William Barry


William Barry

Nancy and Morris John Lurie Investigator
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My general interests are statistical topics related to clinical and translational research in cancer, and methods for investigating molecular data derived from high-throughput biotechnologies. 

This has included the development of the statistical methodology and software, Significance Analysis of Function and Expression (SAFE), that defined several resampling-based approaches, and more recently analytical approximations to empirical tests, for the analysis of pathways in gene expression and other high dimensional genomic datasets.   By accounting for gene-gene correlation, statistical inferences are unbiased, in relation to other methods known to be grossly anti-conservative for transcriptomic data (see Gatti 2010).  SAFE has been implemented as a R package distributed through the Bioconductor repository, as a suite of analytical and graphic functions.  An on-going research project of mine is to extend the methodological framework of SAFE from exploratory investigations of gene-sets, to the evaluation of gene-signatures, as they are being developed and potentially translated into molecular biomarkers of disease.

As a Faculty Statistician of the Alliance for Clinical Trials in Oncology (formerly CALGB), I have lead the development, monitoring and analysis of multiple phase III clinical trials in the Breast Cancer Committee and retrospective/prospective biomarker validations in the Breast Correlative Science Committee. This includes CALGB 40502, Randomized Phase III Trial of Weekly Paclitaxel compared to Weekly Nanoparticle Albumin Bound Nab-Paclitaxel or Ixabepilone +/- Bevacizumab as First-Line Therapy for Locally Recurrent or Metastatic Breast Cancer where the primary clinical findings were recently presented at the 2012 ASCO Annual Meeting. 

As a methodological clinical research topic, I have developed Bayesian hierarchical models for the inclusion of integral biomarkers into randomized phase II studies. Under the Bayesian paradigm, prior selection allows one to control a gradual and seamless transition from randomized-blocks to marker-enrichment during the trial.  Compared to traditional staged designs within biomarker sub-populations, adaptation with a Bayesian hierarchical model is more robust against misspeci cation of marker prevalence, and has improved performance in identifying the sub-population where therapeutics are effective, which would better inform the target population of a subsequent phase III study.



Dr. Barry received a PhD in Biostatistics from the University of North Carolina School of Public Health in 2006, and a BS in Biology and BA in Physics from Duke University in 1996.  He joined DFCI in 2012 as the Nancy and Morris John Lurie Investigator at Dana-Faber Cancer Institute.  Dr. Barry has served since 2007 as Faculty Statistician of the Alliance for Clinical Trials in Oncology (formerly CALGB), a national clinical research group sponsored by the National Cancer Institute. From 2007 to 2012 Dr Barry was an Assistant Professor at Duke University, and during that time served as the Co-Director of the Duke SPORE in Breast Cancer, and as the Director of Bioinformatics Shared Resource to the Duke Cancer Institute.


Recent Publications

Haga SB, Barry WT, Mills R, Ginsburg GS, Svetkey L, Sullivan J, Willard HF. Public knowledge of and attitudes toward genetics and genetic testing. Genet Test Mol Biomarkers. 2013 Apr;17(4):327-35.

Bydlon TM, Barry WT, Kennedy SA, Brown JQ, Gallagher JE, Wilke LG, Geradts J, Ramanujam N. Advancing optical imaging for breast margin assessment: an analysis of excisional time, cautery, and patent blue dye on underlying sources of contrast. PLoS One. 2012;7(12):e51418.

Liao S, Desouki MM, Gaile DP, Shepherd L, Nowak NJ, Conroy J, Barry WT, Geradts J. Differential copy number aberrations in novel candidate genes associated with progression from in situ to invasive ductal carcinoma of the breast. Genes Chromosomes Cancer. 2012 Dec;51(12):1067-78.

Secord AA, Teoh DK, Barry WT, Yu M, Broadwater G, Havrilesky LJ, Lee PS, Berchuck A, Lancaster J, Wenham RM. A phase I trial of dasatinib, an SRC-family kinase inhibitor, in combination with paclitaxel and carboplatin in patients with advanced or recurrent ovarian cancer. Clin Cancer Res. 2012 Oct 1;18(19):5489-98.

Mandelblatt JS, Faul LA, Luta G, Makgoeng SB, Isaacs C, Taylor K, Sheppard VB,Tallarico M, Barry WT, Cohen HJ. Patient and physician decision styles and breast cancer chemotherapy use in older women: Cancer and Leukemia Group B protocol 369901. J Clin Oncol. 2012 Jul 20;30(21):2609-14.

Stevenson M, Mostertz W, Acharya CR, Kim W, Walters K, Barry W, Higgins K, Tuchman SA, Crawford J, Vlahovic G, Ready N, Onaitis M, Potti A. Retraction: characterizing the clinical relevance of an embryonic stem cell phenotype in lung adenocarcinoma. Clin Cancer Res. 2012 Mar 15;18(6):1818

Kim MK, Osada T, Barry WT, Yang XY, Freedman JA, Tsamis KA, Datto M, Clary BM, Clay T, Morse MA, Febbo PG, Lyerly HK, Hsu DS. Characterization of an oxaliplatin sensitivity predictor in a preclinical murine model of colorectal cancer. Mol Cancer Ther. 2012 Jul;11(7):1500-9


Owzar K, Barry WT, Jung SH. Statistical considerations for analysis of
microarray experiments. Clin Transl Sci. 2011 Dec;4(6):466-77.


Meltzer EB, Barry WT, D'Amico TA, Davis RD, Lin SS, Onaitis MW, Morrison LD, Sporn TA, Steele MP, Noble PW. Bayesian probit regression model for the diagnosis of pulmonary fibrosis: proof-of-principle. BMC Med Genomics. 2011 Oct 5;4:70.

Qureshi A, Wray D, Rhome R, Barry W, Del Poeta M. Detection of antibody against fungal glucosylceramide in immunocompromised patients: a potential new diagnostic approach for cryptococcosis. Mycopathologia. 2012 Jun;173(5-6):419-25.


Related Links

Alliance for Clinical Trials in Oncology 


Significance Analysis of Function and Expression



clinical and translational cancer research, high-throughput biotechnologies