St. Jude Research/Departments and Divisions/Biostatistics

The faculty of the Biostatistics Department is actively engaged in research to develop and improve statistical methods used in biomedical research. Our contributions include:

The beta uniform mixture (BUM) model is useful for quickly computing error rate estimates (such as the false discovery rate) for the analysis of microarray data.
The spacings loess histogram (SPLOSH) method is similar to BUM, but much more robust and flexible.
The pooled p-value and error-minimizing pooled p-value filters are approximately statistically optimal methods for filtering Affymetrix gene expression data on the basis of the present-absent p-values used to make the present-absent calls.
We have developed a method to calculate the sample size for a planned microarray study that will use the false discovery rate as the final measure of statistical significance. S-plus and R routines are available to perform the calculations for planning a study that will compare the gene expression of two or more groups in a one-way layout.
We have developed a code library of R/S-plus routines to implement several FDR methods.
We have developed a code library of R/S-plus routines to implement a robust method of FDR estimation.
The sequential conditional probability ratio test (SCPRT) has a special property that the conclusion of the sequential test based on interim data should have held if the testing were not stopped as it should but had continued to the planned end and drawn conclusion from the full data. The SCPRT is especially suitable for the design of clinical trials by providing this feature of consistency desirable for interim analyses. The SCPRT on Information Time is for the design of clinical trials for which the sequential test statistic can be approximated by a Brownian motion on the information time interval [0, 1].
We have developed R code to compute a shrunken F-statistic
We have developed a code library of R routines to implement the reference-marker based normalization of SNP array data utilized by Mullighan et al. (2007).
We have developed a code library of R routines to implement the assumption adequacy averaging method proposed by Pounds and Rai (2008).

Any damages arising from the use of software associated with the above links are NOT the responsibility of its developer(s) nor St. Jude Children's Research Hospital.

Publications

Identification of genes associated with chemotherapy cross-resistance and treatment response in childhood acute lymphoblastic leukemia.
Sanne Lugthart , Meyling H. Cheok , Monique L. den Boer , Wenjian Yang , Amy Holleman , Cheng Cheng , Ching-Hon Pui , Mary V. Relling , Gritta E. Janka-Schaub , Rob Pieters, William E. Evans

Arf induces p53-dependent and independent anti-proliferative genes
Mei-Ling Kuo, Eric J. Duncavage, Rose Mathew, Willem den Besten, Dequing Pei, Deanna Naeve, Tadashi Yamamoto, Cheng Cheng, Charles J. Sherr and Martine F. Roussel
2004

Gene-expression patterns in drug resistant acute lymphoblastic leukemia cells and response to treatment.
Amy Holleman, Meyling H. Cheok, Monique L. den Boer, Wenjian Yang, Anjo J.P. Veerman, Karin M. Kazemier, Deqing Pei, Cheng Cheng, Ching-Hon Pui, Mary V. Relling, Gritta E. Janka-Schaub, Rob Pieters, and William E. Evans
2004

Pediatric Lymphoblastic Leukemia by Gene Expression Profiling
Eng-Juh Yeoh, Mary E. Ross, Shelia A. Shurtleff, W. Kent Williams, Divyen Patel, Rami Mahfouz, Fred G. Behm, Susana C. Raimondi, Mary V. Relling, Anami Patel, Cheng Cheng, Dario Campana, Dawn Wilkins, Xiaodong Zhou, Jinyan Li, Huiqing Liu, Ching-Hon Pui, William E. Evans, Clayton Naeve, Limsoon Wong, James R. Downing
Cancer Cell 2002 Volume 1:133-143

Treatment-specific Changes in Gene Expression Discriminate in vivo Drug
response in Human Leukemia Cells
Meyling H. Cheok, Wenjian Yang, Ching Hon Pui, James R. Downing, CHeng Cheng, Clayton W. Naeve, Mary V. Relling, William E. Evans
Nature Genetics 2003

Gene Expression Profiling of Pediatric Acute Myelogenous Leukemia
Mary E. Ross, Rami Mahfouz, Mihaela Onciu, Hsi-Che Liu, Xiadong Zhou, Guangchun Song, Shelia A. Shurtleff, Stanley Pounds, Cheng Cheng, Jing Ma, Raul C. Riberiro, Jeffrey E. Rubnitz, Kevin Girtman, W. Kent Williams, Susana C. Raimondi, Der-Chemg Liang, Lee-Yung Shih, Ching-Hon Pui & James R. Downing
Blood 2004

Expression of the outcome predictor in acute leukemia 1 (OPAL1) gene is not an independent prognostic factor in patients treated according to COALL or St Jude protocols.
Holleman A, den Boer ML, Cheok MH, Kazemier KM, Pei D, Downing JR, Janka-Schaub GE, Gobel U, Graubner UB, Pui CH, Evans WE, Pieters R.
Blood. 2006 Sep 15;108(6): 1984-90.

Gene expression profiling of childhood adrenocortical tumors.
West AN, Neale GA, Pounds S, Figueredo BC, Rodriguez Galindo C, Pianovski MA,
Oliveira Filho AG, Malkin D, Lalli E, Ribeiro R, Zambetti GP.