Skip to main content
Cheng Cheng, PhD
Cheng Cheng, PhD

Cheng Cheng, PhD

Member, St. Jude Faculty



BS – Beijing Computer Institute, China (1984)
PhD – Texas A & M University (1993)

Research Interests

I collaborate with St. Jude investigators in the areas of hematological malignancies, pharmaceutical sciences, molecular pathology, bioinformatics, and computational biology. I am interested in developing statistical methodologies for biomedical sciences.

  • Statistical inference methods in system biology and genome-wide integrated analyses, with emphasis on applications to cancer genomics
  • Validation inference in genome-wide studies
  • Assessment of levels of statistical errors and significance in massive multiple comparisons applied to biomedical research, such as genome-wide studies
  • Efficient non-inferiority trial designs, phase-II or phase-III
  • Analysis of high-dimensional and large data sets, data mining, dimension reduction and visualization, variable (feature) selection for cluster analysis, modeling, and classification
  • Methodologies of multivariate analysis: nonparametric methods combining linear or nonlinear projections and function estimation
  • Applications of percentiles (quantiles) in data analysis and modeling
  • Methods of analyzing general distance (similarity) and non-dimensional data, visualization, cluster analysis, and multidimensional scaling.

Selected Publications

Qian M, Cao X, Devidas M, Yang W, Cheng C, Dai Y, Carroll A, Heerema NA, Zhang H, Moriyama T, Gastier-Foster JM, Xu H, Raetz E, Larsen E, Winick N, Bowman WP, Martin PL, Mardis ER, Fulton R, Zambetti G, Borowitz M, Wood B, Nichols KE, Carroll WL, Pui CH, Mullighan CG, Evans WE, Hunger SP, Relling MV, Loh ML, Yang JJ. TP53 Germline variations influence the predisposition and prognosis of B-Cell Acute Lymphoblastic Leukemia in children. J Clin Oncol Feb;36(6):591-599, 2018.

Liu Y, Easton J, Shao Y, Maciaszek J, Wang Z, Wilkinson MR, McCastlain K, Edmonson M, Pounds SB, Shi L, Zhou X, Ma X, Sioson E, Li Y, Rusch M, Gupta P, Pei D, Cheng C, Smith MA, Auvil JG, Gerhard DS, Relling MV, Winick NJ, Carroll AJ, Heerema NA, Raetz E, Devidas M, Willman CL, Harvey RC, Carroll WL, Dunsmore KP, Winter SS, Wood BL, Sorrentino BP, Downing JR, Loh ML, Hunger SP, Zhang J, Mullighan CG. The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia. Nat Genet Aug;49(8):1211-1218, 2017.

Stock W, Diouf B, Crews KR, Pei D, Cheng C, Laumann K, Mandrekar SJ, Luger S, Advani A, Stone RM, Larson RA, Evans WE. An inherited genetic variant in CEP72 promoter predisposes to vincristine-induced peripheral neuropathy in adults with acute lymphoblastic leukemia. Clin Pharmacol Ther Mar;101(3):391-395, 2017.

Cheng, C. Exploratory failure time analysis in large scale genomics. Computational Statistics and Data Analysis 95:192-206, 2016. Download pdf NIHMS733642.

Diouf B, Crews KR, Lew G, Pei D, Cheng C, Bao J, Zheng J, Yang W, Fan Y, Wheeler HE, Wing C, Delaney S, Komatsu M, Paugh SW, McCorkle JR, Lu X, Winick NJ, Carroll WL, Loh ML, Hunger SP, Devidas M, Pui C-H, Dolan EM, Relling MV, Evans WE. Association of an Inherited Genetic Variant with Vincristine-Related Peripheral Neuropathy in Children with Acute Lymphoblastic Leukemia. Journal of American Medical Association 313(8):815-823, 2015.

Pui CH, Pei D, Coustan-Smith E, Jeha S, Cheng C, Bowman WP, Sandlund JT, Ribeiro RC, Rubnitz JE, Inaba H, Bhojwani D, Gruber TA, Leung WH, Downing JR, Evans WE, Relling MV, Campana D. Clinical utility of sequential minimal residual disease measurements in the context of risk-based therapy in childhood acute lymphoblastic leukaemia: a prospective study. Lancet Oncol 16:465-474, 2015.

Roberts K … Cheng C … Mullighan C. Targetable kinase activating lesions in Ph-like acute lymphoblastic leukemia. New England Journal of Medicine 371:1005-15, 2014. PMCID: PMC4191900

Roberts KG, Pei D, Campana D, Payne-Turner D, Li Y, Cheng C, Sandlund JT, Jeha S, Easton J, Becksfort J, Zhang J, Coustan-Smith E, Raimondi SC, Leung WH, Relling MV, Evans WE, Downing JR, Mullighan CG, Pui C-H. Outcomes of children with BCR-ABL1-like acute lymphoblastic leukemia treated with risk-directed therapy based on the levels of minimal residual disease. Journal of Clinical Oncology 32(27):3012-3020, 2014. PMCID: PMC4162497

Perez-Andreu V, Roberts KG, Harvey RC, Yang W, Cheng C, Pei D, Xu H, Gastier-Foster J, E S, Lim JY, Chen IM, Fan Y, Devidas M, Borowitz MJ, Smith C, Neale G, Burchard EG, Torgerson DG, Klussmann FA, Villagran CR, Winick NJ, Camitta BM, Raetz E, Wood B, Yue F, Carroll WL, Larsen E, Bowman WP, Loh ML, Dean M, Bhojwani D, Pui CH, Evans WE, Relling MV, Hunger SP, Willman CL, Mullighan CG, Yang JJ. Inherited GATA3 variants are associated with Ph-like childhood acute lymphoblastic leukemia and risk of relapse. Nat Genet 45:1494-1498, 2013.

Cheng C. Integration of diverse statistical evidence of gene-trait association in systems biology studies. Chem Biodivers 9(5):935-44, 2012. *Invited paper for a special issue of Chemistry and Biodiversity.

Yang JJ, Cheng C, Devidas M, Cao X, Campana D, Yang W, Fan Y, Neale G, Cox N, Scheet P, Borowitz MJ, Winick NJ, Martin PL, Bowman WP, Camitta B, Reaman GH, Carroll WL, Willman CL, Hunger SP, Evans WE, Pui CH, Loh M, Relling MV. Genome-wide association study identifies germline polymorphisms associated with relapse of childhood acute lymphoblastic leukemia. Blood 120:4197-4204, 2012.

Xu H, Cheng C, Devidas M, Pei D, Fan Y, Yang W, Neale G, Scheet P, Burchard EG, Torgerson DG, Eng C, Dean M, Antillon F, Winick NJ, Martin PL, Willman CL, Camitta BM, Reaman GH, Carroll WL, Loh M, Evans WE, Pui CH, Hunger SP, Relling MV, Yang JJ. ARID5B genetic polymorphisms contribute to racial disparities in the incidence and treatment outcome of childhood acute lymphoblastic leukemia. J Clin Oncol 30(7):751-757, 2012.

Gao C, Cheng C. A Phenotype-driven dimension reduction (PhDDR) approach to integrated genomic association analyses. Proceedings of 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society pp.6837-6840, 2011. PMCID: PMC3652376 *Invited paper for the special session on Informatics for Integrated Genomics.

Cheng C, Wu J. Interval estimation of quantile ratios applied to anti-cancer drug screening by xenograft experiments. Statistics in Medicine 29:2669-2678, 2010.

Cheng C. Internal validation inferences of significant genomic features in genome-wide screening. Comput Stat Data Anal 53:788-800, 2009.

Pounds S, Cheng C, Mullighan CG, Raimondi, SC, Shurtleff S, and Downing, JR. Reference alignment of SNP microarray signals for copy number analysis of tumors. Bioinformatics 25:315-321, 2009. PMCID: PMC2639073

Pounds S, Cheng C, Cao X, Crews KR, Plunkett W, Gandhi V, Rubnitz J, Raul C. Ribeiro RC, Downing JR, Lamba J. PROMISE: A Tool to Identify Genomic Features with a Specific Biologically Interesting Pattern of Correlations with Multiple Endpoint Variables. Bioinformatics 25:2013-2019, 2009. PMCID: PMC2723006

Pui C-H, Campana D, Pei D, Bowman PW, Sandlund JT, Kaste SC, Ribeiro RC, Rubnitz JE, Raimondi SC, Onciu M, Coustan-Smith E, Kun LE, Jeha S, Cheng C, Howard SC, Simmons V, Bayles A, Metzger ML, Boyett JM, Leung W, Downing JR, Evans WE, Relling MV. Treatment of childhood acute lymphoblastic leukemia without prophylactic cranial irradiation. New England Journal of Medicine 360(26):2730-2741, 2009. PMCID: PMC2754320

Mullighan CG, Su X, Zhang J, Radtke I, Phillips LAA, Miller CB, Ma J, Liu W, Cheng C, Schulman BA, Harvey RC, Chen I-M, Clifford RJ, Carroll WL, Reaman G, Bowman PW, Devidas M, Gerhard DS, Yang W, Relling MV, Shurtleff  SA, Campana D, Borowitz MJ, Pui C-H, Smith M, Hunger SP, Willman CL, Downing JR, and the Children's Oncology Group. Deletion of IKZF1 (IKSROS) is associated with poor prognosis in acute lymphoblastic leukemia. New England Journal of Medicine 360:470-480, 2009. PMCID: PMC2674612

Pounds S, Cheng C, Onar A. Statistical Inference for Microarray Studies. Handbook of Statistical Genetics, Third Edition (David Balding et al. Eds.) 1:231-266, 2007. *Invited paper.

Cheng C, Pounds S. False discovery rate paradigms for analysis of microarray gene expression data. Bioinformation 1(10): 436-446, 2007. *Invited paper.

Cheng C. An adaptive significance threshold criterion for massive multiple hypothesis testing. In Optimality: The Second Erich L. Lehmann Symposium, Institute of Mathematical Statistics, Beachwood, OH, USA; 49:51-76, 2006. Download pdf

Pounds S, Cheng C. Sample size determination for the false discovery rate. Bioinformatics 21:4263-4271, 2005.

Pui C-H, Cheng C, Rivera GK, Leung W, Sandlund JT, Riberio RC, Relling RV, Kun LE, Evans, WE, and Hudson MM. Extended follow up of long-term survivors of childhood acute lymphoblastic leukemia. New England Journal of Medicine 349:640-649, 2003.

Cheng C.  Uniform consistency of generalized kernel estimators of quantile density. The Annals of Statistics 23:2285-2291, 1995.

Corresponding author Contributed equally

See full list of publications

Last update: March 2018