New Funding Announcement:
Translational Biomedical Informatics Proposals

April 27, 2016

The Duke Department of Biostatistics and Bioinformatics, the Duke Clinical and Translational Science Award (CTSA), and the Duke Health Technology Solutions (DHTS) will provide pilot awards of up to $50,000 for projects that will promote innovation and collaboration in Duke Biomedical Informatics. The goal of this program is to support collaborative research that advances the field and strengthens the community of biomedical informatics at Duke.  For more information and deadlines, click here.  

Article by Dr. Halabi one of the top fifty cited articles for 2013 in the Journal of the National Cancer Institute

March 28, 2016

In 2013, Dr.  Halabi authored the article “Prognostic Model Predicting Metastatic Castration-Resistant Prostate Cancer Survival in Men Treated With Second-Line Chemotherapy” in the Journal of National Cancer Institute (JNCI).  The JNCI contacted Dr. Halabi to share the news of the large reach and impact this article has had on other scientific research.  It was originally covered by 8 news outlets and currently has 33 citations, and a Web of Science (citation indexing service) score of 27.

In the study, Halabi and colleagues developed a new prognostic tool using data from a pivotal phase III trial of prostate cancer patients whose cancer returned after they had undergone a regimen of docetaxel, the standard first-round chemotherapy that is used after hormone treatments have been ineffective.  Halabi used penalized regression (adaptive LASSO) as a variable selection method and it was challenging to estimate the standard error for the important selected covariates. She and her post-doctoral associate (Chen-Yen Lin) developed a method to estimate the standard error for the important predictors for adaptive LASSO. Furthermore, the model was validated using an external dataset. The model is available online.

Using this tool, doctors can predict the survival of individual patients with advanced prostate cancer, enabling them to better and rapidly assess whether to try additional rounds of treatment or seek clinical trials.  "For patients with metastatic prostate cancer who are appropriate candidates for second-line chemotherapy, this model can be helpful for guiding care.  It could also be used in randomized phase II or phase III clinical trials to assign patients in risk groups" said Susan Halabi, Ph.D., professor of biostatistics and bioinformatics at Duke and lead author of the study. This work was funded by a R01 that the first author received.

Study aims to resolve how to manage pre-cancers of the breast

March 22, 2016

The first large U.S. study aimed at resolving an ongoing debate about the best way to treat an early sign of breast cancer will launch later this year under the direction of a Duke Cancer Institute investigator.

The study, entitled COMET (Comparison of Operative to Medical Endocrine Therapy) for low-risk ductal carcinoma in situ, received funding through a $13.4 million, five-year award from the Patient-Centered Outcomes Research Institute (PCORI), an independent, nonprofit organization authorized by Congress in 2010 to support research that enlightens health care decisions.  Principal investigator E. Shelley Hwang, M.D., chief of breast surgery at the Duke Cancer Institute and vice chair of research in the Duke University Department of Surgery, will lead the study through the cooperative group, The Alliance for Clinical Trials in Oncology.  

The study was designed in collaboration with Terry Hyslop, PhD, and Director of Biostatistics for the Duke Cancer Institute.  Dr. Hyslop will direct the biostatistical aspects of the study.  The design of the study was particularly challenging in that, it is anticipated that patients may not want to remain in their randomized assignment arm, particularly if assigned to active surveillance.  The notion of active surveillance, which focuses on trying to minimize over-treatment of patients, may be hard for some patients to accept.  Thus, intention-to-treat may not be a viable option due to bias from non-compliance.  Additional challenges analytically include the development of an observational registry study that will incorporate all eligible patients across the Alliance and other centers whether they were approached to participate in the trial or not.  This pragmatic component adds to the richness of the data, providing for collection of long-term outcomes, yet generates a mixture or randomized and observational data.  The study team plans to generate simulated data throughout the trial, using actual patient compliance data, to determine the best analytic approach for causal inference in this setting.  Click here to read more.  

Frank Rockhold, PhD joins the B&B Department

March 21, 2016

The B&B Department is pleased to announce that Frank Rockhold, PhD,  a leading biostatistician and proven leader in research and development, will be joining the Department as professor of biostatistics and bioinformatics.  Rockhold has more than 30 years of diverse experience in clinical trial design, data monitoring, decision sciences, statistical research, and epidemiology. He has a consistent record of leadership in improving the quality and safety of clinical trial protocols and increasing trial efficacy through innovative design, data mining, and extended use of epidemiology.  His appointment will be associated with the Duke Clinical Research Institute (DCRI).

“Throughout his impressive career, Dr. Rockhold has championed the importance of open access to patient-level clinical data,” said DCRI Executive Director Eric Peterson, MD, MPH. “With his expertise in biostatistics research and clinical trial design and data monitoring, Dr. Rockhold is an invaluable addition to our team of some of the world’s foremost authorities on clinical research.”

Rockhold was most recently senior vice president of Global Clinical Safety and Pharmacovigilance at GlaxoSmithKline, and prior to that ran Cardiovascular and Metabolic Development and the Biostatistics, Epidemiology and Healthcare Informatics departments. Earlier in his career, he held positions with Merck Research Laboratories and Lilly Research Laboratories. Rockhold is a well-respected researcher with more than 175 publications and presentations in major scientific journals across a wide variety of topics. He holds adjunct professor appointments at two leading Pennsylvania universities.

Roclhold served on the board of directors of the Clinical Data Interchange Standards Consortium, most recently as Chairman, is past president of the Society for Clinical Trials, is a fellow of both the American Statistical Association and the Society for Clinical Trials, and is an accredited professional statistician. Rockhold received his PhD in biostatistics from the Medical College of Virginia, his ScM in biostatistics from The Johns Hopkins University, and his BA in statistics from the University of Connecticut.

B&B Faculty Megan Neely selected as a Distinguished Nominee for the Gordon G. Hammes Faculty Teaching Award

March 10, 2016

The Vice Dean for Faculty, Ann Brown, MD recently announced the 2016 faculty awards for the School of Medicine.  The B&B Department is pleased to recognize faculty member Megan Neely who was selected as a distinguished nominee for the Gordon G. Hammes Faculty Teaching Award at the annual Spring Faculty Meeting in May.

The Hammes award is intended to recognize continuing excellence in teaching and mentoring, and exemplary commitment to the education of graduate students within Basic Science Departments and Graduate Training Programs of the School of Medicine. Dr. Neely teaches in both the Masters in Biostatistics program and also in the Clinical Research Training Program as well as serving as Co-Director of Graduate Studies for the both the Biostistics Masters and PhD programs.  

This award is named for Gordon G. Hammes, who served as Vice Chancellor for Academic Affairs from 1991 to 1998. In view of his longstanding commitments to Duke University School of Medicine graduate students, and his contributions as a gifted teacher and mentor, the School of Medicine established this award in his honor to recognize each year a Faculty member for continuing excellence in teaching and mentoring, and for exemplary commitment to the education of graduate students within Basic Science Departments and Graduate Training Programs of the School of Medicine.  Congratulations Dr. Neely!

CTSA Spotlight: Erich Huang, MD, PhD “Putting Big Data Ideas Into Action”

March 9, 2016

Dr. Erich Huang is featured this week on the Duke Translational Medicine Institute (DTMI) website.  As the faculty recruit to the Division of Translational Biomedical Informatics within the Department, Duke was familiar territory, he had completed the MD/PhD program in 2003 and was an assistant professor in Surgery before going to Seattle to become the director for cancer research at Sage Bionetworks.  “But what attracted me to return to Duke was the opportunity to actually implement some of these ideas in an academic health system.” 

Discussing his current projects included the Duke Data Service to create an infrastructure that makes it easy for investigators to gather and store the data they collect and generate it in a transparent manner so that others can reproduce their scientific findings.  Another project is CALYPSO – the Clinical and Analytic Learning Platform for Surgical Outcomes where machine learning and electronic health records are used to predict whether a surgical patient is going to have one of a variety of complications. The aim is to provide predictions in real time so that rounding teams can have the information at hand during their rounds. 

Dr. Huang also discussed the big data challenge of interoperability, that is finding easy ways for information to be securely exchanged between providers and platforms.  We gather so much data, but often we can’t share it. We need to find tools that allow us to move and share data. It is absolutely essential for improving healthcare nationally.  Click here to see the full article.

B&B Department offers new summer course on High-Throughput Sequencing 

March 1, 2016

The Department of Biostatistics and Bioinformatics is pleased to offer its second annual High-Throughput Sequencing Summer Short Course. This course will extend and expand upon the material from the inaugural 2015 course on proper procedures to ensure experimental and statistical validity. In addition to faculty and research staff from our department, this course will also now feature the expertise from the Duke Center for Genomic and Computational Biology. The target audience for the course is advanced undergraduates, graduate students, postdocs, research staff and junior faculty in the STEM fields. The six-week course will be held from July 5 to August 11.  For more information, including the material from the 2015 course, visit our course page.  
To Apply: click here for Application  Questions?  Email: htscourse@duke.edu for further information.

Duke CTSA Biostatistics Seminars Not Just for Statisticians

Jan 27, 2016

The Duke Translational Medicine Institute (DTMI) Biostatistics Core is featured this week on the DTMI website.  The Biostatistics Core is housed in the Department of Biostatistics and Bioinformatics.  The Core is a team of faculty and staff biostatisticians with diverse and extensive experience in conducting a broad range of research projects. It supports an interdisciplinary network of clinical investigators conducting research at Duke by providing expertise in the implementation of statistical methodology. 

It is essential for clinical researchers to understand basic statistical concepts and understand how to collaborate with statisticians. The Biostatistics Core offers seminars, workshops, office hours, and training programs focused on developing these interdisciplinary skills.  The Biostatistics Core monthly applied seminar exposes statisticians and clinicians to new statistical methodology and resources. Presenters include Duke staff and faculty, as well as guests from other universities. Past seminars have included a REDCap demonstration by DOCR and an introduction on survey design by SSRI. Last fall, Dr. Sujit Ghosh, Professor of Statistics at NC State and Deputy Director of SAMSI, presented “A (small) Bag of Bayesian Tools for Biostatisticians.” Dr. Andrzej Kosinski from Duke gave a talk on generalized estimating equations (GEE). 

The next seminar will be Tuesday, February 9th  from 3-4pm in Hock Plaza 11025 and Dr. Maren Olsen will present "Association between bariatric surgery and long-term survival in veterans: an illustration of sequential stratification matching" Seminars are typically held the second Tuesday of the month 3-4pm in Hock Plaza 11025 and are open to anyone in the Duke community.   Click here to see the full article. 

Masters Students Present to the Biostatistics Core

Jan. 15, 2016

As part of their internships with the Biostatistics Core, second year students Zinan Chen, Xin Liu, and Victor Poon gave presentations of their work during the past semester.  Zinan Chen presented her work on “Unfavorable versus favorable intermediate risk in prostate cancer,” Xin Liu discussed “Perspectives On Clergy Health Problems, and Victor Poon examined "Analysis of Pulmonary Hypertension in Patients with Mitral Valve Surgery.”  

Zinan Chen has been working with Lauren Howard of the Biostatistics Core and under Dr. Stephen Freedland's prostate cancer research team. In her presentation, she introduced a project she worked on using survival analysis.  She validated this classification method for intermediate risk prostate cancer by comparing the cancer outcomes.  This new method allows doctors to group patients based on their baseline characteristics and provide better, more targeted help for them. 

In the study that Victor Poon completed, “Analysis of Pulmonary Hypertension in Patients with Mitral Valve Surgery,” survival analysis was utilized to examine the differences in expected time to death between patients with and without pulmonary hypertension pre mitral valve surgery. Results from a preliminary analysis suggest that patients with pulmonary hypertension pre mitral valve surgery have lower survival when compared to patients without pulmonary hypertension pre mitral valve surgery.

Xin Liu has been doing her internship as a collaborative biostatistician with Clergy Health Initiative Team funded by Duke Endowment, part of the Duke Divinity School. She discussed an observational study based on the clergy health initiative longitudinal survey data collected in 2014. She used hierarchical modelling to evaluate the effect of taking international Sabbath day on clergy's physical, mental health and spiritual vitality. Her presentation successfully interpreted the findings, how she handled the challenges of missing data and confounding variables."

All Masters of Biostatistics degree candidates complete a practicum which usually includes an internship.  This allows students to develop their analytic ability, biological knowledge, and communication skills. The practicum is typically completed during the summer after the first year, but can be completed during the second year. 

B&B Faculty Shein-Chung Chow, PhD publishes book on Quantitative Methods for Traditional Chinese Medicine Development 

Nov. 20, 2015

In recent years, many pharmaceutical companies and clinical research organizations have been focusing on the development of traditional Chinese (herbal) medicines (TCMs) as alternatives to treating critical or life-threatening diseases and as pathways to personalized medicine.  Dr. Chow’s new book is the first book entirely devoted to the design and analysis of TCM development from a Western perspective, i.e., evidence-based clinical research and development. It provides a comprehensive summary of innovative quantitative methods for developing TCMs but also a useful desk reference for principal investigators involved in personalized medicine and connects the pharmaceutical industry, regulatory agencies, and academia.

This book covers all of the statistical issues encountered at various stages of pharmaceutical/clinical development of a TCM. It explains regulatory requirements; product specifications and standards; and various statistical techniques for evaluation of TCMs, validation of diagnostic procedures, and testing consistency. It also contains an entire chapter of case studies and addresses critical issues in TCM development and FAQs from a regulatory perspective.  This book is published by Chapman and Hall/CRC Press, Taylor & Francis, New York.  


AMIA Spotlight:  Jessica Tenenbaum, PhD

Nov. 9, 2015

Dr. Jessica Tenenbaum is featured this week on the American Medical Informatics Association (AMIA) website.  She discusses her choice to work in informatics as it “has been the perfect combination of my passion for biology, and making people’s health better. It also utilizes my love of computer science, programming, and thinking about data and algorithms, and getting to write code.”

Dr. Tenenbaum’s research is focused around informatics infrastructure to support translational research and precision medicine. She serves as the data science lead for the Alzheimer ’s Disease Metabolomics Consortium (ADMC) and provides domain expertise for the Data Standards Coordinating Center under the NIH’s BD2K initiative. Finally, she is interested in informatics infrastructure to enable precision medicine through genomic clinical decision support and incorporation of genomic data in the electronic health record.  Click here to see the full article.

Ross Prentice visits B & B Department

Nov.5, 2015

The B&B Department was honored to host Ross Prentice, Professor of Biostatistics and former Director of the Public Health Sciences Division at Fred Hutchinson Cancer Research Center as the fifth annual Distinguished Speaker.  

Dr. Prentice gave two lectures, the first, “Multivariate Failure Time Data Analysis Methods” where he presented a new nonparametric estimator of the bivariate survivor function.  This would find applications to genetic epidemiological studies or group randomized clinical trials.  His second lecture was on the “Women's Health Initiative, History, Contributions and On-Going Research” which highlighted his impressive career in cancer research and epidemiology.  

B&B Faculty Laine Thomas receives 2 year AHRQ grant to study of matching methods for comparative effectiveness studies of longitudinal treatments

Nov. 2, 2015

The problem of causal inference from observational data becomes particularly challenging when treatments are initiated over longitudinal follow-up.  Robins and colleagues contributed various methods including marginal structural models (MSMs) and g-estimation of structural nested models (SNMs).  Matching methods for time-dependent treatments offer a convenient alternative.  In essence, the idea is to create pairs of patients, one of whom initiates treatment at time T and another who doesn’t, who are comparable: both eligible for treatment at time T and having a similar covariate history, where that history may include the full, time-dependent information available before time T.  This creates a pseudo-experiment for every treated patient.  The pairs can be combined to create a matched sample and analyzed using standard methods for matched data.  On the surface, this approach produces clinically intuitive results that look just like randomized trials, or observational studies of baseline treatment, including hazard ratios, and survival functions.  That is a tremendous advantage, however, there are important complexities in how to define comparable and eligible patients over time.  Thus, many variations have been proposed for specific applications, with unique terminology such as sequential stratification matching, propensity score matching with time-dependent covariates, and balanced risk set matching.

A researcher, desiring to understand and apply these methods, will encounter various challenges.  Even within the field of biostatistics and epidemiology, related methods use distinct jargon so they are not easily found by searching.  In addition, the existing articles are framed around solving a specific problem, and not in terms of generalizable principles and alternatives.  Aim 1 will address this gap by conducting a comprehensive review of longitudinal matching methods in order to identify the relevant alternatives, advantages, disadvantages and choices that should be considered explicitly in all longitudinal matched analyses.

Statistical methods for time-dependent confounding are under-utilized and poorly appreciated in clinical research.  This gap is exemplified by the fact that propensity score matching with time-dependent covariates has only been referenced in one cardiovascular publication that did not apply the method, but recommended it for future studies.  Similarly, a rigorous statistical paper on sequential stratification matching appeared in the Journal of the American Statistical Association in 2009, but does not appear to have been referenced beyond studies conducted by the original authors, colleagues and ourselves.  Perhaps the most powerful way to promote the use of statistical methods is to show that they matter in real applications.  In Aim 2, we will use the data sources available at Duke Clinical Research Institute, such as the Framingham Heart Study, to assess the impact of longitudinal matching methods when compared to na├»ve methods and alternative strategies for time-dependent confounding.  

Enthusiastic response to the Duke-Industry Statistics Symposium

Oct 25, 2015

On Oct. 22-23 more than 160 participants from across the country attended the Duke Industry Statistics Symposium.  It was held at the Trent Semans Center on the Duke Campus. 

The first day of the event led off with 4 well attended half day short courses.  On Friday, Biostats Department Chair Liz Delong and Rene Kubiak, Head of US Statistics at Boehringer Ingelheim gave welcoming remarks.  Dr Yi Tsong from the Center for Drug Evaluation and Research (CDER) of the Food and Drug Administration gave the keynote address on Duality of significance tests and confidence intervals in drug development. 

The welcoming and keynote was followed by nine sessions that offered 30 presentations, in addition to a poster session, and a closing panel discussion.  There were over 15 posters presented at the Symposium.  Prizes for best posters were awarded to Hyang Kim from Parexel and Laine Thomas of the Biostat Department.  Two Biostats Masters students, Tongrong Wang and Meng Chen also received poster awards.  

B&B Faculty Terry Hyslop’s interdisciplinary proposal, Research Colloquia in Big Data selected for funding

September 21, 2015

The Duke University School of Medicine provides support for interdisciplinary colloquia to bring together basic science, translational and clinical faculty members with common interests in a biomedical problem or area.  Dr. Hyslop’s proposal was chosen for the 2015-2016 cycle.  

Momentum has been built on campus around a T32 application in big data that encompasses the Schools of Medicine, Engineering, and Arts and Sciences.  Forty-four faculty from across these schools have engaged to train computational scientists in biostatistics, statistics, computational biology, and electrical and computer engineering. 

As PI of the T32 application, Dr. Hyslop will establish bi-monthly colloquia to bring together researchers interested in big data with the goal of establishing partnerships and working groups in the development of new grant applications around methodologies leveraging big data, particularly to deepen our understanding of human disease.  Medical partners with interest in big data from DCI, DCRI and other appropriate Centers and Institutes will be invited to participate.  This application is the first of its kind to blend computational faculty from across the Medical School and University sides of campus and unite students from these departments in a unique inter-disciplinary environment.