platform identifies ALL MRD in leukapheresed PBPC collections. The presence of MRD in the autograft strongly predicts relapse, with only 15% RFS in patients harboring ≥10-6 MRD at stem cell collection versus 73% in patients with undetectable MRD. The absence of MRD in PBPC may thus identify a subset of "high-risk" patients likely to achieve long-term remissions without alloHCT. TKI therapy for patients with Ph+ B-ALL may also, in some cases, abrogate the need for alloHCT, even with quantifiable MRD prior to high-dose therapy. Disclosures Damon: Atara: Consultancy; Sunesis: Research Funding; Sigma-Tau: Research Funding; McGraw-Hill: Patents & Royalties: Book Chapter. Andreadis:McGraw Hill: Honoraria; Novartis: Consultancy; Cellerant: Consultancy; Pharmacyclics: Honoraria. Olin:Daiichi-Sankyo: Research Funding. Kong:Adaptive Biotechnologies: Employment, Equity Ownership. Faham:Adaptive Biotechnologies: Employment, Equity Ownership.

Background: Most patients with multiple myeloma (MM) are considered to be incurable, and relapse, due to minimal residual disease (MRD), is the main cause of death among these patients. Even though allele-specific oligonucleotide real-time quantitative PCR (ASO-qPCR) of immunoglobulin heavy chain gene rearrangement has been used to assess the MRD in MM due to its excellent sensitivity and specificity, ASO-qPCR has a major limitation in its relative quantification method because it needs a reference standard curve, which is usually made with dilutions of diagnostic myeloma DNA or from plasmids containing the target IgH rearrangement gene. Recently, droplet digital PCR (ddPCR) was developed to perform reliable absolute quantification of target genes. Based on the principle of single target gene detection, the sensitivity can be increased when the larger amount of DNA is analyzed. Here we assessed the prognostic value of MRD assessment in autografts from MM patients in the autologous stem cell transplantation (ASCT) setting using ASO-qPCR, ddPCR and next-generation sequencing (NGS) approaches. Methods: Twenty-three Japanese patients with newly diagnosed MM who received various induction regimens prior to ASCT without any post-ASCT therapy were retrospectively analyzed. Median age 57 (range 39-67); males 11, females 12; ISS 1 (n=7), 2 (n=12), 3 (n=3), not assessed (n=1). 11 patients were analyzed by G-banding and FISH (t(4;14), del17p, t(14;16)) and 4 patients showed high-risk chromosomal abnormalities (t(4;14) (n=2), t(14;16) (n=1), -13 by G-banding (n=1)). All patients had achieved a very good partial response (VGPR) or better after ASCT. Analyzed samples included: (1) BM slides from 20 MM patients at diagnosis, (2) fresh/frozen BM cells from 3 MM patients at diagnosis, and (3) obtained autografts. IGH-based ASO-qPCR was performed as described previously (Methods Mol Biol 2009). ddPCR was performed by the QX200 Droplet Digital PCR system (Bio-RAD Inc.) with a total 6000 ng of genomic DNA combined with the same ASO-primers and TaqMan-probes used in the ASO-qPCR. Droplets were generated by the QX200 droplet generator. End-point PCR (40 cycles) was performed on a C1000 Touch Thermal cycler (Bio-RAD Inc). The PCR product was loaded in the QX200 droplet reader and analyzed by QuantaSoft 1.7.4 (Bio-Rad Inc). NGS-based MRD assessment was performed using the immunosequencing platform (Adaptive Biotechnologies, South San Francisco, CA) (Martinez-Lopez et al Blood 2014). Results: Nineteen patients could be analyzed by ASO-qPCR and ddPCR, while all 23 patients could be analyzed by NGS. We compared MRD results in autografts between ddPCR and NGS. We observed a high correlation between ddPCR and NGS results of MRD (r=0.82, P Conclusions: In this study, we showed the prognostic value of ddPCR and NGS-based MRD assessment in autografts of patients with MM. Although the ddPCR had improved sensitivity in detecting MRD in autografts and demonstrated higher prognostic value compared with ASO-qPCR, the NGS platform showed the highest sensitivity and prognostic value among these methods. Disclosures Zheng: Adaptive Biotechnologies Corp: Employment, Equity Ownership. Moorhead:Adaptive Biotechnologies Corp: Employment, Equity Ownership. Faham:Adaptive Biotechnologies Corp.: Employment, Other: Stockholder.

Background: Minimal residual disease (MRD) assessment at the end of induction is critical for risk stratification of B-lineage acute lymphoblastic leukemia (B-ALL) patients. There are multiple techniques for molecular MRD assessment, including next-generation sequencing (NGS) and allele-specific oligonucleotide PCR (ASO-PCR) amplification of immunoglobulin (Ig) or T-cell receptor rearrangements. Leukemia-specific rearrangements can be identified in >97% of B-ALL patients using the NGS-based LymphoSIGHT™ method, while ASO-PCR can typically identify leukemia-specific rearrangements in only 80-90% of B-ALL patients. In this report, we assessed the ability of the NGS method to predict event-free survival (EFS) in a cohort of B-ALL patients who were inevaluable by ASO-PCR. Methods: All patients were treated between 2005-2011 on a clinical trial conducted by the Dana-Farber Cancer Institute (DFCI) ALL Consortium (05-001) on which high levels of end-induction MRD (≥10-3) led to intensified treatment. The 37 pediatric B-ALL patients included in this study were inevaluable by ASO-PCR, and therefore this cohort represents a subset of patients in whom a decision to intensify therapy per protocol could not be made. Archived DNA samples from diagnosis and Day 32 were provided for MRD assessment using the NGS method. Using universal primer sets, we amplified the immunoglobulin (IGH-VDJ, IGH-DJ and IGK) and T cell receptor (TRB, TRD, TRG) loci in diagnostic bone marrow samples. Leukemia-specific clonotypes were identified in the diagnostic sample of each patient based on high-frequency within the B-cell and/or T-cell repertoire. The presence of leukemia-specific clonotypes was then assessed in the end-induction (Day 32) sample. NGS MRD assessment was performed blinded to all clinical and ASO-PCR information on these patients. The association of NGS MRD results and clinical outcome (EFS) was examined, and significance assessed using the log-rank test. Results: Of 37 patients who were inevaluable for end-induction MRD by ASO-PCR, leukemia-specific clonotypes were successfully identified in 35 (95%) by the NGS method. The use of a threshold of 10-3, which is the ASO-PCR threshold used for risk-stratification on DFCI protocols, demonstrated significantly improved EFS between the MRD negative and MRD positive groups (p Conclusions: This study demonstrates the prognostic significance of NGS-based MRD assessment in pediatric patients with B-ALL. This NGS-based assay led to successful assessment of MRD in 95% of patients who were inevaluable by ASO-PCR. The NGS method represents an alternative approach for clinical MRD monitoring that could fundamentally improve the ability to identify high-risk B-ALL patients and potentially improve their outcome. Figure 1A. Kaplan-Meier analysis of event-free survival for A) 30 MRD negative ( Figure 1B Figure 1B. Disclosures Zheng: Sequenta, Inc.: Employment, Equity Ownership. Faham:Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

Background: Immunoglobulin (Ig) gene rearrangement is a hallmark of early B-cell development. Chronic lymphocytic leukemia (CLL) is typically considered a malignancy of mature B-cells and is thought to originate from the oncogenic transformation of a single pre- or post-germinal B-cell. Activation-induced deaminase (AID), an enzyme that induces somatic hypermutation (SHM) at the heavy and light chain Ig loci, has been shown to be active in CLL cells in vitro (Patten et al., Blood 2012). Previous studies suggest that multiple CLL-specific Ig clonotypes related by SHM may be present in patients (pts) with dominant CLL clones possessing somatically mutated or unmutated Ig loci (Logan et al., PNAS 2011; Campbell et al., PNAS 2008). To our knowledge, evolution of the dominant CLL-specific Ig clonotype over the course of treatment has not been demonstrated. Here we utilized the LymphoSIGHT™ method, a next-generation sequencing-based method for lymphocyte characterization and quantification, to quantify clonal evolution at the Ig heavy and kappa chain (IGH and IGK) loci in 63 pts with CLL. Methods: Samples were collected at Stanford University and the Dana-Farber Cancer Institute. Peripheral blood mononuclear cells were isolated, and genomic DNA was extracted. Using unbiased universal primer sets, we amplified IGH and IGK variable, diversity, and joining gene segments. Amplified products were sequenced and analyzed using standardized algorithms for clonotype determination (Faham et al., Blood 2012). CLL-specific clonotypes were identified for each patient based on their high frequency (>5%) within the B-cell repertoire of a diagnostic (dx) sample. The highest frequency CLL clonotype identified in a dx sample is termed the “index clonotype”. Dx and post-treatment peripheral blood samples were assessed for evidence of evolved CLL clonotypes using LymphoSIGHT. A clonotype was considered “evolved” based on CDR3 sequence homology to the dx “index clonotype.” Results: CLL clonotypes were identified in dx samples from 63 pts (51 unmutated IGHV; 12 mutated), and we assessed post-treatment samples for the presence of CLL clonotype-associated oligoclonality. Two of 63 pts exhibited clonal evolution in post-treatment samples. One patient with unmutated CLL was MRD negative for over 7 years following allogeneic hematopoietic cell transplant (HCT), and subsequently became MRD positive with the evolved clonotype (differing by 1 nucleotide from the index clonotype) leading to clinical relapse 9 months after MRD positivity, while the original index clone remained undetectable. The patient was treated with ibrutinib upon clinical relapse and continues to have detectable MRD with the same evolved CLL clonotype (Fig 1A). In a second patient with mutated IGHV, we observed several evolved clonotypes in the dx sample. Multiple evolved clonotypes, including 5 that exhibited a significant increase in their frequency relative to the index clonotype, were present in the follow-up sample after treatment with fludarabine and rituximab (Fig 1B). These evolved clonotypes differed from the index clonotype by 1-4 nucleotides, but otherwise shared CDR3 identity, excluding independently arisen B cell clonotypes. Conclusions: We observed evidence of clonal evolution at Ig loci in a small subset (3.2%) of pts with CLL undergoing treatment. The presence of evolution in pts with CLL indicates that either the SHM mechanism, including the AID enzyme, remains active after neoplastic transformation, or the evolved clonotypes arose through a mechanism distinct from SHM. These evolved CLL clonotypes may have a selective advantage, and may be useful as surrogate markers for other oncogenic mutations providing resistance to therapy. Additional cases are under investigation and updated results will be presented. Figure 1. CLL clonal evolution during therapy. MRD levels of two related Ig clonotypes, expressed as leukemia molecules per million leukocytes in peripheral blood, are shown at multiple time points following allogeneic HCT (A). In another patient undergoing conventional treatment, the level of each individual evolved clonotype as a fraction of the total CLL molecules is plotted at dx and post treatment time points. The index clone, evolved clones with increasing levels post-treatment, and evolved clones with decreasing levels post-treatment are shown in red, blue, and white, respectively (B). Figure 1A. Figure 1A. Figure 1B. Figure 1B. Disclosures Moorhead: Sequenta, Inc.: Employment, Equity Ownership. Carlton:Sequenta, Inc.: Employment, Equity Ownership. Faham:Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

Background: Classical Hodgkin lymphoma (CHL) has been established as B-cell malignancy characterized by a clonal expansion of pathognomonic Reed Sternberg cells (Marafioti et al. Blood 2000). A previous report suggests that clonotypic B-cells may be present in the blood of patients with CHL; however, the relationship between these circulating clonotypic B-cells and CHL is unclear. We utilized the LymphoSIGHT™ method, a next-generation sequencing approach, to detect lymphoma-specific clonotypes in peripheral blood in patients with CHL at diagnosis or disease recurrence as well as in follow-up blood samples. This method has the sensitivity to detect one lymphoma cell per million leukocytes in peripheral blood, and has been applied to minimal residual disease (MRD) detection in multiple B-cell malignancies. We evaluated the extent of somatic hypermutation in the lymphoma clonotypes, and performed sequence and expression level analyses of the lymphoma clonotype repertoire. Methods: Frozen primary tumor biopsy samples were first analyzed for clonality at the immunoglobulin heavy chain (IGH) and kappa chain (IGK) loci using the LymphoSIGHT method. Rearranged immunoglobulin gene segments (IGH-VDJ, IGH-DJ and IGK) in the genomic DNA and/or RNA were amplified with locus-specific primer sets, sequenced, and analyzed using standardized algorithms for clonotype determination. Clonotypes with a frequency >5% in the B-cell repertoire of the tumor biopsy were considered to represent tumor clonotypes. IGH-VDJ clonotypes with a frequency >2% in DNA were deemed to be cancer-specific if the clonotype was not present in the RNA. Such clonotypes were then quantitated in serum and peripheral blood mononuclear cells (PBMC), and DNA sequence and/or RNA expression level analysis was performed. Results: A total of 17 CHL patients were analyzed. A high-frequency clonal rearrangement was identified for at least one receptor (IGH-VDJ, IGH-DJ and IGK) in 12 of 17 cases (71%). Lymphoma-specific clonotypes were detected in blood samples from 8 of 11 patients (73%). Notably, a lymphoma-specific clonotype was detected in the serum compartment in 8 of 9 cases (89%) tested (Figure 1A), while it was detected in PBMC only in 3 of 9 cases (33%) tested (Figure 1B). Follow-up samples obtained from three patients in remission were negative for the tumor-specific clonotype in both the serum and cellular compartments. We conducted sequence and expression level analysis of each IGH-VDJ clonal rearrangement. We calculated the number of somatic mutations in each lymphoma-specific clonotype compared to the germline sequence in the interrogated region. In the ten patients with IGH-VDJ clonal rearrangements, we observed a median of 14 somatic mutations (range 0 to 27). This confirms that HRS cells correspond in their developmental stage to germinal or post-germinal center B-cells. While IGH-VDJ clonotypes were observed frequently in DNA obtained at diagnosis, IGH-VDJ clonotypes were not detected in the RNA from the same sample. We evaluated the relationship between the presence of lymphoma-specific clonotypes in the cellular compartment at diagnosis and eventual progression. All three untreated patients that were positive at baseline in the cellular compartment experienced relapse or progression (at 3, 11 and 17 months). In contrast, zero of 5 patients without detectable lymphoma-specific clonotypes in their cellular compartment at baseline experienced relapse (follow up duration 23-45 months, log-rank test p=0.004). Conclusions: This is the first clinical assay that can be used to detect and monitor MRD in CHL. Lymphoma-specific sequences can be identified in serum in 80% of cases. Our preliminary analysis suggests that the presence of lymphoma-specific clonotypes in PBMCs may indicate high risk for recurrence. This study demonstrates proof-of-principle and underscores the promise of a new methodology to measure disease burden and provide prognostic information from a blood test in patients with CHL. Figure 1. Lymphoma clonotype levels in A) cell-free plasma and B) PBMC samples are shown for the different patients. Figure 1. Lymphoma clonotype levels in A) cell-free plasma and B) PBMC samples are shown for the different patients. Figure 2 Figure 2. Disclosures Klinger: Sequenta, Inc.: Employment, Equity Ownership. Carlton:Sequenta, Inc.: Employment, Equity Ownership. Kong:Sequenta, Inc.: Employment, Equity Ownership. Faham:Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

Introduction : Recent studies have shown that leukemic clones in approximately 10-20% of CLL patients have stereotypic IgH gene sequences (Stamatopoulos et al., Blood 2007). These stereotypic IgH sequences are characterized by closely homologous complementarity-determining regions 3 (CDR3) sequences. The presence of these sequences supports the model of antigen-mediated disease pathogenesis in CLL. While previous studies have focused on the dominant CLL clone present at diagnosis, recent advances in next-generation sequencing enable analysis of the full IgH repertoire. Here we assessed whether stereotypic IgH sequences are present at very low frequency among the total IgH repertoire in diagnostic and follow-up samples from 36 CLL patients. Methods:We utilized the LymphoSIGHT method to sequence the IgH repertoire in 36 CLL patients and 185 patients with non-CLL lymphoid neoplasms. Using universal primer sets, we amplified IGH variable (V), diversity (D), and joining (J) gene segments in diagnostic and follow-up samples. Amplified products were sequenced, and CLL-specific clonotypes were identified in the diagnostic sample of each patient based on high-frequency within the B-cell repertoire. We selected a set of 289 stereotypic IgH CDR3 sequences that were previously curated (Stamatopoulos et al., Blood 2007; Messmer et al., Leukemia Res 2008). We assessed whether the stereotypic CDR3 regions were present in the IgH repertoire of both CLL and non-CLL patients using sequence alignment tools. Results: 154,318 IgH clonotypes were observed in the 36 CLL patients, while we identified 8,248,032 IgH clonotypes from 185 patients with non-CLL lymphoid neoplasms. Specifically, we tested 14 mantle cell lymphoma (MCL), 19 hodgkin disease (HD), and 28 acute lymphoblastic leukemia (ALL) patients as well as three cohorts of multiple myeloma (MM) with 26, 30, and 68 patients. We assessed whether each of the 289 CDR3 stereotypes were present in the IgH repertoire of the CLL or non-CLL patients. Twenty two of the stereotypic IgH sequences were observed in any patient: 2 in CLL patients and 20 in the non-CLL patients. This is not surprising given that non-CLL patients have over 50 times the total number of clones compared to the CLL group. One of the stereotypic IgH clonotypes was detected in one CLL patient (p-value= 0.018; not significant with Bonferroni correction). The other stereotypic IgH clonotype was present in two CLL patients but not in any of the non-CLL lymphoid neoplasm cohorts (p=0.00034; 0.0074 Bonferroni corrected). In contrast, we tested for association between each of the 20 stereotypic sequences and each of the 6 control cohorts (3 MM, 1 MCL, 1 HD, and 1 ALL), and only two significant associations were observed (p=0.045 and p=0.01; neither were significant with Bonferroni correction). This underscores that the only significant association was seen in the tested CLL cohort. Of note, both of these stereotypic IgH clonotypes were present at very low frequency in the IgH repertoire ( Conclusion : Our results demonstrate that CLL patients harbor stereotypic IgH sequences. These sequences were not the dominant, high-frequency clonotypes identified at diagnosis in the CLL patients and were absent in a much larger set of clones derived from a cohort of non-CLL cancer patients. These results suggest that a subset of CLL patients may possess an antigen environment that selects for multiple B cells with stereotypic IgH sequences at low frequencies. This selection process may predispose patients to CLL that develops later via accumulation of multiple genetic hits in a pre-leukemic cell containing the stereotypic IgH sequence driving it to high-frequency. Figure 1. Each clonotype observed in two CLL patients (X axis) is shown as a dot. The Y axis depicts the frequency of the clonotypes. The stereotypic clonotypes are shown in red. Figure 1. Each clonotype observed in two CLL patients (X axis) is shown as a dot. The Y axis depicts the frequency of the clonotypes. The stereotypic clonotypes are shown in red. Disclosures Klinger: Sequenta, Inc.: Employment, Equity Ownership. Hervold:Sequenta, Inc.: Employment, Equity Ownership. Faham:Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

Background: Diffuse large B-cell lymphoma (DLBCL) can be cured with frontline therapy, but the prognosis of patients with relapse in the modern era is poor. Radiology scans (CT and PET) are commonly used as surveillance tools after therapy but do not improve outcomes and are associated with long-term health risks. Interim scans have also been used to identify early treatment failures, but are limited by false positives. Reliable predictive biomarkers that predict relapse may improve clinical outcomes. LymphoSIGHTª is a high-throughput DNA sequencing method that can detect and quantify circulating tumor DNA as minimal residual disease (MRD). We have previously reported its ability to detect circulating tumor DNA in serum after frontline therapy in DLBCL (Roschewski ASH 2013). Here, we analyzed the ability of serum MRD to predict both early treatment failure and relapse from remission in a large cohort of newly diagnosed DLBCL patients treated with curative intent. Methods: Patients with DLBCL and treated at the NCI with EPOCH-based chemotherapy +/-rituximab between July 1996 and October 2013 had research serum samples collected pre-Tx, at each cycle, and at each surveillance visit. Surveillance visits included serum samples with paired CT scans at 3, 4, 6, and 12-month intervals for the first 5 years. Pre-treatment formalin-fixed paraffin embedded (FFPE) tissue specimens and/or baseline serum were de-identified and sent for identification of tumor-specific clonotypes. Tumor DNA was amplified using locus-specific primer sets for the immunoglobulin heavy-chain locus (IGH) complete (IGH-VDJH), IGH incomplete (IGH-DJH), and immunoglobulin k locus (IGK). Amplified products were sequenced, and patients in whom a high-frequency tumor clone (.5%) was not identified were excluded from the MRD analysis. Tumor-specific clonotypes were quantitated in the serum as MRD and analyzed for the ability to predict early treatment failure (interim monitoring) and relapse from remission (surveillance monitoring). Disease progression during therapy or Results: 198 patients with DLBCL had pre-treatment specimens screened for a pre-treatment tumor clonotype with 3 excluded due to 6 mos and underwent surveillance monitoring. Eleven of these relapsed and 10/11 had a positive serum MRD at a median of 7.4 months prior to progression. The other 90 patients had sustained remissions and underwent a median of 11 surveillance CT scans (range 1-18). Dynamic monitoring of interim MRD (each cycle) identified early treatment failure (induction failure or relapse within 6 months) in 25 patients with a sensitivity of 81.8% and specificity of 87.5%. The positive predictive value (PPV) of interim MRD was 60% for predicting early failure while the negative predictive value (NPV) was 95.9%. The 5-year EFS of patients who were interim MRD positive was significantly worse than those who were negative (45.9% vs 83.0%, (p Conclusions: Non-invasive dynamic monitoring of serum MRD during therapy predicts early treatment failure, while serial MRD monitoring during surveillance predicts relapse from remission in DLBCL. This work was supported by the Intramural Research Program of NCI at NIH and Sequenta, Inc. Figure 1 Figure 1. Disclosures Kong: Sequenta: Employment. Zheng:Sequenta: Employment. Willis:Sequenta: Employment, Equity Ownership. Faham:Sequenta: Employment, Equity Ownership.

Background: The majority of multiple myeloma (MM) patients receiving autografts ultimately relapse, and tumor cell contamination of autografts may be a contributing factor. A clinical trial to assess tandem chemo-mobilization with the goal of reducing the myeloma cell burden in the patient and in the apheresis product was conducted and outcomes were previously reported (Chen et al., Bone Marrow Transplant 2012). The effect of myeloma cell depletion using tandem mobilization has not been previously quantified; however, clinical outcomes are comparable with other autotransplant regimens. Here we utilize a sequencing-based minimal residual disease (MRD) technology, termed the LymphoSIGHT™ platform, to assess the effect of tandem chemo-mobilization on myeloma cell contamination in apheresis collections. This sequencing-based method has a sensitivity to detect one tumor-associated immune receptor gene rearrangement molecule per million leukocytes and can be used for MRD quantification in lymphoid neoplasms (Faham et al., Blood 2012; Martinez-Lopez et al., Blood 2014). We analyzed cryopreserved apheresis samples from 19 MM patients to quantify the clonotypicmyeloma cell burden in tandem mobilized apheresis products. Methods: In the two-step chemo-mobilization process, MM patients were first treated with cyclophosphamide (4g/m2) followed by G-CSF (10mcg/kg/day) and an apheresis product collected at hematopoietic recovery was stored ("Cycle 1" apheresis sample). Following subsequent treatment with etoposide (2g/m2) followed by G-CSF (10mcg/kg/day), a second apheresis product was collected ("Cycle 2" apheresis sample). Using universal primer sets, we assessed clonal rearrangements at the immunoglobulin (IGH-VDJ, IGH-DJ and IGK) loci in diagnostic bone marrow aspirate (BMA) slides. Myeloma clonotypes were identified in the diagnostic BMA sample of each patient based on high-frequency within the B-cell repertoire. The level of the myeloma clonotype was then quantified in banked aliquots from the Cycle 1 and Cycle 2 apheresis products. Results: Paired Cycle 1 and Cycle 2 apheresis samples were analyzed, and the total number of rearranged immunoglobulin (Ig) molecules, an approximation of total B-cells, was calculated. An average 5.3 fold reduction in rearranged Ig molecules as a fraction of total cells was observed from Cycle 1 to Cycle 2 (p = 0.004, 2-tailed Wilcoxon) (Figure 1A). Myeloma cell contamination was present at a median level of 62.7 myeloma molecules/million PBMCs (range 0-11,951) after Cycle 1 and 43.6 myeloma molecules/million PBMCs (range 0-4,489) after Cycle 2. Quantitative comparison of MRD levels revealed no significant difference in the absolute number of myeloma molecules/million PBMCs between Cycle 1 and Cycle 2 apheresis products (p = 0.276) (Figure 1B). Analysis of the myeloma clonotype frequency illustrated an average 3.0-fold increase in myeloma clonotype frequency relative to total Ig rearrangements from Cycle 1 to Cycle 2 (p = 0.011) (Figure 1C). MRD levels less than 10-5 in autograftapheresis samples were associated with significantly longer PFS (40 vs 14.3 months, p = 0.003) (Figure 1D). Conclusions: Tandem mobilization fails to decrease myeloma contamination in the second apheresis product, and this practice has been discontinued based on this analysis. Highly sensitive quantification of myeloma clonotype levels in autograft samples may provide improved clinical prognostic information, complement post-transplant MRD quantification, and potentially informtreatment decisions about the timing and intensity of post-transplant maintenance therapies. Figure 1. Comparison of Cycle 1 and Cycle 2 apheresis products and clinical outcome data in MM patients. In Panels A-C, paired Cycle 1 and Cycle 2 values for each patient are connected by a line. Open circles represent A) Total rearranged Ig molecules (an approximation of total B-cells) as a fraction of total cells, B) Number of myeloma molecules per million PBMCs, and C) Myeloma clonotype frequency relative to total Ig rearrangements for each patient in the Cycle 1 and Cycle 2 apheresis products. D) Kaplan-Meier analysis of progression-free survival for 7 MRD negative (10-5) patients. Figure 1. Comparison of Cycle 1 and Cycle 2 apheresis products and clinical outcome data in MM patients. In Panels A-C, paired Cycle 1 and Cycle 2 values for each patient are connected by a line. Open circles represent A) Total rearranged Ig molecules (an approximation of total B-cells) as a fraction of total cells, B) Number of myeloma molecules per million PBMCs, and C) Myeloma clonotype frequency relative to total Ig rearrangements for each patient in the Cycle 1 and Cycle 2 apheresis products. D) Kaplan-Meier analysis of progression-free survival for 7 MRD negative (10-5) patients. Disclosures Klinger: Sequenta, Inc.: Employment, Equity Ownership. Kong:Sequenta, Inc.: Employment, Equity Ownership. Faham:Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

*Equally Contributed Introduction: Recent studies show better progression-free (PFS) and overall survival (OS) for newly diagnosed multiple myeloma (NDMM) pts achieving MRD negativity by multicolor flow cytometry (MFC) or next-generation sequencing (NGS). Here, we report on the comprehensive assessment of MRD in a uniformly treated cohort of 45 MM patients (Korde et al. ASH 2013). Methods: 45 NDMM pts were treated with 8 cycles of combination therapy (carfilzomib, lenalidomide and dexamethasone) followed by 2 years of maintenance lenalidomide. Median potential follow-up was 17.3 mos. All patients were evaluated by NGS by LymphoSIGHT™ method. Briefly, using universal primer sets, we amplified immunoglobulin heavy and kappa chain (IGH and IGK) variable, diversity, and joining (VDJ) gene segments from genomic DNA obtained from CD138+ BM cell lysate or cell free bone marrow (BM) aspirate at baseline. A MM clonotype was defined as an immunoglobulin rearrangement identified by NGS at a frequency >=5%. MRD assessment by NGS, MFC and PET was repeated when patients achieved a complete response (CR) or completed 8 cycles of therapy. In a subset of patients, we performed NGS in peripheral blood (plasma) at baseline and after 2 cycles of treatment. Results: 40/45 (89%) of pts achieved VGPR or better after combination therapy. At least one clonal rearrangement was identified in 31/34 (91%) of BM CD138+ cell samples and in 34/45 (76%) of cell free BM aspirates; overall clonal rearrangement was detected in 37/45 (82%) bone marrow aspirates at baseline. Repeat MRD assessment at CR or the completion of 8 cycles in 32 pts show residual disease in cell free BM aspirates by NGS in 18 (56% of pts tested and 40% of the total study population). Estimated 12-mo and 18-mo PFS for MRD neg vs. pos by NGS was 100% vs 94% and 100% vs 84%, respectively (p=0.025). MFC testing for MRD was feasible in 43/44 pts (98%). PFS probabilities at 12-mo and 18-mo for flow neg vs pos was 100% vs 79% and 100% vs 63%, respectively (p=0.0022). Among pts assessed by both MRD methods (n=31), 23 samples were concordant (9 pos and 14 neg); among 8 discordant cases, all were positive by sequencing and negative by flow (p=0.0078). Abnormal PET scans were noted in 38/45 (84%) of pts at baseline. 24/43 (56%) pts at CR or after 8 cycles of CRd had a neg/dec PET response and 19/43 (44%) pts had a pos/partial PET response. At 12-mo and 18-mo, PFS by a neg/dec PET response vs pos/partial PET response was 100% vs 89% and 92% vs 89%, respectively (p=0.54). Furthermore, in 14 pts, we performed NGS in peripheral blood samples collected at baseline. At least one MM clonotype identified in baseline BM was detectable in corresponding plasma sample in 13/14 pts. Number of myeloma-specific molecules per million diploid genomes in the plasma was 3-log fold lower than in the BM (median 252 vs 730,950 MM specific clonal molecules per million diploid genomes). After 2 cycles of CRd treatment, 12/13 pts were still pos by serum electrophoresis and/or immunofixation while only 1 had detectable myeloma clonotypes in the plasma. Conclusions: This prospective evaluation of MRD testing in MM has several key findings: 1. Detection of myeloma-specific clonotypes by NGS of the Immunoglobulin VDJ segments in the BM is feasible in majority of pts with NDMM. 2. MRD detection by NGS compares favorably to MFC since all pts with residual disease by MFC are also MRD positive by sequencing; an additional 8 pts who were MRD negative by flow MFC were MRD positive by sequencing. 3. MRD negativity by MFC and NGS are both associated with significantly better PFS. 4. Detection of myeloma-specific clonotypes by NGS of the immunoglobulin VDJ segments (i.e. cell free DNA) in the peripheral blood plasma is feasible in NDMM pts at diagnosis; however, since tumor load in the plasma is >2000-fold lower than in the BM; using standard volumes of peripheral blood (plasma), the levels of myeloma-specific clonotypes were too low to be quantified already after 2 cycles of combination therapy. This was true despite presence of positive serum electrophoresis and/or immunofixation. Additional studies to understand the dynamics of the myeloma clonotype level in peripheral blood plasma are necessary to determine optimal MRD testing regimen. Disclosures Faham: Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees. Moorhead:Sequenta, Inc.: Employment.

Introduction: Monitoring for minimal residual disease (MRD) in hematologic malignancies can identify patients at high risk of relapse after standard therapy and hematopoietic stem cell transplantation (HSCT). However, techniques are limited for MRD monitoring of most lymphoma subtypes. The LymphoSIGHTTM method (Sequenta, Inc.) is a high-throughput sequencing-based MRD assay that detects small amounts of circulating tumor DNA (CTD) in patients with lymphoid malignancies. This assayhas shown promise in the monitoring of patients with chronic lymphocytic leukemia (CLL), mantle cell lymphoma (MCL), and diffuse large B-cell lymphoma (DLBCL). We evaluated whether CTD measured by LymphoSIGHTTM pre- and post-allogeneic HSCT predicts relapse and outcome in patients with lymphoid malignancies. Methods: We retrospectively studied patients enrolled between 2009-2012 on a multicenter phase 3 trial comparing sirolimus-containing to non-sirolimus containing GVHD prophylaxis regimens in patients with lymphoma undergoing allogeneic HSCT. Only patients with available archival tumor tissue were included. Patients underwent conventional restaging at 3, 6, 12, 18 and 24 months per protocol. Genomic tumor DNA was extracted from formalin-fixed paraffin-embedded tissue or bone marrow aspirate mononuclear cells. PCR amplification of IGH and IGK regions was performed followed by high-throughput sequencing to determine the tumor clonotype(s). As part of the trial, peripheral blood mononuclear cell (PBMC) and plasma samples were collected pre-HSCT and at days 30, 60, 100, 180, 270, 365, 545 and 730 after HSCT. DNA from plasma (DLBCL) and PBMCs (other histologies) was amplified and sequenced to determine the level of CTD per million diploid genomes. Results: We studied 68 patients with B-cell non-Hodgkin lymphoma, classical Hodgkin lymphoma (HL), or CLL. Clonotype calibration was successful in 51 patients (75%; 82% when excluding diagnostic samples with insufficient DNA). MRD evaluation was performed at >=1 time point in 40 patients (13 CLL, 4 DLBCL, 4 transformed indolent lymphoma (TIL), 8 follicular lymphoma (FL), 7 MCL, 4 HL). Overall, 9/40 patients in the cohort relapsed, with a 2y cumulative incidence of relapse/progression (CIR) of 18%. Thirteen of 26 patients (50%) tested were MRD+ pre-HSCT, including 27% of patients in complete remission (CR) and 71% of patients in partial remission (PR) by conventional criteria. The 2y CIR in MRD+ vs MRD- patients at baseline was 38% vs 7% (p=0.2), 2y non-relapse mortality (NRM) was 15% vs 8% (p=0.6), and 2y progression-free survival (PFS) was 46% vs 85% (p=0.12). At day 100, 12 of 32 patients (38%) tested were MRD+. The 2y CIR in day 100 MRD+ patients was 25% vs 0% for MRD- patients (p=0.25), 2y NRM was 25% vs 5% (p=0.05), and 2y PFS was 50% vs 95% (p=0.01). In multivariable models with histology and disease status at HSCT as covariates, the hazard ratio (HR) for progression or death associated with baseline MRD+ was 2.8 (p=0.3); for day 30 MRD+, HR=6.0 (p=0.1); and for day 100 MRD+, HR=8.3 (p=0.07). When entered into the models as a time-dependent covariate, MRD-positivity was associated with a significantly increased risk of progression or death (HR 5.2, 95% CI 1.8-15.4; p=0.03) and of disease relapse/progression (HR 12.7, 95% CI 2.5-64.3, p=0.002). Histology and disease status were not significantly associated with either outcome in the models. Nine patients relapsed or progressed at a median of 4 (range 1-28) months post-HSCT and 7 (78%) had an MRD+ PB sample at a median of 6 months prior to relapse (Figure). Five patients were persistently MRD+ in all PB samples tested prior to relapse and 2 were initially MRD- then became MRD+. All 5 patients who relapsed after day 100 were MRD+ prior to relapse. Among 31 patients who did not relapse: 16 were MRD- in all PB samples tested; 9 were initially MRD+ then became MRD- by day 365 (4 by d100, 3 by d180, 2 by d365); 2 had a mixed MRD pattern, initially MRD-, then MRD+, then MRD- thereafter; the remaining 4 patients, all of whom had CLL, were persistently MRD+ but had marrow or PB evidence of persistent disease without progression at MRD+ time points. Conclusions: MRD status based on CTD detection in patients with lymphoid malignancies is predictive of outcome after allogeneic HSCT. This technique may provide important prognostic information throughout the HSCT course and identify a target population for early intervention to prevent disease relapse. Figure 1 Figure 1. Disclosures Faham: Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

Background: NDMM patients (pts) treated with KRd in a phase 1/2 trial (NCT01029054) demonstrated high rates of complete response (CR, 64%) and stringent complete response (sCR, 55%) that correlated with excellent estimated 3-year progression-free survival (PFS; 79%) and overall survival (OS; 96%) (Jakubowiak et al, Blood, 2012; Jasielec et al, Blood 2013; 122(21):3220). Furthermore, there was a trend towards superior outcomes in patients with multiparameter flow cytometry (MFC) MRD-negative disease with an estimated 3 year PFS of 84% and OS of 100%, suggesting the importance of MRD analysis in predicting relapse. In this post hoc, retrospective analysis, we present an updated evaluation of PFS based on minimal residual disease (MRD) status. Methods: Pts received 28-day cycles of carfilzomib (CFZ) 20–36 mg/m2 intravenously (days [d]1, 2, 8, 9, 15, 16), lenalidomide (LEN) 25 mg orally (PO; d1–21), and dexamethasone 40/20 mg PO weekly (cycles 1–4/5–8). For cycles 8–24, KRd was given with a modified CFZ schedule (d1, 2, 15, 16), and single-agent LEN was administered after cycle 24. Pts had the option to receive stem cell transplantation after cycle 4. MRD assessment at the time of complete response (CR) was performed using 10-color MFC and next-generation sequencing (NGS) analysis. Fresh bone marrow aspirate (BMA) was used for MFC analysis as previously reported, while archived BMA slides were used for NGS analysis. The LymphoSIGHT™ NGS method employed universal primer sets to assess clonal rearrangements at the immunoglobulin loci (IGH-VDJ, IGH-DJ and IGK) in diagnostic BMA slides. Myeloma clonotypes were identified in the diagnostic BMA sample of each patient based on high-frequency within the B-cell repertoire. The level of the myeloma clonotype was then quantified in BMA slides obtained at the time of CR. Results: Twenty-two pts with CR/sCR were evaluated for MRD by both MFC and NGS methods with a median follow-up of 40 months. Limited input DNA was obtained from BMA slides (range 2,189 to 1,870,960 cell equivalents). Concordance analysis in 21 patients with both MFC and NGS MRD data revealed 11 patients that were MRD-negative by both MFC and NGS, while 2 patients were concordantly MRD-positive. NGS demonstrated greater sensitivity compared to MFC, as 8 patients were MRD-positive by NGS but MRD-negative by MFC. Three of these 8 patients relapsed. We evaluated the correlation between MRD status by NGS and PFS. Six MRD samples had less than 40,000 input cell equivalents and were removed from the progression-free survival analysis due to insufficient sample amount. MRD negativity by NGS in KRd patients at the time of CR was associated with longer progression-free survival (median not reached vs 46 months, p = 0.055) (Figure 1). Conclusions: Our results suggest that achievement of MRD-negative disease by NGS in CR patients is associated with superior PFS. The NGS method appears more sensitive than MFC at detecting residual disease. Finally, MRD assessment by NGS in BMA slides is feasible although may not be the optimal method due to limited input DNA amount. MRD assessment by NGS will be performed on the remainder of the KRd cohort and results will be presented. Figure 1. Kaplan-Meier analysis of progression-free survival for 6 MRD negative (10-6) patients. Figure 1. Kaplan-Meier analysis of progression-free survival for 6 MRD negative (10-6) patients. Disclosures Faham: Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees. Lee:Sequenta, Inc.: Employment, Equity Ownership. Jakubowiak:Bristol Myers-Squib: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Janssen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Millennium: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Onyx: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; SkylineDx: Honoraria, Membership on an entity's Board of Directors or advisory committees.

Background: Successful outcome in childhood acute lymphoblastic leukemia (ALL) relies upon appropriate central nervous system (CNS)-directed therapy for treatment of subclinical or overt CNS leukemia. Patients with leukemia blasts detected in the cerebrospinal fluid (CSF) at diagnosis require intensified intrathecal therapy to avert a higher rate of relapse and poorer survival compared with patients without blasts in the CSF. Traditionally, CSF assessment is performed by morphological analysis of CSF smears with or without TdT assay or via flow cytometry; however, both of these methods are limited in their sensitivity. Moreover, these modalities rely on subjective operator judgment for identification of leukemic blasts, which can result in limited assay reproducibility. A precise definition of CNS involvement is necessary to avoid over- or under- treatment. The LymphoSIGHT™ platform is a next-generation sequencing-based method that is being used for minimal residual disease assessment in lymphoid malignancies (Faham et al., Blood 2012). The LymphoSIGHT™ platform has a sensitivity to detect one leukemic cell per million leukocytes in peripheral blood and/or bone marrow and has been shown to have prognostic value in adult ALL patients (Logan et al., Biol Blood Marrow Transplant 2014). In this pilot study, we assessed whether this sequencing method could be used to detect leukemic clonotypes in CSF samples from newly diagnosed pediatric ALL patients. Methods: Diagnostic bone marrow samples, and paired CSF and peripheral blood samples were obtained from two patients. Using universal primer sets, we amplified variable, diversity, and joining gene segments from immunoglobulin (Ig) heavy chain (IGH), Ig kappa chain (IGK), and T-cell receptor beta (TRB), delta (TRD) and gamma (TRG) loci from genomic DNA. Amplified products were sequenced and analyzed using standardized algorithms for clonotype determination. Tumor-specific clonotypes were identified for each patient based on their high-frequency within the B-cell repertoire. The presence of the tumor-specific clonotype was then quantitated in CSF (cell pellet and supernatant) and peripheral blood samples obtained at diagnosis and interim treatment time points. A quantitative and standardized measure of leukemic clonotype level per million leukocytes in each follow-up sample was determined. Results: Diagnostic bone marrow samples from the two pediatric ALL patients were used to identify the tumor-specific clonotypes. Three IGH tumor clonotyes, one IGK, and one TRD tumor clonotype were observed in the first patient. Three IGH tumor clonotypes were observed in the second patient. The level of tumor burden associated with each leukemic clonotype was then assessed in serial CSF samples from each of the two patients. In the first patient, both the CSF pellet and supernatant were positive by sequencing at diagnosis. Consistent with the sequencing results, this patient was determined to have CNS involvement at the time of diagnosis based on standard testing methods. The patient cleared at Day 22, and the CSF pellet and supernatant from this time point were also negative by sequencing. Serial samples from the second patient, who was shown to lack CNS involvement by standard testing methods, were also tested. Both the CSF cell pellet and supernatant were negative at the Day 0 and Day 22 time points for this patient, showing concordance with available clinical data (Table 1). Conclusions: This study demonstrates proof of principle that the LymphoSIGHT sequencing method can be used to assess CNS involvement in pediatric patients with ALL. Further studies are warranted to assess the diagnostic and prognostic value of the sequencing method for assessment of CNS disease. The study cohort has now been expanded to include an additional 35 pediatric patients with ALL, and data will be presented. Abstract 5343. Table 1. Comparison of results in CSF samples using sequencing and traditional methods. Patient Time Point Standard analysis of CSF samples Sequencing analysis of CSF samples WBC count/µL RBC count/µL Cell number Percent blasts Leukemia molecules/1M diploid genomes (cell pellet) Leukemia molecules/1M diploid genomes (supernatant) 1 Day 0 0 0 85 7 431,100 366,800 1 Day 22 0 0 33 0 0 0 2 Day 0 0 0 25 0 0 0 2 Day 22 0 0 32 0 0 0 Disclosures Weng: Sequenta, Inc.: Employment, Equity Ownership. Carlton:Sequenta, Inc.: Employment, Equity Ownership. Faham:Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

Background: Although molecular complete remission (mCR) in multiple myeloma (MM) can be assessed by allele-specific oligonucleotide (ASO)-PCR, this technique requires preparation of clonotype-specific primers for each individual, which is laborious and time-consuming. We utilized the LymphoSIGHTTM platform, which employs consensus primers and next-generation sequencing (NGS) to amplify and sequence all rearranged immunoglobulin gene segments present in a myeloma clone, to assess mCR. This technique has been shown to have 1-2 logs greater sensitivity compared to ASO-PCR and flow cytometry, respectively (Faham et al, Blood 2012). Usage of the sequencing method for minimal residual disease (MRD) detection in MM may provide increased sensitivity and specificity, while overcoming the challenges associated with ASO-PCR. We compared the LymphoSIGHTTM method with ASO-qPCR for MRD detection in autografts and bone marrow (BM) in the autologous peripheral blood stem cell (PBSC) transplantation (ASCT) setting. Methods: One hundred and nine Japanese patients with newly diagnosed MM who received various induction regimens prior to ASCT were retrospectively analyzed. All patients had achieved a partial response (PR) or better after ASCT. BM slides from 84 MM patients and fresh/frozen BM cells from 25 MM patients at diagnosis, as well as autografts/post-ASCT BM cells from each patient, were obtained for DNA extraction. IGH-based ASO-qPCR was performed as described previously (Methods Mol Biol 2009). Using universal primer sets, we amplified IGH variable (V), diversity (D), and joining (J) gene segments, IGH-DJ, and IGK from genomic DNA. Amplified products were subjected to deep sequencing using NGS. Reads were analyzed using standardized algorithms for clonotype determination. Myeloma-specific clonotypes were identified for each patient based on their high frequency in BM samples. Results : Myeloma clonotypes could be identified in autografts/post-ASCT BM cells in 98 of 109 patients (90%) and by ASO-qPCR in 63 of 101 patients (62%). MRD by NGS was assessed in autografts of 89 patients. 70 of 89 patients (79%) were positive by NGS; 28 of 62 patients (45%) were positive by ASO-qPCR. Although we observed a high correlation between NGS and PCR MRD results at MRD levels of 10-5 or higher, the sensitivity of ASO-PCR was 10-4-10-5, whereas that of NGS was 10-6 or lower when a sufficient amount of DNA was available for analysis. Eight cases where MRD was not detected in the autograft by NGS (MRDNGS(-)) and 38 MRDNGS(+) cases received post-ASCT therapy using novel agents such as bortezomib/lenalidomide/thalidomide, while 11 MRDNGS(-) cases and 32 MRDNGS(+) cases were followed without post-ASCT therapy. The MRDNGS(-) cases without post-ASCT therapy showed significantly better progression-free survival (PFS) than the MRDNGS(+) cases without post-ASCT therapy (P = 0.012) (Figure 1A) although overall survival rates were comparable between these groups. To investigate the value of sensitive detection by NGS, we compared PFS in 11 MRDNGS(-) cases (Group 1) with the 12 MRDNGS(+) cases where MRD was not detected by ASO-qPCR (MRDASO(-)) (Group 2). The patients in both groups did not receive any post-ASCT therapy. Group 1 showed significantly better PFS than Group 2 (P = 0.027) (Figure 1B). Furthermore, 9 MRDNGS(-) in post-ASCT BM cases tended to show a better PFS than 18 MRDNGS(+) in post-ASCT BM cases (P = 0.075) (Figure 1C). In a multivariate analysis, post-ASCT therapy using novel agents (P Conclusions: In this study, we showed the prognostic value of MRD detection using the NGS-based LymphoSIGHT platform in autografts of patients with MM who received and in those who did not receive post-ASCT therapy with novel agents. The NGS platform has improved sensitivity compared with ASO-qPCR in detecting MRD in autografts. Patients with low level MRD detected by NGS but not by ASO-qPCR have worse prognosis compared to patients who are MRD negative by sequencing, which underscores the need for sensitive detection. Figure 1 Figure 1. Disclosures Zheng: Sequenta, Inc.: Employment. Moorhead:Sequenta, Inc.: Employment. Faham:Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

Introduction: Immunoglobulin (Ig) gene rearrangement is a hallmark of early B-cell development. Multiple myeloma (MM) is a malignancy of plasma cells, which are at the post-germinal center stage of B cell development. Therefore, Ig sequences in MM are typically mutated but are thought to be stable throughout the course of the disease. We previously observed that multiple Ig sequences related by somatic hypermutation (SHM) are present in some MM patients at diagnosis. Here we expanded our previous observations and investigated whether continuous evolution in Ig sequences occurs over the course of treatment. Methods: 401 MM patientsenrolled in IFM/DFCI study were included in this analysis. The LymphoSIGHT™ platform was used to detect evidence of oligoclonality at the Ig heavy and kappa chain (IGH and IGK) loci. Using universal primer sets, we amplified IGH and IGK variable, diversity, and joining gene segments from RNA isolated from purified CD138+ MM cells collected at the time of diagnosis. Amplified products were sequenced and analyzed (Faham et al., Blood 2012). MM-specific clonotypes were identified for each patient based on their high frequency (5%) within the B-cell repertoire in the diagnostic sample. The highest frequency MM clonotype in a diagnostic sample is termed the "index clonotype." Diagnostic RNA and post-treatment DNA bone marrow samples were assessed for evidence of evolved MM clonotypes. A clonotype was considered "evolved" based on CDR3 sequence homology to the diagnostic "index clonotype." Results: At diagnosis 10/401 (2.5%) MM patients had 2 unrelated expressed Ig sequences; 4 of these cases (1%) are both functional and therefore are likely to be in 2 different cells. In addition, 71/401 (17.7%) MM patients had evidence of at least 1 evolved clone related through SHM to the index clonotype at diagnosis. 26 of 71 patients had a post-treatment sample tested. Of these 9 are negative for both the index and evolved clone, while 17 are positive for the index clone but not the evolved clone. In 1 of these 17 cases the evolved clone would have been observed if it had the same relative frequency to the index clone as was seen in the diagnostic sample. The observation suggests differential sensitivity to treatment. In a separate analysis, we assessed 120 MRD positive post-induction samples (~6 months after diagnosis) for evidence of evolution. Altogether, 7/120 cases (5.8%) had a pattern of evolution at the post-treatment time point which suggested differential sensitivity to therapy. In 4 patients, the evolved "new" clonotype was not observed at diagnosis but appears in the follow up sample only. In 3 patients, the evolved clonotype either increased or decreased in the post-treatment sample relative to the index clonotype (Fig 1). Interestingly, evolved clones in the follow up sample have 1-4 single base differences compared to the index clone found at diagnosis. Conclusions: We observed multiple evolved clonotypes in a substantial percentage of diagnostic MM samples (17.8%). The presence of multiple clonotypes related by SHM indicates that this mechanism remains active after myeloma development in at least a portion of the cells. We also found marked changes in the relative frequency of the MM clonotypes in post-induction samples in 5.8% of MRD+ cases, even though the period between diagnosis and post-treatment samples was only 6 months. The emergence of new IgH clones may not be due to selective advantage of the newly acquired mutations in the Ig gene, but rather some other ongoing genomic mutation process. Thus, these evolved myeloma clonotypes may be useful as surrogate markers for other oncogenic mutations providing resistance to therapy. A) Figure 1. (A) The top line shows the germline sequence of a section of the V segment. The clonotype in the diagnostic sample has 3 SHMs shown in the section. The clonotype in the follow up sample has acquired an additional SHM. B) Germline V and J sequences are shown on top with the boxed sequences present in the clonotypes and the unboxed bases representing the sequences that were deleted during the VDJ recombination to form the clonotypes. The four arrows denote SHMs that have occurred to generate an inferred but unobserved clonotype. One additional mutation occurs to form the clone seen at diagnosis, while three different mutations appear in the clonotype seen in the follow up sample. Figure 1. (A) The top line shows the germline sequence of a section of the V segment. The clonotype in the diagnostic sample has 3 SHMs shown in the section. The clonotype in the follow up sample has acquired an additional SHM. B) Germline V and J sequences are shown on top with the boxed sequences present in the clonotypes and the unboxed bases representing the sequences that were deleted during the VDJ recombination to form the clonotypes. The four arrows denote SHMs that have occurred to generate an inferred but unobserved clonotype. One additional mutation occurs to form the clone seen at diagnosis, while three different mutations appear in the clonotype seen in the follow up sample. B) Figure 2 Figure 2. Disclosures Munshi: Celgene: Consultancy; Onyx: Consultancy; Janssen: Consultancy; Sanofi-Aventi: Consultancy; Oncopep: Consultancy, Equity Ownership, Patents & Royalties. Faham:Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

Background: Chronic lymphocytic leukemia (CLL) usually develops from asymptomatic monoclonal expansions of CD5 positive B-cells termed monoclonal B-cell lymphocytosis (MBL), present in the peripheral blood (PB) of approximately 5% of otherwise healthy older individuals. Although MBL only occasionally progresses to CLL, cases that do progress typically have higher MBL cell counts in the 1500-4000/µL range. Although antigen selection appears to play a central role in the development CLL, it is unclear whether this occurs at an early MBL stage or primarily during the progression of MBL to CLL. One prior study has reported clonal heterogeneity in MBL finding it in 4 of 6 low count MBL cases from familial CLL kindreds using a single cell PCR technique (Leukemia 2010,24:133-140). In this study, we assessed the VH repertoire and degree of clonal heterogeneity in sporadic MBL cases using next-generation sequencing (NGS) of the rearranged immunoglobulin heavy chain (IgH) locus. Methods: The 35 cases selected for sequencing represented residual, cryopreserved material from PB specimens submitted to ARUP for clinical phenotyping studies. All contained polytypic CD5 negative B-cells in addition to MBL/CLL phenotype cells, and had 2 or more vials for analysis. The majority (80%) had counts of MBL cells below 1000/µL (mean 294/, range 795-30 cells/µL). FACS purification of MBL cells (CD20+CD5+) and CD5 negative B-cells was performed on all samples. The IgH repertoire from the unsorted and two sorted populations was determined by NGS using the LymphoSIGHT method. Results: Five cases could not be analyzed due to insufficient numbers of MBL cells. Clonal VDJ rearrangements or clonotypes were identified in the remaining 30 based on their high frequency within the B-cell repertoire of the unsorted sample, and having a higher frequency in the sorted MBL cells relative to the sorted CD5 negative B-cells. Functional clonotypes were identified in 29 of these 30 cases. Interestingly, 5 cases had 2 functional unrelated clonotypes using different D and/or J segments that also employed different V segments. Of the 5 cases with 2 unrelated clonotypes, 3 had MBL cell counts below 1000/µL (32, 275, and 865) and 2 above (1640, 2600). Moreover, 1 of the clones in the case with 865 cells/µL represented only 25% of the MBL cells or 220 cells/µL, while 1 clone in the case with 2600 MBL cells/µL represented 18% of the MBL cells or 470 cells/µL. By flow cytometry, the CD5+ CD20+ cells in 2 of the cases with 2 functional clonotypes showed polytypic kappa/lambda expression (ratios near 1), 2 cases had uniform dim monotypic kappa expression, and 1 case showed 90% dim kappa and 10% dim lambda expression. The most frequently used VH segments were V4-34 in 6/34 or 18% of functional clonotypes, followed by V3-23 (11%), and V3-21 (9%). The V1-69 segment was used by only 1/34 (3%) functional clonotypes. The VH segments in 72% of cases with functional clonotypes were mutated (homology to germline < 98%), with 6 cases showing clear evidence of ongoing mutation by having 2 or more related clones. Conclusions: We demonstrate that MBL exhibits considerable clonal heterogeneity, with 2 distinct unrelated clones identified in 17% of 30 analyzed cases. Finding 2 distinct clones cannot be explained by a lack of allelic exclusion or the presence of 1 cell with 2 productive IgH rearrangements since each clone had different frequencies within the sorted MBL cell repertoire. This is further supported by finding the ratios of the two MBL clones in 2 cases being different in the unsorted compared to the MBL sorted cells. Clonal heterogeneity appears to occur at an early stage since the majority of clones (6/10) had cell counts below 500 cells/µL. We also found that clonal heterogeneity of MBL may not be detectable by flow cytometry or may appear as polytypic CD5+CD20+ B-cells. To our knowledge, this represents the first report of clonal heterogeneity in sporadic MBL. Our identification of infrequent use of V1-69 (1/34) supports prior studies indicating the VH repertoire of MBL is different than CLL which frequently employs V1-69. Finding evidence of ongoing VH mutation suggests antigen selection may occur in early MBL. Overall, our findings are consistent with recent observations (Cancer Cell 2011, 20;246-259) suggesting that hematopoietic stem cells from CLL patients can generate mono-or oligoclonal MBL phenotype cells that can then be selected through antigen binding for expansion. Disclosures Faham: Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

While treatment with anti-CTLA-4 antibody can induce clinical responses in advanced cancer patients, its effects on the breadth of the T cell response is unknown. We used a next-generation sequencing-based method to assess T cell repertoire diversity in 46 patients with metastatic castration resistant prostate cancer or metastatic melanoma. Peripheral blood mononuclear cells were obtained from patients prior to and during treatment with anti-CTLA-4 antibody. mRNA was amplified using locus-specific primer sets for T cell receptor (TCR) beta, and the amplified product was sequenced. Sequence reads were used to quantitate absolute TCR frequencies using standardized clonotype determination algorithms with normalization by spiked reference TCR sequences. Following clonotype quantitation, repertoire differences between serial samples were assessed by the Morisita index, a statistical measure of population dispersion. 97 paired samples were assessed, of which 46 (47%) had increases and 22 (23%) had decreases in TCR diversity by more than 2-fold. By comparison, none of 9 untreated sample pairs underwent more than a 2-fold change in diversity (P = 0.005, Fisher's exact test, two tailed). TCR repertoire differences between monthly samples were markedly higher than for time-matched controls. After the first treatment, median Morisita index between samples was 0.197 for treated samples versus 0.039 for untreated (P = 0.0005, Mann-Whitney U test). The median number of clones that significantly changed in abundance was 421 for treated versus 45 for controls. In patients with multiple time points, this rapid clonotype evolution continued through treatment. Whereas the number of clonotypes that increased with treatment was not associated with clinical outcome, improved overall survival was associated with maintenance of high frequency clones present at baseline. In contrast the highest frequency clonotypes fell with treatment in patients with shorter overall survival. Stably maintained clonotypes included T cells possessing high avidity TCR such as CMV-reactive T cells. Together, these results suggest that CTLA-4 blockade induces T-cell repertoire evolution and diversification. Moreover, improved clinical outcomes are associated with less clonotype loss, consistent with the maintenance of high frequency TCR clonotypes during treatment. These clones may represent the presence of pre-existing high avidity T cells that may be relevant in the anti-tumor response. Citation Format: Lawrence H. Fong, Edward Cha, Mark Klinger, Yafei Hou, Craig Cummings, Antoni Ribas, Malek Faham. T-cell repertoire turnover induced by anti-CTLA-4 antibody treatment in cancer patients. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5017. doi:10.1158/1538-7445.AM2014-5017

Introduction The evaluation of myeloma cells in multiple myeloma (MM) patients has generally been limited to the assessment of bone marrow involvement because of the sensitivity limitations of traditional minimal-residual-disease–detection methods. Materials and Methods We developed a sequencing-based method to identify myeloma cells in bone marrow (BM) and peripheral blood (PB) samples, based on their unique immunoglobulin gene rearrangements, that can detect cancer clones at levels well below 1 in 1 million leukocytes (0.0001%). In this multisite study, we used this sequencing method to determine the fraction of patients with myeloma cells in their PB at diagnosis and posttreatment time points. Results Using this sequencing approach, we detected myeloma cells in the PB in the vast majority of MM patients (44/46, 96%). We demonstrated a clear correlation ( R 2 = 0.57) between myeloma clone levels in paired BM and PB samples, and noted that PB clone levels were approximately 100-fold lower than levels in BM samples. The sequencing assay demonstrated a clear sensitivity advantage in the BM compartment and at least equivalent sensitivity in the PB compared with that of monoclonal-protein results. Conclusion This study highlights the promise of a blood-based, sequencing minimal-residual-disease assay that can be used to measure MM disease burden at different time points and various disease stages.

Introduction Immunoglobulin (Ig) gene rearrangement is a hallmark of early B-cell development. Multiple myeloma (MM) is a malignancy of the plasma cells, which are at the terminal stage of B cell development. MM is a clonal disease originating from the transformation process of a single plasma cell and, thus, myeloma cells are traditionally thought to have one clonal Ig gene sequence that remains stable throughout the course of the disease. Based on preliminary evidence of oligoclonality, we utilized the LymphoSIGHT™ platform, a high-throughput sequencing method, to detect evidence of oligoclonality at the Ig heavy and kappa chain (IGH and IGK) loci. The sequencing approach can be used to examine two general models for oligoclonality. In the first model, two unrelated clonal Ig sequences are observed indicating the presence of two independent myelomas. Alternatively, in the second model, two related myeloma clonal Ig sequences are observed indicating that both myeloma clones are derived from a common ancestor that arose after the pro B cell stage when VDJ recombination is completed. The common ancestor can be a cell with premalignant lesion or after the MM has developed. Using the sequencing platform, we looked for evidence of these two models of oligoclonality in 193 MM patients. Methods Two cohorts of newly diagnosed MM patients were included in this analysis (N=125, N=68). Using universal primer sets, we amplified IGH and IGK variable, diversity, and joining gene segments from genomic DNA or RNA from bone marrow collected at initial diagnosis. Amplified products were sequenced and analyzed using standardized algorithms for clonotype determination (Faham et al, Blood 2012). In the first cohort (N=125), we assessed gene rearrangement at the IGH-VDJ and IGK loci in 120 patients using RNA only and in 5 patients, we used both DNA and RNA to assess the IGH-VDJ, IGH-DJ and IGK loci. In the second cohort (N=68), we analyzed gene rearrangement at the IGH-VDJ, IGH-DJ and IGK loci using genomic DNA. Myeloma-specific clonotypes were identified for each patient based on their high frequency (5%) within the B-cell repertoire in the diagnostic sample. To identify clonotypes that are present in more than one cell we looked for patterns that are not consistent with having a maximum of one functional and one non-functional clonotype in a cell. Results We observed oligoclonality in 23 of 193 (12%) MM patients. Unrelated Ig sequences, which are consistent with the first model of oligoclonality, were present in 8 of the 193 (4%) patients. Fifteen of 193 (8%) patients exhibited related Ig clones, which is consistent with the second model of oligoclonality. In 4 of the 15 patients clones were related to each other via a somatic hypermutation process and differed by only a few bases (Figure 1), while in other 11 patients, the same VDJ sequence was associated with two distinct isotypes (IgA and IgG). Interestingly, in cases with both RNA and DNA sequencing and oligoclonality, we observed differential expression levels compared to clonal content at the DNA level, suggesting that a low frequency clone could be contributing as a predominant secretory clone. Conclusions This study demonstrates frequent oligoclonality in MM patients and suggests that this phenomenon does occur due to two distinct processes, either as unrelated sequences consistent with independent clones or as related sequences consistent with evolution after the MM malignant lesions occur. These findings shed light on the biology and pathogenesis of MM and may provide prognostic information. Currently, this analysis was limited to high frequency clones, using a threshold of 5% for identification of the myeloma-specific clones. Additional analysis is being performed to assess the presence of lower frequency clones, and data will be presented. Disclosures: Carlton: Sequenta, Inc. : Employment, Equity Ownership. Moorhead:Sequenta, Inc.: Employment, Equity Ownership. Faham:Sequenta, Inc. : Employment, Equity Ownership, Membership on an entity’s Board of Directors or advisory committees.

Background The prognostic significance of minimal residual disease (MRD) quantification in the post-transplant setting has been demonstrated in multiple lymphoid malignancies, including acute lymphoblastic leukemia (ALL), mantle cell lymphoma (MCL) and chronic lymphocytic leukemia (CLL). Previous studies support the clinical utility of molecular MRD quantification of tumor burden after allogeneic hematopoietic cell transplantation (allo-HCT) (Logan et al, Leukemia 2013). We have developed the ClonoSIGHT™ test, which is based on the deep sequencing of immunoglobulin and T-cell receptor rearrangements and has a detection limit of one cancer cell per million leukocytes in peripheral blood or bone marrow (Faham et al, Blood 2012; Armand et al, Brit J Haematol 2013). In this report, we will discuss the technical performance of the ClonoSIGHT test for routine MRD quantification after allo-HCT and present a case study on a patient with T-cell prolymphocytic leukemia (T-PLL). Methods A 55 year old female presented with T-PLL including symptomatic CNS disease, received 12 weeks of Alemtuzumab therapy and then 12 weeks following her last Alemtuzumab treatment received an unrelated donor myeloablative allo-HCT using Fludarabine, BCNU and Melphalan conditioning with antithymoglobulin, Mycophenolate mofetil and cyclosporine primary immune prophylaxis. Peripheral blood samples were collected for MRD assessment before and serially after allo-HCT. Using universal primer sets, we amplified T-cell receptor beta (TRB), delta (TRD) and gamma (TRG) variable, diversity, and joining gene segments from genomic DNA isolated from peripheral blood mononuclear cells (PBMC). Amplified products were sequenced and analyzed using standardized algorithms for clonotype determination, and leukemia-specific clonotypes were identified based on their frequency within the T-cell repertoire (>5%). The leukemia-specific clonotype was then quantified in serial peripheral blood samples and reported as the absolute number of leukemic-specific clones among total leukocytes. Results A single clonal TRG gene rearrangement accounting for 26.1% WBC in the pre-transplant sample was identified and quantified in serial peripheral blood samples. A 4-log decline in MRD levels occurred post allo-HCT (Figure 1) thru 56 days following graft infusion; however, serial MRD monitoring demonstrated increasing levels of leukemia-specific clonotypes in the peripheral blood over time (Figure 1). Immunosuppression tapering strategies were employed in response to clinical events and MRD levels. Specifically, the patient developed an EBV+ post-transplant lymphoproliferative disease (PTLD) 60 days post allo-HCT, and cyclosporine was tapered in addition to instituting anti-CD20 rituximab treatment. As per institutional practice, a bone marrow biopsy 84 days post-HCT showed full donor engraftment with normal cellularity and no evidence of PLL was detected by flow cytometry when ClonoSIGHT detected 0.013% PLL in the patient's blood. Unfortunately, in the setting of immune suppression taper at 100 days post allo-HCT, the patient developed Grade II skin GVHD and was treated with 0.5mg/kg prednisone daily and tapered as indicated. At 160 days post allo-HCT, the patient presented with new skin papules suspected to be leukemia cutis. The PLL clonotype was detected in the skin biopsy; however, it was present at lower frequency in the TRG repertoire than in the blood, thus not supporting a diagnosis of leukemia cutis. In agreement, skin pathology revealed Verruca Vulgaris (warts). However, the patient's MRD continued to increase in the blood while immunosuppression was tapered and stopped completely 6 months post-HCT. Conclusions MRD assessment can be used to monitor a patient's disease progression after immune cellular therapy and aids immune suppression management following allo-HCT. Further, as presented in this case study, ClonoSIGHT detection of the leukemia clone in the blood compared with other tissues can sensitively and specifically assess extramedullary relapse. Disclosures: Kong: Sequenta, Inc.: Employment, Equity Ownership. Faham:Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity’s Board of Directors or advisory committees.

Background Detection of minimal residual disease (MRD) by t(14;18) Real-Time Quantitative (RQ) PCR is an important tool during clinical follow-up in patients (pts) with follicular lymphoma (FL). However, only the major breakpoint region (MBR) and minor cluster region (mcr) breakpoints have been currently exploited as MRD targets. Therefore, only 50% to 65% of pts can be assessed by t(14;18) RQ-PCR. Alternative targets such as the immunoglobulin heavy chain variable region (IGH) can be used only with limitations due to somatic hypermutation. IGH-based next-generation sequencing (NGS) might provide an alternative approach and provide increased sensitivity, specificity, accuracy and reproducibility. We performed a comparison of the two approaches in 29 FL pts. Patients and Methods Overall, 206 samples (85 bone marrow, 114 peripheral blood, 6 stem cell aliquots and one lymph node sample) were investigated from 29 FL pts in which RQ-PCR based MRD analysis had been performed in the context of prospective clinical trials. Overall, 33 dx and 173 follow-up (FU) samples were analyzed. 23/29 pts had a PCR detectable t(14;18) rearrangement, 5 pts had a clonal IGH rearrangement only and one patient had no marker by consensus PCR. NGS was performed at Sequenta in South San Francisco. Using universal primer sets, we amplified IGH variable, diversity, and joining gene segments from genomic DNA. Amplified products were sequenced to obtain a high degree of coverage and analyzed using standardized algorithms for clonotype determination. Tumor-specific clonotypes were identified for each patient based on their high-frequency in the dx sample and then quantitated in FU samples. Overall comparability of MRD results by RQ-PCR and NGS was assessed using correlation analysis. A positive/negative discordance between two results was defined as major when the positive result was >1E-05 and minor when ≤1E-05; a quantitative discordance was defined as the presence of two positive results with a quantitative discrepancy >1 log. Results All 29 pts were evaluable with at least one method. IGH NGS identified an index clone in 22/29 cases. Seven patients pts were only quantifiable by t(14;18) RQ-PCR while IGH NGS did not identify an index clone for sequencing. In all but one dx sample demonstrated low level lymphoma infiltration with MRD level below 10-3. In one of these cases, IG kappa could be successfully sequenced for MRD indicating that not only low level MRD but also somatic mutation of IGH is a potential pitfall for MRD detection by NGS in FL. 15 pts were evaluable for MRD by t(14;18) RQ-PCR and NGS. In 97 FU samples, a significant concordance between MRD methods could be demonstrated (r2=0.80) (p In 5 t(14;18) negative cases and one with an unusual large t(14;18) rearrangement MRD was quantified by IGH-RQ-PCR using cloned plasmids and IGH NGS. In all cases both methods also showed excellent concordance. One advantage of the IGH NGS approach is its ability to detect different IGH sequences generated by the somatic hypermutation process. We have seen in some patients a dynamic picture of the IGH clonotypes with the rise and fall of different clonotypes at different time points (Fig 1). Conclusions NGS represents a feasible tool for IGH-based MRD monitoring that allows analysis of a larger group of FL pts. Our results show that the two methods have a high level of correlation. Lymphoma infiltration of dx samples and somatic mutation of IGH is a critical point for identification of the tumor-specific clonotypes by NGS, therefore different MRD methods should complement each other to allow MRD assessment for the majority of pts. Furthermore IGH NGS sequencing has the potential to detect and track IGH evolution in FL. Disclosures: Kneba: Roche: Consultancy, Research Funding. Faham:Sequenta, Inc.: Employment, Patents & Royalties.