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1.  Protective effect of CMV reactivation on relapse after allogeneic hematopoietic cell transplantation in AML patients is influenced by their conditioning regimen 
Cytomegalovirus (CMV) reactivation after allogeneic hematopoietic cell transplant (allo-HCT) has been associated with reduced risk of relapse in patients with acute myeloid leukemia (AML). However the influence of the conditioning regimen on this protective effect of CMV reactivation after allo-HCT is relatively unexplored. To address this, we evaluated the risk of relapse in 264 AML patients who received T cell replete, 6/6 HLA matched sibling or 10/10 HLA matched unrelated donor transplantation at a single institution between 2006 and 2011. Out of these 264 patients, 206 received myeloablative (MA) and 58 received reduced intensity conditioning (RIC) regimens. CMV reactivation was observed in 88 patients with MA conditioning and 37 patients with RIC. At a median follow up of 299 days, CMV reactivation was associated with significantly lower risk of relapse in patients who received MA conditioning both in univariate (P= .01) and multivariate analyses (hazard ratio of 0.5246, P= .006), however CMV reactivation did not significantly affect the risk of relapse in our RIC cohort. These results confirm the protective effect of CMV reactivation on relapse in AML patients after allo-HCT reported by previous studies, however they suggest that this protective effect of CMV reactivation on relapse is influenced by the conditioning regimen used with the transplant.
PMCID: PMC4029772  PMID: 24120526
2.  Assessment of imipenem-cilastatin 500mg q6h, meropenem 1g q8h and meropenem 500mg q6h following cefepime use in adult patients with neutropenic fever 
Pharmacotherapy  2009;29(8):914-923.
Study objective
An alternative meropenem dosing strategy (500mg q6h) has been postulated to provide similar pharmacodynamics based on %T>MIC as traditional dosing with 1gm q8h while decreasing total daily dose. However, this dosing strategy has not been formally evaluated for empiric treatment of febrile neutropenic patients. The aim of this study was to compare clinical outcomes in patients treated with alternatively-dosed meropenem at 500mg q6h (Mero500q6), traditionally-dosed meropenem at 1gm q8h (Mero1q8), and imipenem-cilastatin at 500mg q6h (Imi500q6) following failure or intolerance of cefepime for febrile neutropenia.
A retrospective, single-center, observational cohort study was performed.
Barnes-Jewish Hospital, a 1,250 bed urban academic medical center in St. Louis, MO.
Adult neutropenic fever patients admitted to either the Hematologic Malignancy or Hematopoietic Stem Cell Transplant service.
A total of 127 patients were included: 40 patients treated with Imi500q6 from September 1, 2005, to August 31, 2006, and 87 patients treated with meropenem (Mero1q8=29, Mero500q6=58) from September 1, 2006, to August 31, 2007.
Measurements and main results
Primary outcomes including time to defervescence (median 3 vs. 2 vs. 3 days), need for additional antibiotics (20% vs. 17.2% vs. 13.8%), and time to additional antibiotics (median 5 vs. 2 vs. 1 days) were not statistically different between the Imi500q6, Mero1q8 and Mero500q6 groups, respectively. Differences in secondary outcomes including treatment duration (median 10 vs. 8 vs. 8 days), seizure incidence (0% vs. 0% vs. 0%), in-hospital mortality (5% vs. 6% vs. 7%), and 30-day mortality (12.5% vs. 6% vs. 14%) were not identified.
Mero500q6h yielded similar patient outcomes, including time to defervescence, need for additional antibiotics, duration of therapy, and mortality as compared to traditional dosing of meropenem and imipenem-cilastatin in adult patients with febrile neutropenia and had no observed adverse impact on clinical outcomes.
PMCID: PMC4256050  PMID: 19637944
imipenem-cilastatin; meropenem; neutropenic fever
3.  Dose Intensification of Daunorubicin and Cytarabine during Treatment of Adult Acute Lymphoblastic Leukemia: Results of Cancer and Leukemia Group B Study 19802 
Cancer  2012;119(1):90-98.
CALGB 19802, a phase II study, evaluated whether dose intensification of daunorubicin and cytarabine could improve disease-free survival (DFS) of adults with acute lymphoblastic leukemia (ALL), and whether high-dose systemic and intrathecal methotrexate could replace cranial radiotherapy for central nervous system (CNS) prophylaxis.
Patients and Methods
One hundred sixty-one eligible, previously untreated patients age 16–82 years (median, 40 years) were enrolled; 33 (20%) were ≥60years old.
One hundred twenty-eight patients (80%) achieved a complete remission (CR). Dose intensification of daunorubicin and cytarabine was feasible. With a median follow-up of 10.4 years for surviving patients, 5-year DFS was 25% (95% CI, 18–33%) and overall survival (OS) was 30% (95% CI, 23–37%). Patients <60 years who received the 80 mg/m2 dose of daunorubicin had a DFS of 33% (22–44%) and OS of 39% (29–49%) at 5 years. Eighty-four (52%) patients relapsed, including nine (6%) with isolated CNS relapses. Omission of cranial irradiation did not result in higher than historical CNS relapse rates.
Intensive systemic, oral, and intrathecal methotrexate dosing permitted omission of CNS irradiation. This intensive approach using higher doses of daunorubicin and cytarabine failed to result in an overall improvement in DFS or OS compared with historical CALGB studies. Future therapeutic strategies for adults with ALL should be tailored to specific age and molecular genetic subsets.
PMCID: PMC4220742  PMID: 22744771
4.  Clonal Architecture of Secondary Acute Myeloid Leukemia Defined by Single-Cell Sequencing 
PLoS Genetics  2014;10(7):e1004462.
Next-generation sequencing has been used to infer the clonality of heterogeneous tumor samples. These analyses yield specific predictions—the population frequency of individual clones, their genetic composition, and their evolutionary relationships—which we set out to test by sequencing individual cells from three subjects diagnosed with secondary acute myeloid leukemia, each of whom had been previously characterized by whole genome sequencing of unfractionated tumor samples. Single-cell mutation profiling strongly supported the clonal architecture implied by the analysis of bulk material. In addition, it resolved the clonal assignment of single nucleotide variants that had been initially ambiguous and identified areas of previously unappreciated complexity. Accordingly, we find that many of the key assumptions underlying the analysis of tumor clonality by deep sequencing of unfractionated material are valid. Furthermore, we illustrate a single-cell sequencing strategy for interrogating the clonal relationships among known variants that is cost-effective, scalable, and adaptable to the analysis of both hematopoietic and solid tumors, or any heterogeneous population of cells.
Author Summary
Human cancers are genetically diverse populations of cells that evolve over the course of their natural history or in response to the selective pressure of therapy. In theory, it is possible to infer how this variation is structured into related populations of cells based on the frequency of individual mutations in bulk samples, but the accuracy of these models has not been evaluated across a large number of variants in individual cells. Here, we report a strategy for analyzing hundreds of variants within a single cell, and we apply this method to assess models of tumor clonality derived from bulk samples in three cases of leukemia. The data largely support the predicted population structure, though they suggest specific refinements. This type of approach not only illustrates the biological complexity of human cancer, but it also has the potential to inform patient management. That is, precise knowledge of which variants are present in which populations of cells may allow physicians to more effectively target combinations of mutations and predict how patients will respond to therapy.
PMCID: PMC4091781  PMID: 25010716
5.  An exploratory phase 2 study of investigational Aurora A kinase inhibitor alisertib (MLN8237) in acute myelogenous leukemia and myelodysplastic syndromes 
Leukemia Research Reports  2014;3(2):58-61.
Alisertib (MLN8237) is an investigational, oral, selective, Aurora A kinase (AAK) inhibitor. In this phase 2 trial, 57 patients with acute myeloid leukemia (AML) or high-grade myelodysplastic syndrome received alisertib 50 mg BID for 7 days in 21-day cycles. Responses in 6/35 AML patients (17% response rate with an additional 49% stable disease, 34% transfusion independence) included 1 complete response lasting >1 year. No responses were observed in MDS patients. Adverse events >30% included diarrhea, fatigue, nausea, febrile neutropenia, and stomatitis. Results suggest modest activity in AML, supporting further research to better understand how AAK inhibition may induce leukemic cell senescence.
•The efficacy and safety of alisertib, an AAK inhibitor, in AML/MDS was evaluated.•57 patients received alisertib 50 mg twice-daily for 7 days in 21-day cycles.•The ORR in AML was 17%, with 49% stable disease; no responses were observed in MDS.•Common AEs included diarrhea, fatigue, nausea, febrile neutropenia, and stomatitis.•Our results suggest that alisertib has modest single-agent activity in AML.
PMCID: PMC4110881  PMID: 25068104
Aurora A kinase inhibitor; Alisertib; Safety; Acute myeloid leukemia (AML); Myelodysplastic syndrome (MDS)
6.  Myelodysplastic Syndromes 
PMCID: PMC4000017  PMID: 23847220
NCCN Clinical Practice Guidelines; NCCN Guidelines; myelodysplastic syndromes; chronic myelomonocytic leukemia; refractory anemia; cytopenias; treatment
7.  Peripheral-Blood Stem Cells versus Bone Marrow from Unrelated Donors 
The New England journal of medicine  2012;367(16):10.1056/NEJMoa1203517.
Randomized trials have shown that the transplantation of filgrastim-mobilized peripheral-blood stem cells from HLA-identical siblings accelerates engraftment but increases the risks of acute and chronic graft-versus-host disease (GVHD), as compared with the transplantation of bone marrow. Some studies have also shown that peripheral-blood stem cells are associated with a decreased rate of relapse and improved survival among recipients with high-risk leukemia.
We conducted a phase 3, multicenter, randomized trial of transplantation of peripheral-blood stem cells versus bone marrow from unrelated donors to compare 2-year survival probabilities with the use of an intention-to-treat analysis. Between March 2004 and September 2009, we enrolled 551 patients at 48 centers. Patients were randomly assigned in a 1:1 ratio to peripheral-blood stem-cell or bone marrow transplantation, stratified according to transplantation center and disease risk. The median follow-up of surviving patients was 36 months (interquartile range, 30 to 37).
The overall survival rate at 2 years in the peripheral-blood group was 51% (95% confidence interval [CI], 45 to 57), as compared with 46% (95% CI, 40 to 52) in the bone marrow group (P = 0.29), with an absolute difference of 5 percentage points (95% CI, −3 to 14). The overall incidence of graft failure in the peripheral-blood group was 3% (95% CI, 1 to 5), versus 9% (95% CI, 6 to 13) in the bone marrow group (P = 0.002). The incidence of chronic GVHD at 2 years in the peripheral-blood group was 53% (95% CI, 45 to 61), as compared with 41% (95% CI, 34 to 48) in the bone marrow group (P = 0.01). There were no significant between-group differences in the incidence of acute GVHD or relapse.
We did not detect significant survival differences between peripheral-blood stem-cell and bone marrow transplantation from unrelated donors. Exploratory analyses of secondary end points indicated that peripheral-blood stem cells may reduce the risk of graft failure, whereas bone marrow may reduce the risk of chronic GVHD. (Funded by the National Heart, Lung, and Blood Institute–National Cancer Institute and others; number, NCT00075816.)
PMCID: PMC3816375  PMID: 23075175
8.  Myelodysplastic Syndromes 
PMCID: PMC3768131  PMID: 21233243
NCCN Clinical Practice Guidelines; NCCN Guidelines; myelodysplastic syndromes; chronic myelomonocytic leukemia; refractory anemia; cytopenias; treatment
9.  The origin and evolution of mutations in Acute Myeloid Leukemia 
Cell  2012;150(2):264-278.
Most mutations in cancer genomes are thought to be acquired after the initiating event, which may cause genomic instability, driving clonal evolution. However, for acute myeloid leukemia (AML), normal karyotypes are common, and genomic instability is unusual. To better understand clonal evolution in AML, we sequenced the genomes of AML samples with a known initiating event (PML-RARA) vs. normal karyotype AML samples, and the exomes of hematopoietic stem/progenitor cells (HSPCs) from healthy people. Collectively, the data suggest that most of the mutations found in AML genomes are actually random events that occurred in HSPCs before they acquired the initiating mutation; the mutational history of that cell is “captured” as the clone expands. In many cases, only one or two additional, cooperating mutations are needed to generate the malignant founding clone. Cells from the founding clone can acquire additional cooperating mutations, yielding subclones that can contribute to disease progression and/or relapse.
PMCID: PMC3407563  PMID: 22817890
10.  Use of Cytomegalovirus Intravenous Immune Globulin for the Adjunctive Treatment of Cytomegalovirus in Hematopoietic Stem Cell Transplant Patients 
Pharmacotherapy  2010;30(6):554-561.
Study Objective
To describe characteristics and clinical outcomes of hematopoietic stem cell transplant (HSCT) patients who received adjunctive Cytomegalovirus Intravenous Immune Globulin (CMV-IVIG) for probable or proven cytomegalovirus (CMV) disease.
Retrospective cohort study.
A large, university-affiliated, tertiary-care medical center.
Thirty-five adult HSCT patients receiving at least one dose of CMV-IVIG for adjunctive treatment of probable or proven CMV disease over an eight-year period.
Measurements and Main Results
All-cause mortality at hospital discharge was the primary outcome. All patients received an allogeneic HSCT. Twenty-six patients had pneumonitis (74%), nine had enteritis (26%), and 29 had CMV viremia (83%). All patients received concomitant antiviral therapy; 31 (89%) received ganciclovir and 14 (40%) received foscarnet. All-cause mortality at hospital discharge was 49%. Patient characteristics associated with mortality included requiring intubation for CMV pneumonia (79% of non-survivors vs. 25% of survivors, p=0.016) and earlier disease onset following HSCT (median of 48 days for non-survivors vs. 106 days for survivors, p<0.001). In multivariable analysis, only requiring intubation for CMV pneumonia remained a significant risk factor for increased mortality. CMV-IVIG was attributed with a low rate of adverse events; mild hypertension (5.7%) and erythema/chills (2.9%) were most common.
The mortality rate in our population is similar to previous reports in the literature, and may be somewhat lower than rates reported with antiviral monotherapy. Our analysis suggests that factors associated with mortality include the need for intubation and, possibly, earlier onset of CMV disease following HSCT. CMV-IVIG appears to be well-tolerated in HSCT patients. These findings support further trials of CMV-IVIG efficacy in this setting.
PMCID: PMC3668347  PMID: 20500045
Cytomegalovirus intravenous immune globulin; Cytomegalovirus disease; Hematopoietic stem cell transplantation
11.  Recognizing and managing the expanded risk of tumor lysis syndrome in hematologic and solid malignancies 
Tumor lysis syndrome (TLS) is widely recognized as a serious adverse event associated with the cytotoxic therapies primarily used in hematologic cancers, such as Burkitt lymphoma and acute lymphoblastic leukemia. In recent years, TLS has been more widely observed, due at least in part to the availability of more effective cancer treatments. Moreover, TLS is seen with greater frequency in solid tumors, and particularly in bulky tumors with extensive metastases and tumors with organ or bone marrow involvement. The consequences of TLS include the serious morbidity and high risk of mortality associated with the condition itself. Additionally, TLS may delay or force an alteration in the patient’s chemotherapy regimen. The changing patterns of TLS, as well as its frequency, in the clinical setting, result in unnecessarily high rates of illness and/or fatality. Prophylactic measures are widely available for patients at risk of TLS, and are considered highly effective. The present article discusses the various manifestations of TLS, its risk factors and management options to prevent TLS from occurring.
PMCID: PMC3544586  PMID: 23237230
Acute renal failure; Allopurinol; Adverse events; Hematologic malignancies; Management; Prophylactic therapy; Solid tumors; Tumor lysis syndrome (TLS); Rasburicase; Uric acid
12.  Prognostic Significance of FDG-PET in Relapsed or Refractory Classical Hodgkin Lymphoma Treated with Standard Salvage Chemotherapy and Autologous Stem Cell Transplantation 
Positron emission tomography using [18F]fluorodeoxyglucose (FDG-PET) has emerged as the standard response assessment tool in front-line therapy for classical Hodgkin lymphoma (cHL). The ability of FDG-PET to predict outcomes in patients with relapsed cHL treated with modern standard salvage chemotherapy and autologous stem cell transplantation (ASCT) remains uncertain. Forty-six patients with relapsed/refractory cHL treated from 2001–2007 with standard salvage/ASCT therapy had FDG-PET available for blinded review. The results of pre-ASCT FDG-PET interpreted by the international harmonization project (IHP) criteria were compared to published prognostic models for prediction of event free survival (EFS) and overall survival (OS). Overall, 3 year EFS was 62% and OS was 78% with a median follow-up of 38 months. Pre-ASCT FDG-PET response significantly predicted 3 year EFS in FDG-PET negative (82%) versus FDG-PET positive (41%) patients (p=0.02). A trend was observed for 3 year OS comparing FDG-PET negative (91%) versus positive (64%) patients (p=0.08). Multivariate analysis demonstrated the independent prognostic significance of pre-ASCT FDG-PET for EFS with a HR of 3.2 (CI 1.1–9.0, p=0.03). Pre-ASCT FDG-PET scans predict EFS in patients with relapsed cHL patients treated with modern salvage/ASCT therapy, and warrant prospective evaluation.
PMCID: PMC3166401  PMID: 21601641
autologous stem cell transplantation; classical Hodgkin lymphoma; FDG-PET; prognosis
13.  Clonal Architecture of Secondary Acute Myeloid Leukemia 
The New England Journal of Medicine  2012;366(12):1090-1098.
The myelodysplastic syndromes are a group of hematologic disorders that often evolve into secondary acute myeloid leukemia (AML). The genetic changes that underlie progression from the myelodysplastic syndromes to secondary AML are not well understood.
We performed whole-genome sequencing of seven paired samples of skin and bone marrow in seven subjects with secondary AML to identify somatic mutations specific to secondary AML. We then genotyped a bone marrow sample obtained during the antecedent myelodysplastic-syndrome stage from each subject to determine the presence or absence of the specific somatic mutations. We identified recurrent mutations in coding genes and defined the clonal architecture of each pair of samples from the myelodysplastic-syndrome stage and the secondary-AML stage, using the allele burden of hundreds of mutations.
Approximately 85% of bone marrow cells were clonal in the myelodysplastic-syndrome and secondary-AML samples, regardless of the myeloblast count. The secondary-AML samples contained mutations in 11 recurrently mutated genes, including 4 genes that have not been previously implicated in the myelodysplastic syndromes or AML. In every case, progression to acute leukemia was defined by the persistence of an antecedent founding clone containing 182 to 660 somatic mutations and the outgrowth or emergence of at least one subclone, harboring dozens to hundreds of new mutations. All founding clones and subclones contained at least one mutation in a coding gene.
Nearly all the bone marrow cells in patients with myelodysplastic syndromes and secondary AML are clonally derived. Genetic evolution of secondary AML is a dynamic process shaped by multiple cycles of mutation acquisition and clonal selection. Recurrent gene mutations are found in both founding clones and daughter subclones. (Funded by the National Institutes of Health and others.)
PMCID: PMC3320218  PMID: 22417201
14.  Reduced Intensity Allogeneic Transplantation Provides High Event-Free And Overall Survival In Patients With Advanced Indolent B Cell Malignancies: CALGB 109901 
CALGB conducted a Phase II study to evaluate the safety and efficacy of a reduced-intensity conditioning regimen with allogeneic transplantation to treat patients with recurrent low grade B cell malignancies. Patients over age 18 with a diagnosis of relapsed, chemotherapy-sensitive disease underwent transplantation with a matched sibling donor and conditioning with cyclophosphamide (1 g/m2/d × 3) and fludarabine phosphate (25 mg/m2/d × 5). GVH prophylaxis included cyclosporine or tacrolimus plus low-dose methotrexate. Forty-four evaluable patients with a median age of 53 and median of two prior regimens were accrued. Sixteen patients had follicular NHL and 28 had histologies including 7 indolent B cell lymphomas, 4 mantle cell, 15 chronic lymphocytic leukemia, and 2 prolymphocytic leukemia pts. The six-month treatment-related mortality (TRM) was 2.4% and three-year TRM was 9%. Three-year event-free and overall survival were.75 and .81 for the follicular patients, .59 and .71 for the CLL/PLL patients, and .55 and .64 for the other histologies. The incidence of grade 2–4 acute graft vs host disease (GVHD) was 29% and extensive chronic GVHD was 18%. This report demonstrates that allogeneic sibling transplantation with a reduced intensity conditioning regimen is safe and efficacious for patients with advanced indolent B cell malignancies enrolled on a Cooperative Group study.
PMCID: PMC3134602  PMID: 21296675
15.  Clonal evolution in relapsed acute myeloid leukemia revealed by whole genome sequencing 
Nature  2012;481(7382):506-510.
Most patients with acute myeloid leukemia (AML) die from progressive disease after relapse, which is associated with clonal evolution at the cytogenetic level1,2. To determine the mutational spectrum associated with relapse, we sequenced the primary tumor and relapse genomes from 8 AML patients, and validated hundreds of somatic mutations using deep sequencing; this allowed us to precisely define clonality and clonal evolution patterns at relapse. Besides discovering novel, recurrently mutated genes (e.g. WAC, SMC3, DIS3, DDX41, and DAXX) in AML, we found two major clonal evolution patterns during AML relapse: 1) the founding clone in the primary tumor gained mutations and evolved into the relapse clone, or 2) a subclone of the founding clone survived initial therapy, gained additional mutations, and expanded at relapse. In all cases, chemotherapy failed to eradicate the founding clone. The comparison of relapse-specific vs. primary tumor mutations in all 8 cases revealed an increase in transversions, probably due to DNA damage caused by cytotoxic chemotherapy. These data demonstrate that AML relapse is associated with the addition of new mutations and clonal evolution, which is shaped in part by the chemotherapy that the patients receive to establish and maintain remissions.
PMCID: PMC3267864  PMID: 22237025
Nature Genetics  2011;44(1):53-57.
Myelodysplastic syndromes (MDS) are hematopoietic stem cell disorders that often progress to chemotherapy-resistant secondary acute myeloid leukemia (sAML). We used whole genome sequencing to perform an unbiased comprehensive screen to discover all the somatic mutations in a sAML sample and genotyped these loci in the matched MDS sample. Here we show that a missense mutation affecting the serine at codon 34 (S34) in U2AF1 was recurrently mutated in 13/150 (8.7%) de novo MDS patients, with suggestive evidence of an associated increased risk of progression to sAML. U2AF1 is a U2 auxiliary factor protein that recognizes the AG splice acceptor dinucleotide at the 3′ end of introns and mutations are located in highly conserved zinc fingers in U2AF11,2. Mutant U2AF1 promotes enhanced splicing and exon skipping in reporter assays in vitro. This novel, recurrent mutation in U2AF1 implicates altered pre-mRNA splicing as a potential mechanism for MDS pathogenesis.
PMCID: PMC3247063  PMID: 22158538
17.  Recurrent DNMT3A Mutations in Patients with Myelodysplastic Syndromes 
Alterations in DNA methylation have been implicated in the pathogenesis of myelodysplastic syndromes (MDS), although the underlying mechanism remains largely unknown. Methylation of CpG dinucleotides is mediated by DNA methyltransferases, including DNMT1, DNMT3A, and DNMT3B. DNMT3A mutations have recently been reported in patients with de novo acute myeloid leukemia (AML), providing a rationale for examining the status of DNMT3A in MDS samples. Here, we report the frequency of DNMT3A mutations in patients with de novo MDS, and their association with secondary AML. We sequenced all coding exons of DNMT3A using DNA from bone marrow and paired normal cells from 150 patients with MDS and identified 13 heterozygous mutations with predicted translational consequences in 12/150 patients (8.0%). Amino acid R882, located in the methyltransferase domain of DNMT3A, was the most common mutation site, accounting for 4/13 mutations. DNMT3A mutations were expressed in the majority of cells in all tested mutant samples regardless of blast counts, suggesting that DNMT3A mutations occur early in the course of MDS. Patients with DNMT3A mutations had worse overall survival compared to patients without DNMT3A mutations (p=0.005) and more rapid progression to AML (p=0.007), suggesting that DNMT3A mutation status may have prognostic value in de novo MDS.
PMCID: PMC3202965  PMID: 21415852
myelodysplastic syndrome; DNMT3A; mutation
18.  Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome 
The New England journal of medicine  2009;361(11):1058-1066.
The full complement of DNA mutations that are responsible for the pathogenesis of acute myeloid leukemia (AML) is not yet known.
We used massively parallel DNA sequencing to obtain a very high level of coverage (approximately 98%) of a primary, cytogenetically normal, de novo genome for AML with minimal maturation (AML-M1) and a matched normal skin genome.
We identified 12 acquired (somatic) mutations within the coding sequences of genes and 52 somatic point mutations in conserved or regulatory portions of the genome. All mutations appeared to be heterozygous and present in nearly all cells in the tumor sample. Four of the 64 mutations occurred in at least 1 additional AML sample in 188 samples that were tested. Mutations in NRAS and NPM1 had been identified previously in patients with AML, but two other mutations had not been identified. One of these mutations, in the IDH1 gene, was present in 15 of 187 additional AML genomes tested and was strongly associated with normal cytogenetic status; it was present in 13 of 80 cytogenetically normal samples (16%). The other was a nongenic mutation in a genomic region with regulatory potential and conservation in higher mammals; we detected it in one additional AML tumor. The AML genome that we sequenced contains approximately 750 point mutations, of which only a small fraction are likely to be relevant to pathogenesis.
By comparing the sequences of tumor and skin genomes of a patient with AML-M1, we have identified recurring mutations that may be relevant for pathogenesis.
PMCID: PMC3201812  PMID: 19657110
19.  DNMT3A Mutations in Acute Myeloid Leukemia 
The New England journal of medicine  2010;363(25):2424-2433.
The genetic alterations responsible for an adverse outcome in most patients with acute myeloid leukemia (AML) are unknown.
Using massively parallel DNA sequencing, we identified a somatic mutation in DNMT3A, encoding a DNA methyltransferase, in the genome of cells from a patient with AML with a normal karyotype. We sequenced the exons of DNMT3A in 280 additional patients with de novo AML to define recurring mutations.
A total of 62 of 281 patients (22.1%) had mutations in DNMT3A that were predicted to affect translation. We identified 18 different missense mutations, the most common of which was predicted to affect amino acid R882 (in 37 patients). We also identified six frameshift, six nonsense, and three splice-site mutations and a 1.5-Mbp deletion encompassing DNMT3A. These mutations were highly enriched in the group of patients with an intermediate-risk cytogenetic profile (56 of 166 patients, or 33.7%) but were absent in all 79 patients with a favorable-risk cytogenetic profile (P<0.001 for both comparisons). The median overall survival among patients with DNMT3A mutations was significantly shorter than that among patients without such mutations (12.3 months vs. 41.1 months, P<0.001). DNMT3A mutations were associated with adverse outcomes among patients with an intermediate-risk cytogenetic profile or FLT3 mutations, regardless of age, and were independently associated with a poor outcome in Cox proportional-hazards analysis.
DNMT3A mutations are highly recurrent in patients with de novo AML with an intermediate-risk cytogenetic profile and are independently associated with a poor outcome. (Funded by the National Institutes of Health and others.)
PMCID: PMC3201818  PMID: 21067377
20.  Use of whole genome sequencing to diagnose a cryptic fusion oncogene 
Whole genome sequencing (WGS) is becoming increasingly available for research purposes, but it has not yet been routinely used for clinical diagnosis.
To determine whether whole genome sequencing can identify cryptic, actionable mutations in a clinically relevant time frame.
Design, Setting, and Patient
We were referred a difficult diagnostic case of acute promyelocytic leukemia with no pathogenic X-RARA fusion identified by routine metaphase cytogenetics or interphase FISH. The patient was enrolled in an IRB approved protocol, with consent specifically tailored to the implications of whole genome sequencing. The protocol employs a ‘movable firewall,’ which maintains patient anonymity within the entire research team, but allows the research team to communicate medically relevant information to the treating physician.
Main Outcome Measure
Clinical relevance of whole genome sequencing and time to communicate validated results to the treating physician.
Massively parallel paired-end sequencing allowed us to identify a cytogenetically cryptic event: 77 kilobases from chromosome 15 was inserted en bloc into the second intron of the RARA gene on chromosome 17, resulting in a classic bcr3 PML-RARA fusion gene. RT-PCR subsequently validated the expression of the fusion transcript. Novel FISH probes identified two additional cases of t(15;17)-negative acute promyelocytic leukemia that had cytogenetically invisible insertions. Whole genome sequencing and validation were completed in seven weeks, and changed the treatment plan for the patient.
Whole genome sequencing can identify cytogenetically invisible oncogenes in a clinically relevant timeframe.
PMCID: PMC3156695  PMID: 21505136
21.  DNA sequencing of a cytogenetically normal acute myeloid leukemia genome 
Nature  2008;456(7218):66-72.
Lay Summary
Acute myeloid leukemia is a highly malignant hematopoietic tumor that affects about 13,000 adults yearly in the United States. The treatment of this disease has changed little in the past two decades, since most of the genetic events that initiate the disease remain undiscovered. Whole genome sequencing is now possible at a reasonable cost and timeframe to utilize this approach for unbiased discovery of tumor-specific somatic mutations that alter the protein-coding genes. Here we show the results obtained by sequencing a typical acute myeloid leukemia genome and its matched normal counterpart, obtained from the patient’s skin. We discovered 10 genes with acquired mutations; two were previously described mutations thought to contribute to tumor progression, and 8 were novel mutations present in virtually all tumor cells at presentation and relapse, whose function is not yet known. Our study establishes whole genome sequencing as an unbiased method for discovering initiating mutations in cancer genomes, and for identifying novel genes that may respond to targeted therapies.
We used massively parallel sequencing technology to sequence the genomic DNA of tumor and normal skin cells obtained from a patient with a typical presentation of FAB M1 Acute Myeloid Leukemia (AML) with normal cytogenetics. 32.7-fold ‘haploid’ coverage (98 billion bases) was obtained for the tumor genome, and 13.9-fold coverage (41.8 billion bases) was obtained for the normal sample. Of 2,647,695 well-supported Single Nucleotide Variants (SNVs) found in the tumor genome, 2,588,486 (97.7%) also were detected in the patient’s skin genome, limiting the number of variants that required further study. For the purposes of this initial study, we restricted our downstream analysis to the coding sequences of annotated genes: we found only eight heterozygous, non-synonymous somatic SNVs in the entire genome. All were novel, including mutations in protocadherin/cadherin family members (CDH24 and PCLKC), G-protein coupled receptors (GPR123 and EBI2), a protein phosphatase (PTPRT), a potential guanine nucleotide exchange factor (KNDC1), a peptide/drug transporter (SLC15A1), and a glutamate receptor gene (GRINL1B). We also detected previously described, recurrent somatic insertions in the FLT3 and NPM1 genes. Based on deep readcount data, we determined that all of these mutations (except FLT3) were present in nearly all tumor cells at presentation, and again at relapse 11 months later, suggesting that the patient had a single dominant clone containing all of the mutations. These results demonstrate the power of whole genome sequencing to discover novel cancer-associated mutations.
PMCID: PMC2603574  PMID: 18987736
22.  Cellular immune therapy for refractory cancers: novel therapeutic strategies 
Experimental hematology  2005;33(12):1427-1435.
Allogeneic stem cell transplantation is curative for certain cancers, but the high doses of chemotherapy and radiotherapy may lead to toxicity. This review summarizes the field of cellular immune therapy using very-low–dose conditioning for refractory cancers.
In our initial study, we treated 25 patients with refractory cancers with 100 cGy total body irradiation followed by allogeneic, nonmobilized peripheral blood cells. Eighteen patients received sibling and seven patients received unrelated cord blood stem cells.
None of the 13 patients with solid tumors achieved donor chimerism or had a sustained response. Twelve patients with hematologic malignancies were treated, 1 received a cord blood transplant and 11 received sibling donor cells. Nine of these 11 patients achieved donor chimerism, ranging from 5% to 100%. Four patients had sustained complete remission of their cancers. The patients who received cord blood transplants did not respond. Development of chimerism correlated with total previous myelotoxic chemotherapy (p < 0.001). We review additional studies in this area, including data in the haploidentical and unrelated donor setting. The data presented comprises studies performed at the four institutions represented by the authors, and a review of other pertinent studies in this area.
Cellular immune therapy is an emerging application of transplantation therapy, which may be appropriate for refractory cancers. New studies in solid tumors, and with alternative donors, will expand the application of this new and promising treatment.
PMCID: PMC1986765  PMID: 16338484

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