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1.  Second Malignant Neoplasms After Treatment of Childhood Acute Lymphoblastic Leukemia 
Journal of Clinical Oncology  2013;31(19):2469-2476.
Purpose
Second malignant neoplasms (SMNs) after diagnosis of childhood acute lymphoblastic leukemia (ALL) are rare events.
Patients and Methods
We analyzed data on risk factors and outcomes of 642 children with SMNs occurring after treatment for ALL from 18 collaborative study groups between 1980 and 2007.
Results
Acute myeloid leukemia (AML; n = 186), myelodysplastic syndrome (MDS; n = 69), and nonmeningioma brain tumor (n = 116) were the most common types of SMNs and had the poorest outcome (5-year survival rate, 18.1% ± 2.9%, 31.1% ± 6.2%, and 18.3% ± 3.8%, respectively). Five-year survival estimates for AML were 11.2% ± 2.9% for 125 patients diagnosed before 2000 and 34.1% ± 6.3% for 61 patients diagnosed after 2000 (P < .001); 5-year survival estimates for MDS were 17.1% ± 6.4% (n = 36) and 48.2% ± 10.6% (n = 33; P = .005). Allogeneic stem-cell transplantation failed to improve outcome of secondary myeloid malignancies after adjusting for waiting time to transplantation. Five-year survival rates were above 90% for patients with meningioma, Hodgkin lymphoma, thyroid carcinoma, basal cell carcinoma, and parotid gland tumor, and 68.5% ± 6.4% for those with non-Hodgkin lymphoma. Eighty-nine percent of patients with brain tumors had received cranial irradiation. Solid tumors were associated with cyclophosphamide exposure, and myeloid malignancy was associated with topoisomerase II inhibitors and starting doses of methotrexate of at least 25 mg/m2 per week and mercaptopurine of at least 75 mg/m2 per day. Myeloid malignancies with monosomy 7/5q− were associated with high hyperdiploid ALL karyotypes, whereas 11q23/MLL-rearranged AML or MDS was associated with ALL harboring translocations of t(9;22), t(4;11), t(1;19), and t(12;21) (P = .03).
Conclusion
SMNs, except for brain tumors, AML, and MDS, have outcomes similar to their primary counterparts.
doi:10.1200/JCO.2012.47.0500
PMCID: PMC3807139  PMID: 23690411
2.  Considerations in the design of clinical trials for pediatric acute lymphoblastic leukemia 
Clinical investigation  2013;3(9):10.4155/cli.13.71.
Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy. Although outcomes for children with ALL have improved dramatically over the last 50 years, ALL remains the leading cause of childhood cancer death. In addition, high-risk patient subsets can be identified with significantly inferior survival. In the current era of therapies directed at specific molecular targets, the use of conventional randomized Phase III trials to show benefit from a new treatment regimen may not be feasible when these biologically defined subsets are small. This review presents the traditional approaches to designing trials for children with ALL, as well as innovative approaches attempting to study the benefit of new treatments as reliably as possible for patient subsets with distinctive biological characteristics.
doi:10.4155/cli.13.71
PMCID: PMC3834963  PMID: 24273641
acute lymphoblastic leukemia; clinical trials; historical controls
3.  Children’s Oncology Group’s 2013 Blueprint for Research: Acute Lymphoblastic Leukemia 
Pediatric blood & cancer  2012;60(6):957-963.
Approximately 90% of the 2,000 children, adolescents, and young adults enrolled each year in Children’s Oncology Group acute lymphoblastic leukemia (ALL) trials will be cured. However, high-risk subsets with significantly inferior survival remain, including infants, newly diagnosed patients with age ≥10 years, white blood count ≥50,000/µl, poor early response or T-cell ALL, and relapsed ALL patients. Effective strategies to improve survival include better risk stratification, optimizing standard chemotherapy and combining targeted therapies with cytotoxic chemotherapy, the latter of which is dependent upon identification of key driver mutations present in ALL.
doi:10.1002/pbc.24420
PMCID: PMC4045498  PMID: 23255467
acute lymphoblastic leukemia (ALL); COG ALL trials
4.  Novel Susceptibility Variants at 10p12.31-12.2 for Childhood Acute Lymphoblastic Leukemia in Ethnically Diverse Populations 
Background
Acute lymphoblastic leukemia (ALL) is the most common cancer in children and the incidence of ALL varies by ethnicity. Although accumulating evidence indicates inherited predisposition to ALL, the genetic basis of ALL susceptibility in diverse ancestry has not been comprehensively examined.
Methods
We performed a multiethnic genome-wide association study in 1605 children with ALL and 6661 control subjects after adjusting for population structure, with validation in three replication series of 845 case subjects and 4316 control subjects. Association was tested by two-sided logistic regression.
Results
A novel ALL susceptibility locus at 10p12.31-12.2 (BMI1-PIP4K2A, rs7088318, P = 1.1×10−11) was identified in the genome-wide association study, with independent replication in European Americans, African Americans, and Hispanic Americans (P = .001, .009, and .04, respectively). Association was also validated at four known ALL susceptibility loci: ARID5B, IKZF1, CEBPE, and CDKN2A/2B. Associations at ARID5B, IKZF1, and BMI1-PIP4K2A variants were consistent across ethnicity, with multiple independent signals at IKZF1 and BMI1-PIP4K2A loci. The frequency of ARID5B and BMI1-PIP4K2A variants differed by ethnicity, in parallel with ethnic differences in ALL incidence. Suggestive evidence for modifying effects of age on genetic predisposition to ALL was also observed. ARID5B, IKZF1, CEBPE, and BMI1-PIP4K2A variants cumulatively conferred strong predisposition to ALL, with children carrying six to eight copies of risk alleles at a ninefold (95% confidence interval = 6.9 to 11.8) higher ALL risk relative to those carrying zero to one risk allele at these four single nucleotide polymorphisms.
Conclusions
These findings indicate strong associations between inherited genetic variation and ALL susceptibility in children and shed new light on ALL molecular etiology in diverse ancestry.
doi:10.1093/jnci/djt042
PMCID: PMC3691938  PMID: 23512250
5.  Modifications to Induction Therapy Decrease Risk of Early Death in Infants With Acute Lymphoblastic Leukemia Treated on Children’s Oncology Group P9407 
Pediatric blood & cancer  2012;59(5):834-839.
Background
Infants (<366 days of age) with acute lymphoblastic leukemia (ALL) have a poor prognosis. Most treatment failures occur within 6–9 months of diagnosis, primarily from relapse.
Procedure
The Children’s Oncology Group P9407 study was designed to test if early intensified treatment would improve outcome for infants with ALL. Due to a significant number of early deaths (< 90 days from enrollment), Induction therapy was amended three times. Cohorts 1 + 2 (n = 68), received identical Induction therapy except for reduced daunorubicin dose in Cohort 2. Cohort 3 (n = 141) received prednisone (40 mg/m2/day) instead of dexamethasone (10 mg/m2/day) and short infusion daunorubicin (30 minutes) instead of continuous infusion (48 hours), as well as additional supportive care measures throughout therapy.
Results
Early deaths occurred in 17/68 (25%) infants in Cohorts 1 + 2 and 8/141 (5.7%) infants in Cohort 3 (P < 0.0001). Among infants ≤90 days of age at diagnosis, early death occurred in 10/17 (58.8%) in Cohorts 1 + 2 and 4/27 (14.8%) in Cohort 3 (P = 0.006). Among infants >90 days of age at diagnosis, early death occurred in 7/51 (13.7%) in Cohorts 1 + 2 and 4/114 (3.5%) in Cohort 3 (P = 0.036). Bacterial, viral, and fungal infections were more common in Cohorts 1 + 2 versus Cohort 3.
Conclusions
Early morbidity and mortality for infants with ALL were reduced by substitution of prednisone (40 mg/m2/day) for dexamethasone (10 mg/m2/day), the delivery of daunorubicin over 30 minutes instead of a continuous infusion for 48 hours, and the provision of more specific supportive care measures.
doi:10.1002/pbc.24132
PMCID: PMC4008315  PMID: 22488662
infant acute lymphoblastic leukemia; mortality
6.  Treatment of Relapsed Precursor-B Acute Lymphoblastic Leukemia With Intensive Chemotherapy: POG (Pediatric Oncology Group) Study 9411 (SIMAL 9) 
Summary
Pediatric patients who experience a bone marrow relapse of precursor-B acute lymphoblastic leukemia are cured < 50% of the time. This study was designed to determine if intensification of therapies with known activity in this disease would improve the cure rates for patients with relapsed acute lymphoblastic leukemia. Patients were treated with intensive asparaginase during induction followed by repeated cycles of ifosfamide/etoposide and cytarabine/idarubicin. Patients with well-matched related donors were encouraged to undergo hematopoietic stem cell transplant as consolidation. The results of this study demonstrate no significant difference in disease-free survival in patients who received chemotherapy alone (45%) or chemotherapy followed by allogeneic stem cell transplant (50%). Furthermore, results from this study show no significant difference in event-free survival (39.9% ± 6.2%) or overall survival (41.6% ± 6.1%) at 8 years when compared with previous studies using less intensive regimens. Our results suggest that alternative therapies are needed to improve cure rates for pediatric patients with relapsed leukemia.
doi:10.1097/MPH.0b013e31829f3235
PMCID: PMC3957178  PMID: 23887024
relapsed precursor-B; ALL; intensive chemotherapy; POG study 9411; SIMAL 9
7.  THE GENOMIC LANDSCAPE OF HYPODIPLOID ACUTE LYMPHOBLASTIC LEUKEMIA 
Nature genetics  2013;45(3):242-252.
The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), a subtype of ALL characterized by aneuploidy and poor outcome, is unknown. Genomic profiling of 124 hypodiploid ALL cases, including whole genome and exome sequencing of 40 cases, identified two subtypes that differ in severity of aneuploidy, transcriptional profile and submicroscopic genetic alterations. Near haploid cases with 24–31 chromosomes harbor alterations targeting receptor tyrosine kinase- and Ras signaling (71%) and the lymphoid transcription factor IKZF3 (AIOLOS; 13%). In contrast, low hypodiploid ALL with 32–39 chromosomes are characterized by TP53 alterations (91.2%) which are commonly present in non-tumor cells, and alterations of IKZF2 (HELIOS; 53%) and RB1 (41%). Both near haploid and low hypodiploid tumors exhibit activation of Ras- and PI3K signaling pathways, and are sensitive to PI3K inhibitors, indicating that these drugs should be explored as a new therapeutic strategy for this aggressive form of leukemia.
doi:10.1038/ng.2532
PMCID: PMC3919793  PMID: 23334668
8.  Chemotherapy for Initial Induction Failures in Childhood Acute Lymphoblastic Leukemia: a Children’s Oncology Group Study (POG 8764) 
Children with acute lymphocytic leukemia (ALL) who fail to enter remission have a poor prognosis. In a previous study, 9 of 14 children with induction failure entered remission after teniposide (VM26) plus cytosine arabinoside (Ara-C). We attempted to confirm these results. Twenty children received teniposide (200 mg/m2/day IV) for 3 days and cytosine arabinoside (100 mg/m2/day continuous IV infusion) for 7 days. There were 3 complete and 3 partial responses. Two additional patients achieved a complete response after a second, shorter course of the same agents. Although VM26 plus Ara-C is an active combination for treatment of ALL induction failure, it does not appear as effective as in the initial report. Better treatments for this problem are needed.
doi:10.1097/MPH.0b013e318279afdd
PMCID: PMC3587335  PMID: 23211688
9.  Plasma Methotrexate, Red Blood Cell Methotrexate and Red Blood Cell Folate Values and Outcome in Children with Precursor B Acute Lymphoblastic Leukemia: A Report from the Children’s Oncology Group 
Plasma steady state methotrexate (MTX) level and red blood cell (RBC) MTX and folate concentrations were evaluated in 1124 children with newly diagnosed acute lymphoblastic leukemia (ALL) enrolled on the Pediatric Oncology Group studies 9005 (lower risk; Regimens A and C) and 9006 (higher risk; Regimen A). These regimens included intermediate dose MTX (1 gram/m2) given as a 24 hour infusion every other week for 12 doses during intensification. Plasma MTX level was evaluated at the end of MTX infusions. RBC MTX and folate concentrations were measured at the end of intensification. The five year continuous complete remission (CCR) was 76 ± 1.4% versus 85 ± 3.0% for those patients with steady state MTX levels ≤ and > 14 µM, respectively (p=0.0125). Hispanic children had significantly reduced median steady state MTX levels, 8.7 µM, compared to non-Hispanic children, 9.95 µM (p=0.0015), but this did not correlate with a difference in outcome. Neither RBC MTX, RBC folate, nor the RBC MTX:folate ratio identified children at increased risk of failure.
doi:10.1097/MPH.0b013e31820ee239
PMCID: PMC3771527  PMID: 21364468
Red Blood Cell Methotrexate and Folate; Childhood Acute Lymphoblastic Leukemia
10.  Acute Lymphoblastic Leukemia (ALL) with t(8;14)(q11.2;q32): B-cell disease with high proportion of Down Syndrome. A Children's Oncology Group (COG) Study 
Cancer genetics  2012;205(9):453-458.
The rare translocation t(8;14)(q11.2;q32) has been described in patients with B-cell acute lymphoblastic leukemia (ALL), particularly patients with Down Syndrome (DS).
We describe patients with t(8;14)(q11.2;q32) that were identified by the Children's Oncology Group (COG) ALL cytogenetics database, expanding our previous report of 10 patients with this translocation. Twenty-two such patients were treated with COG protocols. All patients had B-cell ALL and 7 (31.8%) had DS. None of the children with DS had an event, thus these patients had a superior estimated 5-year event-free survival (EFS) compared to non-DS patients (100% vs. 50.1 ± 17.7%; p=0.04). Only one patient (4.5%) had a concomitant Philadelphia chromosome t(9;22)(q34;q11.2). The cytogenetics data of two additional patients, who were not eligible for COG protocols, are also included in this report.
In conclusion, ALL patients with the recurring translocation t(8;14)(q11.2;q32) have B-cell phenotype and a high percentage have DS. Children with DS and t(8;14)(q11.2;q34) have improved event-free survival using standard COG therapy compared to non-DS patients. We did not find an increased number of patients with a concomitant Philadelphia chromosome in this population.
doi:10.1016/j.cancergen.2012.07.016
PMCID: PMC3432955  PMID: 22939398
Acute Lymphoblastic Leukemia; B-cell; translocation; Down Syndrome
11.  Alternate-Week versus Continuous Dexamethasone Scheduling on the Risk of Osteonecrosis in Acute Lymphoblastic Leukemia: Results from the CCG-1961 Randomized Cohort Trial 
The lancet oncology  2012;13(9):906-915.
SUMMARY
Background
Acute lymphoblastic leukemia (ALL) is curable in over 80% of children and adolescents with high-risk features. However, current therapies are associated with symptomatic osteonecrosis that disproportionately affects adolescents, often requires surgery, and is one of the most common causes of short- and long-term morbidity. A strategy is needed to lessen this risk.
Methods
CCG-1961, a multi-cohort randomized cooperative group trial, evaluated components of therapeutic intensification in 2056 eligible, newly diagnosed high-risk patients (white blood cell count ≥50×109/L and/or age ≥10 years). To address osteonecrosis, a novel alternate-week dexamethasone schedule (10 mg/m2/day on days 0-6 and 14-20) was compared to standard continuous dexamethasone (10 mg/m2/day on days 0-20) in randomized regimens with either double or single delayed intensification phases, respectively. Randomization was done based on a randomization schedule generated using permuted blocks within strata. Patients were prospectively monitored clinically for osteonecrosis, with confirmatory imaging of suspected sites. Primary analyses were performed on an intent-to-treat basis and focused on the estimation and comparison of cumulative incidence rates of osteonecrosis both overall and in patient subgroups (age, gender, marrow early response status); final results are herein reported. This study is registered with ClinicalTrials.gov, number NCT00002812.
Findings
Symptomatic osteonecrosis was diagnosed in 143 patients at 377 confirmed skeletal sites, resulting in 139 surgeries. The overall cumulative incidence of osteonecrosis was 7·7% (N=2056) at 5 years, correlating with age at ALL diagnosis (1-9 years 1·0% (N=769), 10-15 years 9·9% (N=1025), ≥16 years 20·0% (N=262), p<0·0001) and gender (≥10 years, female 15·7% (N=525) versus male 9·3% (N=762), p=0·0010). For patients ≥10 years old with a rapid response to induction therapy, the use of alternate-week dexamethasone during delayed intensification phases significantly reduced osteonecrosis incidence compared with continuous dexamethasone (8·7±2·1% (N=420) versus 17·0±2·9% (N=403), p=0·0005), especially those ≥16 years (11·3±5·3% (N=84) versus 37·5±11·1% (N=79), p=0·0003; females 17·2±8·1% (N=32) versus 43·9±14·1% (N=23), p=0·050; males 7·7±5·9% (N=53) versus 34·6±11·6% (N=56), p=0·0014).
Interpretation
Alternate-week dexamethasone during delayed intensification phases effectively reduces osteonecrosis risk in children and adolescents receiving intensified therapy for high-risk ALL.
doi:10.1016/S1470-2045(12)70274-7
PMCID: PMC3448283  PMID: 22901620
12.  Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia 
Cancer cell  2012;22(2):153-166.
SUMMARY
Genomic profiling has identified a subtype of high-risk B-progenitor acute lymphoblastic leukemia (B-ALL) with alteration of IKZF1, a gene expression profile similar to BCR-ABL1-positive ALL and poor outcome (Ph-like ALL). The genetic alterations that activate kinase signaling in Ph-like ALL are poorly understood. We performed transcriptome and whole genome sequencing on 15 cases of Ph-like ALL, and identified rearrangements involving ABL1, JAK2, PDGFRB, CRLF2 and EPOR, activating mutations of IL7R and FLT3, and deletion of SH2B3, which encodes the JAK2 negative regulator LNK. Importantly, several of these alterations induce transformation that is attenuated with tyrosine kinase inhibitors, suggesting the treatment outcome of these patients may be improved with targeted therapy.
doi:10.1016/j.ccr.2012.06.005
PMCID: PMC3422513  PMID: 22897847
13.  Pilot Study of Nelarabine in Combination With Intensive Chemotherapy in High-Risk T-Cell Acute Lymphoblastic Leukemia: A Report From the Children's Oncology Group 
Journal of Clinical Oncology  2012;30(22):2753-2759.
Purpose
Children's Oncology Group study AALL00P2 was designed to assess the feasibility and safety of adding nelarabine to a BFM 86–based chemotherapy regimen in children with newly diagnosed T-cell acute lymphoblastic leukemia (T-ALL).
Patients and Methods
In stage one of the study, eight patients with a slow early response (SER) by prednisone poor response (PPR; ≥ 1,000 peripheral blood blasts on day 8 of prednisone prephase) received chemotherapy plus six courses of nelarabine 400 mg/m2 once per day; four patients with SER by high minimal residual disease (MRD; ≥ 1% at day 36 of induction) received chemotherapy plus five courses of nelarabine; 16 patients with a rapid early response (RER) received chemotherapy without nelarabine. In stage two, all patients received six 5-day courses of nelarabine at 650 mg/m2 once per day (10 SER patients [one by MRD, nine by PPR]) or 400 mg/m2 once per day (38 RER patients; 12 SER patients [three by MRD, nine by PPR]).
Results
The only significant difference in toxicities was decreased neutropenic infections in patients treated with nelarabine (42% with v 81% without nelarabine). Five-year event-free survival (EFS) rates were 73% for 11 stage one SER patients and 67% for 22 stage two SER patients treated with nelarabine versus 69% for 16 stage one RER patients treated without nelarabine and 74% for 38 stage two RER patients treated with nelarabine. Five-year EFS for all patients receiving nelarabine (n = 70) was 73% versus 69% for those treated without nelarabine (n = 16).
Conclusion
Addition of nelarabine to a BFM 86–based chemotherapy regimen was well tolerated and produced encouraging results in pediatric patients with T-ALL, particularly those with a SER, who have historically fared poorly.
doi:10.1200/JCO.2011.40.8724
PMCID: PMC3402886  PMID: 22734022
14.  Phase II Trial of Trastuzumab in Combination With Cytotoxic Chemotherapy for Treatment of Metastatic Osteosarcoma With Human Epidermal Growth Factor Receptor 2 Overexpression: A Report From the Children's Oncology Group 
Journal of Clinical Oncology  2012;30(20):2545-2551.
Purpose
Despite efforts to intensify chemotherapy, survival for patients with metastatic osteosarcoma remains poor. Overexpression of human epidermal growth factor receptor 2 (HER2) in osteosarcoma has been shown to predict poor therapeutic response and decreased survival. This study tests the safety and feasibility of delivering biologically targeted therapy by combining trastuzumab with standard chemotherapy in patients with metastatic osteosarcoma and HER2 overexpression.
Patients and Methods
Among 96 evaluable patients with newly diagnosed metastatic osteosarcoma, 41 had tumors that were HER2-positive by immunohistochemistry. All patients received chemotherapy with cisplatin, doxorubicin, methotrexate, ifosfamide, and etoposide. Dexrazoxane was administered with doxorubicin to minimize the risk of cardiotoxicity from treatment with trastuzumab and anthracycline. Only patients with HER2 overexpression received concurrent therapy with trastuzumab given for 34 consecutive weeks.
Results
The 30-month event-free and overall survival rates for patients with HER2 overexpression treated with chemotherapy and trastuzumab were 32% and 59%, respectively. For patients without HER2 overexpression, treated with chemotherapy alone, the 30-month event-free and overall survival rates were 32% and 50%, respectively. There was no clinically significant short-term cardiotoxicity in patients treated with trastuzumab and doxorubicin.
Conclusion
Despite intensive chemotherapy plus trastuzumab for patients with HER2-positive disease, the outcome for all patients was poor, with no significant difference between the HER2-positive and HER2-negative groups. Although our findings suggest that trastuzumab can be safely delivered in combination with anthracycline-based chemotherapy and dexrazoxane, its therapeutic benefit remains uncertain. Definitive assessment of trastuzumab's potential role in treating osteosarcoma would require a randomized study of patients with HER2-positive disease.
doi:10.1200/JCO.2011.37.4546
PMCID: PMC3397787  PMID: 22665540
15.  Germline genetic variation and treatment response on CCG-1891 
Pediatric blood & cancer  2011;58(5):695-700.
Background
Recent studies suggest that polymorphisms in genes encoding enzymes involved in drug detoxification and metabolism may influence disease outcome in pediatric acute lymphoblastic leukemia (ALL). We sought to extend current knowledge by using standard and novel statistical methodology to examine polymorphic variants of genes and relapse risk, toxicity, and drug dose delivery in standard risk ALL.
Procedure
We genotyped and abstracted chemotherapy drug dose data from treatment roadmaps on 557 patients on the Children’s Cancer Group ALL study, CCG-1891. Fourteen common polymorphisms in genes involved in folate metabolism and/or phase I and II drug detoxification were evaluated individually and clique-finding methodology was employed for detection of significant gene-gene interactions.
Results
After controlling for known risk factors, polymorphisms in four genes: GSTP1*B (HR=1.94, p=0.047), MTHFR (HR=1.61, p=0.034), MTRR (HR=1.95, p=0.01), and TS (3R/4R, HR=3.69, p=0.007), were found to significantly increase relapse risk. One gene-gene pair, MTRR A/G and GSTM1 null genotype, significantly increased the risk of relapse after correction for multiple comparisons (p=0.012). Multiple polymorphisms were associated with various toxicities and there was no significant difference in dose of chemotherapy delivered by genotypes.
Conclusions
These data suggest that various polymorphisms play a role in relapse risk and toxicity during childhood ALL therapy and that genotype does not play a role in adjustment of drug dose administered. Additionally, gene-gene interactions may increase the risk of relapse in childhood ALL and the clique method may have utility in further exploring these interactions. childhood ALL therapy.
doi:10.1002/pbc.23192
PMCID: PMC3165089  PMID: 21618417
genotype; acute lymphoblastic leukemia; prognosis; toxicity; gene-gene interactions
16.  ARID5B Genetic Polymorphisms Contribute to Racial Disparities in the Incidence and Treatment Outcome of Childhood Acute Lymphoblastic Leukemia 
Journal of Clinical Oncology  2012;30(7):751-757.
Purpose
Recent genome-wide screens have identified genetic variations in ARID5B associated with susceptibility to childhood acute lymphoblastic leukemia (ALL). We sought to determine the contribution of ARID5B single nucleotide polymorphisms (SNPs) to racial disparities in ALL susceptibility and treatment outcome.
Patients and Methods
We compared the association between ARID5B SNP genotype and ALL susceptibility in whites (> 95% European genetic ancestry; 978 cases and 1,046 controls) versus in Hispanics (> 10% Native American ancestry; 330 cases and 541 controls). We determined the relationships between ARID5B SNP genotype and ALL relapse risk in 1,605 children treated on the Children's Oncology Group (COG) P9904/9905 clinical trials.
Results
Among 49 ARID5B SNPs interrogated, 10 were significantly associated with ALL susceptibility in both whites and Hispanics (P < .05), with risk alleles consistently more frequent in Hispanics than in whites. rs10821936 exhibited the most significant association in both races (P = 8.4 × 10−20 in whites; P = 1 × 10−6 in Hispanics), and genotype at this SNP was highly correlated with local Native American genetic ancestry (P = 1.8 × 10−8). Multivariate analyses in Hispanics identified an additional SNP associated with ALL susceptibility independent of rs10821936. Eight ARID5B SNPs were associated with both ALL susceptibility and relapse hazard; the alleles related to higher ALL incidence were always linked to poorer treatment outcome and were more frequent in Hispanics.
Conclusion
ARID5B polymorphisms are important determinants of childhood ALL susceptibility and treatment outcome, and they contribute to racial disparities in this disease.
doi:10.1200/JCO.2011.38.0345
PMCID: PMC3295551  PMID: 22291082
17.  Non-metastatic unresected paediatric non-rhabdomyosarcoma soft tissue sarcomas: Results of a pooled analysis from United States and European groups 
Background
Non-rhabdomyosarcoma soft tissue sarcomas (NRSTS) with initially unresected tumours represent a particular subset of patients with a poor outcome. Various international research groups pooled their data in a joint study in order to investigate prognostic variables and treatment modalities.
Methods
The study population consisted of 304 patients <21 years old treated between 1980 and 2005 using a multimodality therapeutic strategy.
Results
Synovial sarcoma and malignant peripheral nerve sheath tumour (MPNST) were the most frequent histotypes. Most patients received initial chemotherapy: major responses were recorded in 41% and minor in 16% of cases. Overall survival (OS) was 60.0% and 51.5% at 5 and 10 years, respectively, and it was significantly associated with patient's age, histological subtype, tumour site and size, quality of delayed surgical resection, radiotherapy administration and response to induction chemotherapy. MPNST associated to neurofibromatosis type 1 was the tumour type with the worst rate of response to chemotherapy and the worst outcome.
Conclusions
In unresected NRSTS patients, radiotherapy and delayed surgery are of crucial importance. Patients who respond to chemotherapy have better chance of survival. However, given the relatively poor prognosis, research on intensive multimodal treatment approaches and novel strategies is warranted.
doi:10.1016/j.ejca.2010.11.013
PMCID: PMC3539303  PMID: 21145727
Non-rhabdomyosarcoma soft tissue sarcomas; Unresected sarcoma; Paediatric sarcoma; Synovial sarcoma, malignant peripheral nerve sheath tumour; Chemotherapy, response to chemotherapy; Radiotherapy; Surgery; Prognostic factors
18.  Outcomes after Induction Failure in Childhood Acute Lymphoblastic Leukemia 
The New England Journal of Medicine  2012;366(15):1371-1381.
BACKGROUND
Failure of remission-induction therapy is a rare but highly adverse event in children and adolescents with acute lymphoblastic leukemia (ALL).
METHODS
We identified induction failure, defined by the persistence of leukemic blasts in blood, bone marrow, or any extramedullary site after 4 to 6 weeks of remission-induction therapy, in 1041 of 44,017 patients (2.4%) 0 to 18 years of age with newly diagnosed ALL who were treated by a total of 14 cooperative study groups between 1985 and 2000. We analyzed the relationships among disease characteristics, treatments administered, and outcomes in these patients.
RESULTS
Patients with induction failure frequently presented with high-risk features, including older age, high leukocyte count, leukemia with a T-cell phenotype, the Philadelphia chromosome, and 11q23 rearrangement. With a median follow-up period of 8.3 years (range, 1.5 to 22.1), the 10-year survival rate (±SE) was estimated at only 32±1%. An age of 10 years or older, T-cell leukemia, the presence of an 11q23 rearrangement, and 25% or more blasts in the bone marrow at the end of induction therapy were associated with a particularly poor outcome. High hyperdiploidy (a modal chromosome number >50) and an age of 1 to 5 years were associated with a favorable outcome in patients with precursor B-cell leukemia. Allogeneic stem-cell transplantation from matched, related donors was associated with improved outcomes in T-cell leukemia. Children younger than 6 years of age with precursor B-cell leukemia and no adverse genetic features had a 10-year survival rate of 72±5% when treated with chemotherapy only.
CONCLUSIONS
Pediatric ALL with induction failure is highly heterogeneous. Patients who have T-cell leukemia appear to have a better outcome with allogeneic stem-cell transplantation than with chemotherapy, whereas patients who have precursor B-cell leukemia without other adverse features appear to have a better outcome with chemotherapy. (Funded by Deutsche Krebshilfe and others.)
doi:10.1056/NEJMoa1110169
PMCID: PMC3374496  PMID: 22494120
19.  Augmented Therapy Improves Outcome For Pediatric High Risk Acute Lymphocytic Leukemia: Results Of Children’s Oncology Group Trial P9906 
Pediatric blood & cancer  2011;57(4):569-577.
Background
The augmented BFM regimen improves outcome for children with NCI high acute lymphoblastic leukemia (ALL). Patient age, sex, and presenting white blood cell count (WBC) can be used to identify a subset of approximately 12% of children with B-precursor ALL that had a 5-year continuous complete remission (CCR) rate of only about 50% on earlier Pediatric Oncology Group (POG) trials.
Procedures
Children’s Oncology Group trial P9906 evaluated a modified augmented BFM regimen in 267 patients with particularly high risk B-precursor ALL. Minimal residual disease (MRD) was assessed in blood at day 8 and in marrow at day 29 of Induction and correlated with outcome.
Results
The 5-year CCR probability for patients in P9906 was significantly better than that observed for similar patients on POG trials 8602/9006 (62.2 ±3.7% versus 50.6 ±2.4%; p=0.0007) but similar to POG 9406 (63.5±2.4%; p=0.81). Interim analysis showed poor central nervous system (CNS) control, especially in patients with initial WBC ≥100,000/microliter. Day 29 marrow MRD positive (>=0.01%) vs. negative patients had 5 year CCR rates of 37.1±7.4% vs. 72.6±4.3%; day 8 blood MRD positive vs. negative patients had 5 year CCR rates of 57.1 ±4.6 % vs.83.6±6.3%. End induction marrow MRD predicted marrow but not CNS relapse. In multivariate analysis, day 29 MRD>0.01%, initial WBC≥100,000/µl, male gender, and day 8 blood MRD>0.01% were significant prognostic factors.
Conclusions
Augmented BFM therapy improved outcome for children with higher risk ALL. Day 8 blood and day 29 marrow MRD were strong prognostic factors in these patients.
doi:10.1002/pbc.22944
PMCID: PMC3136564  PMID: 21360654
Acute lymphocytic leukemia; Phase III clinical trial; Prognostic factors; Minimal residual disease
20.  The genetic basis of early T-cell precursor acute lymphoblastic leukaemia 
Nature  2012;481(7380):157-163.
Early T-cell precursor acute lymphoblastic leukaemia (ETP ALL) is an aggressive malignancy of unknown genetic basis. We performed whole-genome sequencing of 12 ETP ALL cases and assessed the frequency of the identified somatic mutations in 94 T-cell acute lymphoblastic leukaemia cases. ETP ALL was characterized by activating mutations in genes regulating cytokine receptor and RAS signalling (67% of cases; NRAS, KRAS, FLT3, IL7R, JAK3, JAK1, SH2B3 and BRAF), inactivating lesions disrupting haematopoietic development (58%; GATA3, ETV6, RUNX1, IKZF1 and EP300) and histone-modifying genes (48%; EZH2, EED, SUZ12, SETD2 and EP300). We also identified new targets of recurrent mutation including DNM2, ECT2L and RELN. The mutational spectrum is similar to myeloid tumours, and moreover, the global transcriptional profile of ETP ALL was similar to that of normal and myeloid leukaemia haematopoietic stem cells. These findings suggest that addition of myeloid-directed therapies might improve the poor outcome of ETP ALL.
doi:10.1038/nature10725
PMCID: PMC3267575  PMID: 22237106
22.  Analysis of the Role of Hematopoietic Stem-Cell Transplantation in Infants With Acute Lymphoblastic Leukemia in First Remission and MLL Gene Rearrangements: A Report From the Children's Oncology Group 
Journal of Clinical Oncology  2010;29(2):214-222.
Purpose
Although the majority of children with acute lymphoblastic leukemia (ALL) are cured with current therapy, the event-free survival (EFS) of infants with ALL, particularly those with mixed lineage leukemia (MLL) gene rearrangements, is only 30% to 40%. Relapse has been the major source of treatment failure for these patients. The parallel Children's Cancer Group (CCG) 1953 and Pediatric Oncology Group (POG) 9407 studies were designed to test the hypothesis that more intensive therapy, including dose intensification of chemotherapy, and hematopoietic stem-cell transplantation (HSCT) would improve the outcome for this group of patients.
Patients and Methods
One hundred eighty-nine infants (CCG 1953, n = 115; POG 9407, n = 74) were enrolled between October 1996 and August 2000. For infants with the MLL gene rearrangement and an appropriate donor, HSCT was the preferred treatment on CCG 1953 and investigator option on POG 9407 after completion of the second phase of therapy. Fifty-three infants underwent HSCT.
Results
The 5-year EFS rate was 48.8% (95% CI, 33.9% to 63.7%) in patients who received HSCT and 48.7% (95% CI, 33.8% to 63.6%) in patients treated with chemotherapy alone (P = .60). Transplantation outcomes were not affected by the preparatory regimen or donor source.
Conclusion
Our data suggest that routine use of HSCT for infants with MLL-rearranged ALL is not indicated. However, limited by small numbers, this study should not be considered the definitive answer to this question.
doi:10.1200/JCO.2009.26.8938
PMCID: PMC3058277  PMID: 21135279
23.  Folylpolyglutamate Synthetase Gene Transcription is Regulated by a Multiprotein Complex that Binds the TEL-AML1 Fusion in Acute Lymphoblastic Leukemia 
Leukemia research  2010;34(12):1601-1609.
Acute Lymphoblastic Leukemia (ALL) non-random fusions influence clinical outcome and alter the accumulation of MTX-PGs in vivo. Analysis of primary ALL samples uncovered subtype-specific patterns of folate gene expression. Using an FPGS-luciferase reporter gene assay, we determined that E2A-PBX1 and TEL-AML1 expression decreased FPGS transcription. ChIP assays uncovered HDAC1,AML1, mSin3A, E2F, and Rb interactions with the FPGS promoter region. We demonstrate that FPGS expression is epigenetically regulated through binding of selected ALL fusions to a multiprotein complex, which also controls the cell cycle dependence of FPGS expression. This study provides insights into the pharmacogenomics of MTX in ALL subtypes.
doi:10.1016/j.leukres.2010.05.012
PMCID: PMC2946984  PMID: 20538338
FPGS; TEL-AML1; Rb/E2F; Chromatin remodeling; ALL; leukemia; HDAC1; methotrexate
24.  The use of central laboratories and remote electronic data capture to risk-adjust therapy for pediatric acute lymphoblastic leukemia and neuroblastoma 
Seminars in oncology  2010;37(1):53-59.
The Children’s Oncology Group (COG) is a National Cancer Institute sponsored cooperative clinical trials group with the primary mission of conducting pediatric cancer clinical trials. COG has complex risk classification systems that are used to deliver risk-stratified therapy for many pediatric cances, including clinical trials for Acute Lymphoblastic Leukemia (ALL) and Neuroblastoma (NB). Classification of patients is based on biological, clinical, and genomic data obtained at initial diagnosis and during the initial phases of therapy. The COG web-based remote data entry (RDE) system enables submission of data in real time from central laboratories and treating institutions. The data are then used in an automated fashion to determine the risk group and corresponding treatment assignment for individual patients enrolled in COG clinical trials.
doi:10.1053/j.seminoncol.2009.12.007
PMCID: PMC2843557  PMID: 20172365
25.  Improved Early Event-Free Survival With Imatinib in Philadelphia Chromosome–Positive Acute Lymphoblastic Leukemia: A Children's Oncology Group Study 
Journal of Clinical Oncology  2009;27(31):5175-5181.
Purpose
Imatinib mesylate is a targeted agent that may be used against Philadelphia chromosome–positive (Ph+) acute lymphoblastic leukemia (ALL), one of the highest risk pediatric ALL groups.
Patients and Methods
We evaluated whether imatinib (340 mg/m2/d) with an intensive chemotherapy regimen improved outcome in children ages 1 to 21 years with Ph+ ALL (N = 92) and compared toxicities to Ph− ALL patients (N = 65) given the same chemotherapy without imatinib. Exposure to imatinib was increased progressively in five patient cohorts that received imatinib from 42 (cohort 1; n = 7) to 280 continuous days (cohort 5; n = 50) before maintenance therapy. Patients with human leukocyte antigen (HLA) –identical sibling donors underwent blood and marrow transplantation (BMT) with imatinib given for 6 months following BMT.
Results
Continuous imatinib exposure improved outcome in cohort 5 patients with a 3-year event-free survival (EFS) of 80% ± 11% (95% CI, 64% to 90%), more than twice historical controls (35% ± 4%; P < .0001). Three-year EFS was similar for patients in cohort 5 treated with chemotherapy plus imatinib (88% ± 11%; 95% CI, 66% to 96%) or sibling donor BMT (57% ± 22%; 95% CI, 30.4% to 76.1%). There were no significant toxicities associated with adding imatinib to intensive chemotherapy. The higher imatinib dosing in cohort 5 appears to improve survival by having an impact on the outcome of children with a higher burden of minimal residual disease after induction.
Conclusion
Imatinib plus intensive chemotherapy improved 3-year EFS in children and adolescents with Ph+ ALL, with no appreciable increase in toxicity. BMT plus imatinib offered no advantage over BMT alone. Additional follow-up is required to determine the impact of this treatment on long-term EFS and determine whether chemotherapy plus imatinib can replace BMT.
doi:10.1200/JCO.2008.21.2514
PMCID: PMC2773475  PMID: 19805687

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