Cheng Cheng

Summary

Affiliation: St. Jude Children's Research Hospital
Country: USA

Publications

  1. ncbi request reprint Statistical significance threshold criteria for analysis of microarray gene expression data
    Cheng Cheng
    Department of Biostatistics, St Jude Children s Research Hospital
    Stat Appl Genet Mol Biol 3:Article36. 2004
  2. pmc False discovery rate paradigms for statistical analyses of microarray gene expression data
    Cheng Cheng
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, TN, USA
    Bioinformation 1:436-46. 2007
  3. pmc Integration of diverse statistical evidence of gene-trait association in systems biology studies
    Cheng Cheng
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Chem Biodivers 9:935-44. 2012
  4. ncbi request reprint Design options for case-control studies of gene-environment interactions
    Cheng Cheng
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, Tennessee
    Pediatr Blood Cancer 48:373-4. 2007
  5. pmc Interval estimation of quantile ratios applied to anti-cancer drug screening by xenograft experiments
    Cheng Cheng
    Department of Biostatistics, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 2794, USA
    Stat Med 29:2669-78. 2010
  6. pmc Treating childhood acute lymphoblastic leukemia without cranial irradiation
    Ching Hon Pui
    Department of Oncology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    N Engl J Med 360:2730-41. 2009
  7. pmc Acquired variation outweighs inherited variation in whole genome analysis of methotrexate polyglutamate accumulation in leukemia
    Deborah French
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, TN 38105 2794, USA
    Blood 113:4512-20. 2009
  8. pmc Genome-wide interrogation of germline genetic variation associated with treatment response in childhood acute lymphoblastic leukemia
    Jun J Yang
    St Jude Children s Research Hospital, Memphis, TN 38105, USA
    JAMA 301:393-403. 2009
  9. ncbi request reprint Identification of genes associated with chemotherapy crossresistance and treatment response in childhood acute lymphoblastic leukemia
    Sanne Lugthart
    Hematological Malignancy Program, St Jude Children s Research Hospital, Memphis, Tennessee 38105, USA
    Cancer Cell 7:375-86. 2005
  10. pmc Novel susceptibility variants at 10p12.31-12.2 for childhood acute lymphoblastic leukemia in ethnically diverse populations
    Heng Xu
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, TN 38105 3678, USA
    J Natl Cancer Inst 105:733-42. 2013

Collaborators

Detail Information

Publications104 found, 100 shown here

  1. ncbi request reprint Statistical significance threshold criteria for analysis of microarray gene expression data
    Cheng Cheng
    Department of Biostatistics, St Jude Children s Research Hospital
    Stat Appl Genet Mol Biol 3:Article36. 2004
    ..A guideline for using these criteria is provided. Splus/R code is available from the corresponding author upon request...
  2. pmc False discovery rate paradigms for statistical analyses of microarray gene expression data
    Cheng Cheng
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, TN, USA
    Bioinformation 1:436-46. 2007
    ..The goal is not to do an exhaustive literature survey, but rather to review the current state of the field...
  3. pmc Integration of diverse statistical evidence of gene-trait association in systems biology studies
    Cheng Cheng
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Chem Biodivers 9:935-44. 2012
    ..A novel integrated statistical analysis procedure is developed in this paper and is illustrated by an application in studying childhood leukemia...
  4. ncbi request reprint Design options for case-control studies of gene-environment interactions
    Cheng Cheng
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, Tennessee
    Pediatr Blood Cancer 48:373-4. 2007
  5. pmc Interval estimation of quantile ratios applied to anti-cancer drug screening by xenograft experiments
    Cheng Cheng
    Department of Biostatistics, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 2794, USA
    Stat Med 29:2669-78. 2010
    ....
  6. pmc Treating childhood acute lymphoblastic leukemia without cranial irradiation
    Ching Hon Pui
    Department of Oncology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    N Engl J Med 360:2730-41. 2009
    ..Prophylactic cranial irradiation has been a standard treatment in children with acute lymphoblastic leukemia (ALL) who are at high risk for central nervous system (CNS) relapse...
  7. pmc Acquired variation outweighs inherited variation in whole genome analysis of methotrexate polyglutamate accumulation in leukemia
    Deborah French
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, TN 38105 2794, USA
    Blood 113:4512-20. 2009
    ..We conclude that acquired genetic variation in leukemia cells has a stronger influence on MTXPG accumulation than inherited genetic variation...
  8. pmc Genome-wide interrogation of germline genetic variation associated with treatment response in childhood acute lymphoblastic leukemia
    Jun J Yang
    St Jude Children s Research Hospital, Memphis, TN 38105, USA
    JAMA 301:393-403. 2009
    ..Pediatric acute lymphoblastic leukemia (ALL) is the prototype for a drug-responsive malignancy. Although cure rates exceed 80%, considerable unexplained interindividual variability exists in treatment response...
  9. ncbi request reprint Identification of genes associated with chemotherapy crossresistance and treatment response in childhood acute lymphoblastic leukemia
    Sanne Lugthart
    Hematological Malignancy Program, St Jude Children s Research Hospital, Memphis, Tennessee 38105, USA
    Cancer Cell 7:375-86. 2005
    ..The expression of these genes discriminated treatment outcome in two independent patient populations, identifying a subset of patients with a markedly inferior outcome (37% +/- 13% 5 year DFS)...
  10. pmc Novel susceptibility variants at 10p12.31-12.2 for childhood acute lymphoblastic leukemia in ethnically diverse populations
    Heng Xu
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, TN 38105 3678, USA
    J Natl Cancer Inst 105:733-42. 2013
    ..Although accumulating evidence indicates inherited predisposition to ALL, the genetic basis of ALL susceptibility in diverse ancestry has not been comprehensively examined...
  11. pmc Germline genetic variation in an organic anion transporter polypeptide associated with methotrexate pharmacokinetics and clinical effects
    Lisa R Treviño
    St Jude Children s Research Hospital, Memphis, TN 38105 2794, USA
    J Clin Oncol 27:5972-8. 2009
    ..Our aim was to identify the genetic basis of interindividual variability in methotrexate pharmacokinetics in children with newly diagnosed acute lymphoblastic leukemia (ALL)...
  12. pmc The SWI/SNF chromatin-remodeling complex and glucocorticoid resistance in acute lymphoblastic leukemia
    Nicolas Pottier
    Hematological Malignancies Program, St Jude Children s Research Hospital, Memphis, TN, USA
    J Natl Cancer Inst 100:1792-803. 2008
    ....
  13. pmc Improved prognosis for older adolescents with acute lymphoblastic leukemia
    Ching Hon Pui
    St Jude Children s Research Hospital, Memphis, TN 38105, USA
    J Clin Oncol 29:386-91. 2011
    ..We reviewed the outcome of older adolescents (age 15 to 18 years) treated in four consecutive Total Therapy studies to determine if recent improved treatment extended to this high-risk group...
  14. pmc Genome-wide study of methotrexate clearance replicates SLCO1B1
    Laura B Ramsey
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Blood 121:898-904. 2013
    ..This study is registered at http://www.clinicaltrials.gov as NCT00005585 and NCT00005596...
  15. pmc Genome-wide association study identifies germline polymorphisms associated with relapse of childhood acute lymphoblastic leukemia
    Jun J Yang
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Blood 120:4197-204. 2012
    ..All trials are registered at www.clinicaltrials.gov or www.cancer.gov (COG P9904: NCT00005585; COG P9905: NCT00005596; COG P9906: NCT00005603; St Jude Total XIIIB: NCI-T93-0101D; and St Jude Total XV: NCT00137111)...
  16. pmc Dexamethasone exposure and asparaginase antibodies affect relapse risk in acute lymphoblastic leukemia
    Jitesh D Kawedia
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, TN 38105 2794, USA
    Blood 119:1658-64. 2012
    ..019). In conclusion, systemic clearance of dexamethasone is higher in patients with anti-asparaginase antibodies. Lower exposure to both drugs was associated with an increased risk of relapse...
  17. pmc Impact of tyrosine kinase inhibitors on minimal residual disease and outcome in childhood Philadelphia chromosome-positive acute lymphoblastic leukemia
    Sima Jeha
    Department of Oncology, St Jude Children s Research Hospital, Memphis, Tennessee
    Cancer 120:1514-9. 2014
    ..To date, no data are available on the impact of TKIs on minimal residual disease (MRD) at the end of induction therapy among patients who have a poor early response to 2 weeks of induction therapy that does not include TKIs...
  18. ncbi request reprint Risk of adverse events after completion of therapy for childhood acute lymphoblastic leukemia
    Ching Hon Pui
    Department of Hematology Oncology, St Jude Children s Research Hospital, Memphis, TN 38105 2794, USA
    J Clin Oncol 23:7936-41. 2005
    ..Our goal was to use the information to further refine therapy and advance cure rates...
  19. pmc A set of genes that regulate cell proliferation predicts treatment outcome in childhood acute lymphoblastic leukemia
    Christian Flotho
    Departments of Pathology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Blood 110:1271-7. 2007
    ..Incorporation of the expression levels of these genes into existing strategies of risk classification could improve clinical management...
  20. pmc Rare versus common variants in pharmacogenetics: SLCO1B1 variation and methotrexate disposition
    Laura B Ramsey
    Pharmaceutical Sciences Department, St Jude Children s Research Hospital, Memphis, Tennessee 38105, USA
    Genome Res 22:1-8. 2012
    ..8% of SLCO1B1's effects (1.9% of total variation) and had larger effect sizes than common NS variants. Our results show that rare variants are likely to have an important effect on pharmacogenetic phenotypes...
  21. pmc Methotrexate-induced neurotoxicity and leukoencephalopathy in childhood acute lymphoblastic leukemia
    Deepa Bhojwani
    All authors St Jude Children s Research Hospital and Deepa Bhojwani, Jun J Yang, Hiroto Inaba, Jeffrey E Rubnitz, Monika L Metzger, Scott C Howard, Raul C Ribeiro, Sima Jeha, John T Sandlund, and Ching Hon Pui, University of Tennessee Health Sciences Center, College of Medicine, Memphis, TN
    J Clin Oncol 32:949-59. 2014
    ....
  22. pmc Prognostic significance of CD20 expression in childhood B-cell precursor acute lymphoblastic leukemia
    Sima Jeha
    Department of Hematology Oncology, St Jude Children s Research Hospital, 332 N Lauderdale St, Memphis, TN 38105, USA
    Blood 108:3302-4. 2006
    ..9% versus 78% +/- 3.1% (P = .08). These data suggest that CD20 expression is not associated with inferior outcome in pediatric patients treated with contemporary regimens...
  23. pmc ARID5B genetic polymorphisms contribute to racial disparities in the incidence and treatment outcome of childhood acute lymphoblastic leukemia
    Heng Xu
    St Jude Children s Research Hospital, Memphis, TN 38105 3678, USA
    J Clin Oncol 30:751-7. 2012
    ..We sought to determine the contribution of ARID5B single nucleotide polymorphisms (SNPs) to racial disparities in ALL susceptibility and treatment outcome...
  24. ncbi request reprint Robust estimation of the false discovery rate
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital 332 N Lauderdale Street, Memphis, TN 38135, USA
    Bioinformatics 22:1979-87. 2006
    ..Therefore, it is difficult to reliably estimate the FDR when p-values are discrete or based on one-sided tests...
  25. ncbi request reprint Lymphoid gene expression as a predictor of risk of secondary brain tumors
    Mathew J Edick
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, University of Tennessee, Memphis, Tennessee, USA
    Genes Chromosomes Cancer 42:107-16. 2005
    ..These data suggest that gene expression profiling from accessible tissues may identify targets involved in therapy-related malignancies in unrelated tissues...
  26. pmc Between-course targeting of methotrexate exposure using pharmacokinetically guided dosage adjustments
    Jennifer L Pauley
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 3678, USA
    Cancer Chemother Pharmacol 72:369-78. 2013
    ..It is advantageous to individualize high-dose methotrexate (HDMTX) to maintain adequate exposure while minimizing toxicities. Previously, we accomplished this through within-course dose adjustments...
  27. pmc Early T-cell precursor leukaemia: a subtype of very high-risk acute lymphoblastic leukaemia
    Elaine Coustan-Smith
    Department of Oncology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Lancet Oncol 10:147-56. 2009
    ..We studied leukaemic cells, collected at diagnosis, to identify cases with ETP features and determine their clinical outcome...
  28. pmc Integrated analysis of pharmacologic, clinical and SNP microarray data using Projection Onto the Most Interesting Statistical Evidence with Adaptive Permutation Testing
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Int J Data Min Bioinform 5:143-57. 2011
    ..In the analysis of a paediatric leukaemia data set, PROMISE effectively identifies genomic features that exhibit a biologically meaningful pattern of association with multiple endpoint variables...
  29. pmc Ancestry and pharmacogenomics of relapse in acute lymphoblastic leukemia
    Jun J Yang
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, Tennessee, USA
    Nat Genet 43:237-41. 2011
    ..017). Ancestry-related differences in relapse risk were abrogated by the addition of a single extra phase of chemotherapy, indicating that modifications to therapy can mitigate the ancestry-related risk of relapse...
  30. pmc Reference alignment of SNP microarray signals for copy number analysis of tumors
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
    Bioinformatics 25:315-21. 2009
    ..In our study of acute lymphoblastic leukemia, RSA-RAP gives copy number analysis results that show substantially better concordance with cytogenetics than do two other alignment procedures...
  31. ncbi request reprint Improved outcome for children with acute lymphoblastic leukemia: results of Total Therapy Study XIIIB at St Jude Children's Research Hospital
    Ching Hon Pui
    Department of Hematology Oncology, St Jude Children s Research Hospital, Memphis, TN 38105 2794, USA
    Blood 104:2690-6. 2004
    ..01% or more at the end of the 6-week remission induction phase. Our results suggest the efficacy of early intensification of intrathecal chemotherapy and provide the basis for studies omitting cranial irradiation altogether...
  32. pmc Genes contributing to minimal residual disease in childhood acute lymphoblastic leukemia: prognostic significance of CASP8AP2
    Christian Flotho
    Department of Pathology, St Jude Children s Research Hospital, 332 N Lauderdale, Memphis, TN 38105, USA
    Blood 108:1050-7. 2006
    ..Therefore, this gene is a strong candidate for inclusion in gene expression arrays specifically designed for leukemia diagnosis...
  33. ncbi request reprint Sample size determination for the false discovery rate
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital 332 N Lauderdale Street, Memphis, TN 38135, USA
    Bioinformatics 21:4263-71. 2005
    ..There is not a widely applicable method to determine the sample size for experiments basing statistical significance on the false discovery rate (FDR)...
  34. pmc Shortening infusion time for high-dose methotrexate alters antileukemic effects: a randomized prospective clinical trial
    Torben S Mikkelsen
    St Jude Children s Research Hospital, 262 Danny Thomas Pl, Memphis, TN 38105, USA
    J Clin Oncol 29:1771-8. 2011
    ....
  35. doi request reprint Genetic predictors of glucocorticoid-induced hypertension in children with acute lymphoblastic leukemia
    Landry K Kamdem
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, Tennessee 38105 2794, USA
    Pharmacogenet Genomics 18:507-14. 2008
    ..One of the adverse effects of glucocorticoids is hypertension. Our aim was to define the frequency of and clinical and genetic risk factors for steroid-induced hypertension...
  36. pmc Ancestry and pharmacogenetics of antileukemic drug toxicity
    Shinji Kishi
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, TN 38105 2794, USA
    Blood 109:4151-7. 2007
    ..026). The genotype-phenotype associations were similar whether analyses were adjusted by self-reported race or ancestry-informative genetic markers. Germ-line polymorphisms are significant determinants of toxicity of antileukemic therapy...
  37. pmc Treatment outcomes in black and white children with cancer: results from the SEER database and St Jude Children's Research Hospital, 1992 through 2007
    Ching Hon Pui
    St Jude Children s Research Hospital, Memphis, TN 38105, USA
    J Clin Oncol 30:2005-12. 2012
    ..Treatment outcome for black patients with cancer has been significantly worse than for their white counterparts. We determined whether recent improved treatment had narrowed the gap in outcome between black and white pediatric patients...
  38. pmc Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia
    Charles G Mullighan
    Department of Pathology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    N Engl J Med 360:470-80. 2009
    ..Recent genomewide analyses have identified a high frequency of DNA copy-number abnormalities in ALL, but the prognostic implications of these abnormalities have not been defined...
  39. pmc Pharmacokinetic, pharmacodynamic, and pharmacogenetic determinants of osteonecrosis in children with acute lymphoblastic leukemia
    Jitesh D Kawedia
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 2794, USA
    Blood 117:2340-7; quiz 2556. 2011
    ..Overall, older age, lower albumin, higher lipid levels, and dexamethasone exposure were associated with osteonecrosis and may be linked by inherited genomic variation...
  40. pmc In vivo response to methotrexate forecasts outcome of acute lymphoblastic leukemia and has a distinct gene expression profile
    Michael J Sorich
    Hematological Malignancies Program and the Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, Tennessee, United States of America
    PLoS Med 5:e83. 2008
    ..Therefore, we measured the in vivo antileukemic effects of MTX and identified genes whose expression differed significantly in patients with a good versus poor response to MTX...
  41. pmc Clinical utility of sequential minimal residual disease measurements in the context of risk-based therapy in childhood acute lymphoblastic leukaemia: a prospective study
    Ching Hon Pui
    Department of Oncology, St Jude Children s Research Hospital, Memphis, TN, USA Department of Pathology, St Jude Children s Research Hospital, Memphis, TN, USA University of Tennessee Health Science Center, Memphis, TN, USA Electronic address
    Lancet Oncol 16:465-74. 2015
    ..We aimed to establish the clinical significance of minimal residual disease in a prospective trial that used sequential minimal residual disease measurements to guide treatment decisions...
  42. pmc Inherited GATA3 variants are associated with Ph-like childhood acute lymphoblastic leukemia and risk of relapse
    Virginia Pérez-Andreu
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, Tennessee, USA
    Nat Genet 45:1494-8. 2013
    ..Our results provide insights into interactions between inherited and somatic variants and their role in ALL pathogenesis and prognosis. ..
  43. pmc PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
    Bioinformatics 25:2013-9. 2009
    ..However, to our knowledge, there is no statistical procedure designed to detect specific patterns of association with multiple endpoint variables...
  44. ncbi request reprint Results of therapy for acute lymphoblastic leukemia in black and white children
    Ching Hon Pui
    Department of Hematology Oncology, St Jude Children s Research Hospital, Memphis, TN 38105 2794, USA
    JAMA 290:2001-7. 2003
    ..Treatment results for acute lymphoblastic leukemia (ALL) clearly have improved over the past decade, but black children have not fared as well as white children in large national trials...
  45. doi request reprint Genome-wide study links PNPLA3 variant with elevated hepatic transaminase after acute lymphoblastic leukemia therapy
    Yiwei Liu
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, TN
    Clin Pharmacol Ther . 2017
    ..024). This is an example of a pharmacogenetic variant overlapping with a disease risk variant. This article is protected by copyright. All rights reserved...
  46. pmc Genetic mediators of neurocognitive outcomes in survivors of childhood acute lymphoblastic leukemia
    Kevin R Krull
    Department of Epidemiology and Cancer Control, St Jude Children s Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN 38105 3678, USA
    J Clin Oncol 31:2182-8. 2013
    ..This study examined genetic polymorphisms associated with variability in neurocognitive outcome...
  47. doi request reprint Asparaginase may influence dexamethasone pharmacokinetics in acute lymphoblastic leukemia
    Lei Yang
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, 332 N Lauderdale, Memphis, TN 38105 2794, USA
    J Clin Oncol 26:1932-9. 2008
    ..Dexamethasone is used widely in oncology, but pharmacokinetic studies are lacking. We evaluated dexamethasone pharmacokinetics in children with acute lymphoblastic leukemia...
  48. pmc Neuropathic pain during treatment for childhood acute lymphoblastic leukemia
    Doralina L Anghelescu
    Division of Anesthesia and Pain Management Service, St Jude Children s Research Hospital, Memphis, TN 38105 2794, USA
    Pediatr Blood Cancer 57:1147-53. 2011
    ..Neuropathic pain (NP) is an unpleasant side effect of chemotherapeutic agents for leukemia, especially vincristine...
  49. pmc Discrete TCR repertoires and CDR3 features distinguish effector and Foxp3+ regulatory T lymphocytes in myelin oligodendrocyte glycoprotein-induced experimental allergic encephalomyelitis
    Phuong Nguyen
    Department of Pathology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    J Immunol 185:3895-904. 2010
    ..Differences in sequence and physical characteristics distinguish Treg and Tconv TCRs and imply dissimilar Ag recognition properties...
  50. pmc The Role of Leukapheresis in the Current Management of Hyperleukocytosis in Newly Diagnosed Childhood Acute Lymphoblastic Leukemia
    Rosa Nguyen
    Department of Oncology, St Jude Children s Research Hospital, Memphis, Tennessee
    Pediatr Blood Cancer 63:1546-51. 2016
    ..Hyperleukocytosis in children with acute lymphoblastic leukemia (ALL) has been associated with early morbidity and mortality. The use of leukapheresis in these children treated with contemporary therapy remains controversial...
  51. pmc Severe hypertriglyceridaemia during therapy for childhood acute lymphoblastic leukaemia
    Deepa Bhojwani
    Department of Oncology, St Jude Children s Research Hospital, Memphis, TN, USA Department of Pediatrics, University of Tennessee Health Sciences Center, Memphis, TN, USA Electronic address
    Eur J Cancer 50:2685-94. 2014
    ..There are no guidelines for screening or management of patients with severe hypertriglyceridaemia (>1000mg/dL) during ALL therapy...
  52. doi request reprint CRHR1 polymorphisms predict bone density in survivors of acute lymphoblastic leukemia
    Terreia S Jones
    Department of Radiology, Colleges of Pharmacy and Medicine, University of Tennessee, Memphis, TN, USA
    J Clin Oncol 26:3031-7. 2008
    ..Because CRHR1 polymorphisms have been associated with other corticosteroid effects, our goal was to define whether CRHR1 polymorphisms predict which patients with ALL are likely to develop bone mineral deficits...
  53. ncbi request reprint Extended follow-up of long-term survivors of childhood acute lymphoblastic leukemia
    Ching Hon Pui
    Department of Hematology Oncology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    N Engl J Med 349:640-9. 2003
    ..We determined the long-term survival and the rates of health insurance coverage, marriage, and employment among patients who had attained at least 10 years of event-free survival...
  54. pmc A Phenotype-Driven Dimension Reduction (PhDDR) approach to integrated genomic association analyses
    Cuilan Gao
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Conf Proc IEEE Eng Med Biol Soc 2011:6837-40. 2011
    ..This approach is then illustrated by an application to gene co-expression analysis of treatment response of childhood leukemia...
  55. pmc Somatic deletions of genes regulating MSH2 protein stability cause DNA mismatch repair deficiency and drug resistance in human leukemia cells
    Barthélémy Diouf
    Hematological Malignancies Program, St Jude Children s Research Hospital, Memphis, Tennessee, USA
    Nat Med 17:1298-303. 2011
    ..These findings reveal a previously unrecognized mechanism whereby somatic deletions of genes regulating MSH2 degradation result in undetectable levels of MSH2 protein in leukemia cells, DNA mismatch repair deficiency and drug resistance...
  56. pmc Prophylactic Trimethoprim-Sulfamethoxazole Does Not Affect Pharmacokinetics or Pharmacodynamics of Methotrexate
    Courtney S Watts
    Departments of Pharmaceutical Sciences Oncology Biostatistics, St Jude Children s Research Hospital, Memphis, TN Department of Pediatric Oncology, Skejby Hospital, Aarhus University, Aarhus, Denmark
    J Pediatr Hematol Oncol 38:449-52. 2016
    ..Thus, we found no evidence for an interaction between methotrexate and TMP/SMX given prophylactically. ..
  57. pmc Germline genetic variation in ETV6 and risk of childhood acute lymphoblastic leukaemia: a systematic genetic study
    Takaya Moriyama
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, TN, USA Department of Pediatrics, Mie University Graduate School of Medicine, Mie, Japan
    Lancet Oncol 16:1659-66. 2015
    ..Our aims in this study were to comprehensively identify ALL predisposition variants in ETV6 and to determine the extent to which they contributed to the overall risk of childhood ALL...
  58. doi request reprint Osteonecrosis is unrelated to hip anatomy in children with acute lymphoblastic leukemia
    Mary V Portera
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, Tennessee
    Pediatr Blood Cancer . 2016
    ..Despite adequate statistical power, we found no association between hip anatomy and osteonecrosis. Investigation of other factors contributing to ALL-associated osteonecrosis is warranted...
  59. pmc Genetic risk factors for the development of osteonecrosis in children under age 10 treated for acute lymphoblastic leukemia
    Seth E Karol
    Department of Oncology, St Jude Children s Research Hospital, Memphis, TN
    Blood 127:558-64. 2016
    ..These data may provide new insights into the pathophysiology of osteonecrosis. ..
  60. pmc Antileukemic Efficacy of Continuous vs Discontinuous Dexamethasone in Murine Models of Acute Lymphoblastic Leukemia
    Laura B Ramsey
    Pharmaceutical Sciences Department, St Jude Children s Research Hospital, Memphis, Tennessee, United States of America
    PLoS ONE 10:e0135134. 2015
    ..002). Our results support the clinical practice of using discontinuous rather than continuous dexamethasone dosing in patients with acute lymphoblastic leukemia. ..
  61. pmc Inherited NUDT15 variant is a genetic determinant of mercaptopurine intolerance in children with acute lymphoblastic leukemia
    Jun J Yang
    Jun J Yang, Wenjian Yang, Chengcheng Liu, Cheng Cheng, Deqing Pei, Kristine R Crews, Nancy Kornegay, William E Evans, Ching Hon Pui, and Mary V Relling, St Jude Children s Research Hospital, Memphis, TN and Wendy Landier, Lindsey Hageman, Yanjun Chen, F Lennie Wong, and Smita Bhatia, City of Hope, Duarte, CA
    J Clin Oncol 33:1235-42. 2015
    ..Mercaptopurine (MP) is the mainstay of curative therapy for acute lymphoblastic leukemia (ALL). We performed a genome-wide association study (GWAS) to identify comprehensively the genetic basis of MP intolerance in children with ALL...
  62. pmc PACSIN2 polymorphism influences TPMT activity and mercaptopurine-related gastrointestinal toxicity
    Gabriele Stocco
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Hum Mol Genet 21:4793-804. 2012
    ..These data indicate that polymorphism in PACSIN2 significantly modulates TPMT activity and influences the risk of GI toxicity associated with mercaptopurine therapy...
  63. pmc Intestinal CYP3A4 and midazolam disposition in vivo associate with VDR polymorphisms and show seasonal variation
    Ranjit K Thirumaran
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, TN, USA
    Biochem Pharmacol 84:104-12. 2012
    ..These data suggest VDR polymorphisms are predictors of intestinal CYP3A4, and that CYP3A4 intestinal expression varies seasonally--likely related to annual changes in UV sunlight and vitamin D levels...
  64. pmc Epigenetic regulation of human gamma-glutamyl hydrolase activity in acute lymphoblastic leukemia cells
    Qing Cheng
    Hematological Malignancies Program, Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Am J Hum Genet 79:264-74. 2006
    ....
  65. ncbi request reprint Gene expression profiling of pediatric acute myelogenous leukemia
    Mary E Ross
    Department of Hematology Oncology, Hartwell Center for Bioinformatics and Biotechnology, St Jude Children s Research Hospital, 332 N Lauderdale, Memphis, TN 38105, USA
    Blood 104:3679-87. 2004
    ..Surprisingly, AMLs containing partial tandem duplications of MLL failed to cluster with MLL chimeric fusion gene cases, suggesting a significant difference in their underlying mechanism of transformation...
  66. ncbi request reprint Utility of automated counting to determine absolute neutrophil counts and absolute phagocyte counts for pediatric cancer treatment protocols
    Nobuko Hijiya
    Department of Hematology Oncology, St Jude Children s Research Hospital, Memphis, Tennessee, USA
    Cancer 101:2681-6. 2004
    ..By analyzing blood samples from children undergoing cancer treatment, the authors determined whether ANCs and APCs obtained by automated methods correlated positively with ANCs and APCs obtained manually...
  67. pmc Association of an inherited genetic variant with vincristine-related peripheral neuropathy in children with acute lymphoblastic leukemia
    Barthélémy Diouf
    Hematological Malignancies Program, Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, Tennessee
    JAMA 313:815-23. 2015
    ..With cure rates of childhood acute lymphoblastic leukemia (ALL) exceeding 85%, there is a need to mitigate treatment toxicities that can compromise quality of life, including peripheral neuropathy from vincristine treatment...
  68. pmc A genomic random interval model for statistical analysis of genomic lesion data
    Stan Pounds
    Department of Biostatistics, Department of Computational Biology and Department of Pathology, St Jude Children s Research Hospital, Memphis, TN 38135, USA
    Bioinformatics 29:2088-95. 2013
    ....
  69. ncbi request reprint Acute lymphoblastic leukemia with TEL-AML1 fusion has lower expression of genes involved in purine metabolism and lower de novo purine synthesis
    Gianluigi Zaza
    St Jude Children s Research Hospital, 332 N Lauderdale St, Memphis, TN 38105, USA
    Blood 104:1435-41. 2004
    ..These findings have established that TEL-AML1 ALL has significantly lower de novo purine synthesis and differential expression of genes involved in purine metabolism...
  70. doi request reprint Impact of neutrophil recovery on oxygenation in pediatric oncology patients with acute hypoxemic respiratory failure
    Lama M Elbahlawan
    Division of Critical Care Medicine, St Jude Children s Research Hospital, Memphis, TN 38103, USA
    J Pediatr Hematol Oncol 33:e296-9. 2011
    ..Our findings suggest that a faster ANC increment in the 2 days after recovery is associated with an increased risk of oxygenation worsening...
  71. ncbi request reprint Modeling oligonucleotide microarray signals
    Yongqing Zhang
    Hartwell Center for Bioinformatics and Biotechnology, St Jude Children s Research Hospital, Memphis, Tennessee 38105 2794, USA
    Appl Bioinformatics 5:151-60. 2006
    ..This correlation between the predicted expression levels and the spike-in concentrations of test transcripts demonstrated good predictive abilities of our model...
  72. pmc Spinal epidural lipomatosis in children with hematologic malignancies
    Rachel C Brennan
    Department of Oncology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Ann Hematol 90:1067-74. 2011
    ..Investigation for SEL in leukemia or lymphoma patients with difficult lumbar punctures is warranted. Placement of an Ommaya reservoir may facilitate safe CNS-directed therapy in severely affected patients...
  73. pmc Long-term outcome and risk factors for uncontrolled seizures after a first seizure in children with hematological malignancies
    Raja B Khan
    Division of Neurology, St Jude Children s Research Hospital, Memphis, TN, USA
    J Child Neurol 29:774-81. 2014
    ..04). In conclusion, seizures are controlled with medications in a majority of patients with hematological cancer. After a period without seizures, antiseizure drug withdrawal in appropriately selected patient has a high success rate. ..
  74. pmc The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias
    Anna K Andersson
    1 Department of Pathology, St Jude Children s Research Hospital, Memphis, Tennessee, USA 2 Department of Clinical Genetics, Lund University, Lund, Sweden
    Nat Genet 47:330-7. 2015
    ..5 mutations/case versus 1.3 mutations/case, P = 7.15 × 10(-5)) and had frequent mutations (45%) in epigenetic regulators, a category of genes that, with the exception of MLL, was rarely mutated in infant MLL-R ALL. ..
  75. pmc Host thiopurine methyltransferase status affects mercaptopurine antileukemic effectiveness in a murine model
    Laura B Ramsey
    Departments of aPharmaceutical Sciences bPathology cBiostatistics dOncology, St Jude Children s Research Hospital Current address Puma Biotechnology Inc, Los Angeles, CA 90024, USA eDepartment of Tumor Cell Biology, Howard Hughes Medical Institute, St Jude Children s Research Hospital, Memphis, Tennessee, USA
    Pharmacogenet Genomics 24:263-71. 2014
    ..Patients with an inherited host defect in thiopurine methyltransferase (TPMT) are at high risk for life-threatening toxicity if treated with conventional dosages, but the impact on antileukemic efficacy is less clear...
  76. pmc Literature aided determination of data quality and statistical significance threshold for gene expression studies
    Lijing Xu
    Bioinformatics Program, Memphis, TN 38152, USA
    BMC Genomics 13:S23. 2012
    ..In addition, selection of expression p-value (EPv) threshold is somewhat arbitrary. In this study, we aimed to develop novel literature based approaches to integrate functional information in analysis of gene expression data...
  77. pmc The genomic landscape of hypodiploid acute lymphoblastic leukemia
    Linda Holmfeldt
    Department of Pathology, St Jude Children s Research Hospital, Memphis, Tennessee, USA
    Nat Genet 45:242-52. 2013
    ....
  78. pmc Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire
    Phuong Nguyen
    Department of Pathology, St, Jude Children s Research Hospital, 262 Danny Thomas Pl, Memphis, TN 38105, USA
    BMC Genomics 12:106. 2011
    ..The resolution of this sequencing is dependent on its accuracy, and direct assessments of the errors formed during high throughput repertoire analyses are limited...
  79. pmc T cell receptor CDR3 sequence but not recognition characteristics distinguish autoreactive effector and Foxp3(+) regulatory T cells
    Xin Liu
    Department of Pathology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Immunity 31:909-20. 2009
    ....
  80. ncbi request reprint Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling
    Eng Juh Yeoh
    Department of Pathology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Cancer Cell 1:133-43. 2002
    ..Thus, the single platform of expression profiling should enhance the accurate risk stratification of pediatric ALL patients...
  81. ncbi request reprint Homocysteine, pharmacogenetics, and neurotoxicity in children with leukemia
    Shinji Kishi
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, 332 North Lauderdale, Memphis, TN 38105, USA
    J Clin Oncol 21:3084-91. 2003
    ....
  82. pmc ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data
    Song Wu
    Department of Biostatistics, St, Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
    Theor Biol Med Model 7:18. 2010
    ..However, high cost and high rate of false discovery of transcription factor binding sites identified from ChIP-Seq data significantly limit its application...
  83. pmc The genetic basis of early T-cell precursor acute lymphoblastic leukaemia
    Jinghui Zhang
    Department of Computational Biology and Bioinformatics, St Jude Children s Research Hospital, Memphis, Tennessee 38105, USA
    Nature 481:157-63. 2012
    ..These findings suggest that addition of myeloid-directed therapies might improve the poor outcome of ETP ALL...
  84. ncbi request reprint Improving false discovery rate estimation
    Stan Pounds
    Department of Biostatistics, MS 262 St Jude Children s Research Hospital, 332 N Lauderdale Street, Memphis, TN 38105 2794, USA
    Bioinformatics 20:1737-45. 2004
    ..Unfortunately, the BUM approach is reliable only in settings where the assumed model accurately represents the actual distribution of p-values...
  85. ncbi request reprint Statistical development and evaluation of microarray gene expression data filters
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, TN 38105 2794, USA
    J Comput Biol 12:482-95. 2005
    ..S-plus and R routines to implement the pooled p-value and error-minimizing pooled p-value filters have been developed and are available from www.stjuderesearch.org/depts/biostats/index.html...
  86. ncbi request reprint MDR1 genotype is associated with hepatic cytochrome P450 3A4 basal and induction phenotype
    Jatinder Lamba
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Clin Pharmacol Ther 79:325-38. 2006
    ..This study investigated whether common single-nucleotide polymorphisms (SNPs) in multidrug resistance 1 (MDR1), encoding P-glycoprotein, or the pregnane X receptor (PXR) were associated with basal or inducible CYP3A4 expression...
  87. ncbi request reprint Distinct gene expression profiles and reduced JNK signaling in retinitis pigmentosa caused by RP1 mutations
    Jiewu Liu
    Department of Developmental Neurobiology, St Jude Children s Research Hospital, Memphis, TN 38105 2794, USA
    Hum Mol Genet 14:2945-58. 2005
    ..Our studies further suggest JNK-related therapeutic strategies for RP1 diseases...
  88. pmc Attention and working memory abilities in children treated for acute lymphoblastic leukemia
    Jason Ashford
    Department of Behavioral Medicine, St Jude Children s Research Hospital, Memphis, Tennessee 38105, USA
    Cancer 116:4638-45. 2010
    ....
  89. pmc Safe anesthesia for radiotherapy in pediatric oncology: St. Jude Children's Research Hospital Experience, 2004-2006
    Doralina L Anghelescu
    Division of Anesthesiology, St Jude Children s Research Hospital, Memphis, TN 38105 2794, USA
    Int J Radiat Oncol Biol Phys 71:491-7. 2008
    ..To determine the incidence of anesthesia-related complications in children undergoing radiotherapy and the associated risk factors...
  90. ncbi request reprint Treatment-specific changes in gene expression discriminate in vivo drug response in human leukemia cells
    Meyling H Cheok
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, 332 N Lauderdale St, Memphis, Tennessee 38105 USA
    Nat Genet 34:85-90. 2003
    ....
  91. doi request reprint Globin lentiviral vector insertions can perturb the expression of endogenous genes in beta-thalassemic hematopoietic cells
    Phillip W Hargrove
    Department of Hematology, St Jude Children s Research Hospital, Memphis, Tennessee 38105, USA
    Mol Ther 16:525-33. 2008
    ..This is the first direct evidence that lentiviral vectors can cause insertional dysregulation of cellular genes at a frequent rate...
  92. pmc Impact of continuous renal replacement therapy on oxygenation in children with acute lung injury after allogeneic hematopoietic stem cell transplantation
    Lama ElBahlawan
    Division of Critical Care Medicine, St Jude Children s Research Hospital, Memphis, Tennessee 38105 3678, USA
    Pediatr Blood Cancer 55:540-5. 2010
    ....
  93. pmc Effector CD8+ T cells recovered from an influenza pneumonia differentiate to a state of focused gene expression
    Dana R Marshall
    Department of Immunology, Hartwell Center for Bioinformatics, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Proc Natl Acad Sci U S A 102:6074-9. 2005
    ....
  94. ncbi request reprint Risk factors for traumatic and bloody lumbar puncture in children with acute lymphoblastic leukemia
    Scott C Howard
    Department of Hematology Oncology, St Jude Children s Research Hospital, Memphis, TN, USA
    JAMA 288:2001-7. 2002
    ..Traumatic or bloody lumbar puncture (LP) reduces the diagnostic value of the procedure and may worsen the outcome of patients with acute lymphoblastic leukemia (ALL). Little is known about the risk factors for traumatic and bloody LP...
  95. ncbi request reprint Arf induces p53-dependent and -independent antiproliferative genes
    Mei Ling Kuo
    Department of Genetics and Tumor Cell Biology, St Jude Children s Research Hospital, Memphis, Tennessee 38105, USA
    Cancer Res 63:1046-53. 2003
    ..Together, the results indicate that p19(Arf) induces a broad spectrum of proteins that likely act in concert to arrest cell proliferation...
  96. ncbi request reprint Haplotype structure of the UDP-glucuronosyltransferase 1A1 promoter in different ethnic groups
    Federico Innocenti
    Department of Medicine, Committee on Clinical Pharmacology and Pharmacogenomics, Cancer Research Center, The University of Chicago, Chicago, IL 60637, USA
    Pharmacogenetics 12:725-33. 2002
    ..This study showed that (i) common promoter variants are in linkage disequilibrium and (ii) the haplotype structure of promoter is probably different between Caucasians and African-Americans...
  97. pmc Pharmacogenetics of outcome in children with acute lymphoblastic leukemia
    Jose Claudio C Rocha
    Department of Pharmaceutical Sciences, Saint Jude Children s Research Hospital of the University of Tennessee, Memphis 38105 2794, USA
    Blood 105:4752-8. 2005
    ..04). The GSTM1 non-null and TYMS 3/3 genotypes are plausibly linked to drug resistance. Polymorphisms interact to influence antileukemic outcome and represent determinants of response that can be used to optimize therapy...
  98. ncbi request reprint Gene-expression patterns in drug-resistant acute lymphoblastic leukemia cells and response to treatment
    Amy Holleman
    Division of Pediatric Oncology Hematology, Erasmus University Medical Center, Sophia Children s Hospital, Rotterdam, The Netherlands
    N Engl J Med 351:533-42. 2004
    ..Childhood acute lymphoblastic leukemia (ALL) is curable with chemotherapy in approximately 80 percent of patients. However, the cause of treatment failure in the remaining 20 percent of patients is largely unknown...
  99. ncbi request reprint A pharmacogenetic study of uridine diphosphate-glucuronosyltransferase 2B7 in patients receiving morphine
    Michael B Sawyer
    Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, IL, USA
    Clin Pharmacol Ther 73:566-74. 2003
    ..045 and P =.004, respectively). Interindividual differences in morphine glucuronidation may be the result of genetic variation in UGT2B7, and further studies are indicated...
  100. ncbi request reprint Antitumor efficacy and tumor-selective replication with a single intravenous injection of OAS403, an oncolytic adenovirus dependent on two prevalent alterations in human cancer
    Patricia C Ryan
    Genetic Therapy, Inc, Gaithersburg, Maryland 20878, USA
    Cancer Gene Ther 11:555-69. 2004
    ..Furthermore, efficacy was significantly improved when OAS403 treatment was combined with doxorubicin. This virus holds promise for the treatment of a broad range of human cancers including metastatic disease...
  101. pmc The expression of 70 apoptosis genes in relation to lineage, genetic subtype, cellular drug resistance, and outcome in childhood acute lymphoblastic leukemia
    Amy Holleman
    Department of Pediatric Oncology and Hematology, Erasmus MC Sophia Children s Hospital, Rotterdam, The Netherlands
    Blood 107:769-76. 2006
    ..051). In conclusion, ALL subtypes have a unique expression pattern of apoptosis genes and our data suggest that selective genes are linked to cellular drug resistance and prognosis in childhood B-lineage ALL...