STAT 509 Design and Analysis of Clinical Trials
Fall 2013 Semester
Co-Instructors
Tonya Sharp King, PhD
Professor
Division of Biostatistics and Bioinformatics
Department of Public Health Sciences, A210
Penn State College of Medicine
600 Centerview Drive, Suite 2200
Hershey, PA 17033-0855
Email: tsk4@psu.edu
Rebecca Antle Lengerich, M. A.
Senior Instructor
Division of Biostatistics and Bioinformatics
Department of Public Health Sciences, A210
Penn State College of Medicine
600 Centerview Drive, Suite 2200
Hershey, PA 17033-0855
Email: ral14@psu.edu
To contact instructors: Use ANGEL email system (check “send copy to internet email” as well).
Course Description
This is a survey course that stresses the concepts of statistical design and analysis in biomedical
research, with special emphasis on clinical trials. SAS for Windows statistical software will be
used throughout the course for data analysis. Penn State offers three opportunities to take a
course in Design and Analysis of Clinical Trials: Stat 509 at the University Park campus, Stat
509 through World Campus and PHS 580 at the Hershey campus. The instructional materials
and requirements for World Campus Stat 509 are similar to those of Stat 509 at University Park
and PHS 580 at Hershey, adapted for online instruction. Dr. Vern Chinchilli was the original
course author for Stat 509.
Course Prerequisites
STAT 500, STAT 501, HES/PHS 520, or an equivalent introductory statistics course. Prior
knowledge of SAS is not required, but students should have some familiarity with operating a
PC in a Windows environment.
Required Course Materials
In order to take this course, you need:


access to a Windows PC that has internet access, SAS, and Microsoft Word
you can purchase your own copy of SAS 9.3 Windows Student License & Media
through Penn State's Computer Store for $30. You will need to have your 9 digit PSU ID
number handy when you make this order.
A Note to MAC users. You could attempt to use a MAC computer and Virtual PC software to
run SAS. However, SAS does not guarantee the outcome. You are, therefore, strongly
discouraged from using anything but a Windows PC for this course.
Recommended Text Books
The majority of the material on the design and analysis of clinical trials is taken from:
Piantadosi S. (2005). Clinical Trials: A Methodologic Perspective, Second Edition. New
York, NY: John Wiley & Sons.
Additional material on the analysis of clinical trials is taken from
Woolson RF, Clarke WR. (2002). Statistical Methods for the Analysis of Biomedical
Data, Second Edition. New York, NY: John Wiley & Sons.
Learning Assessment Plan
5 Homework Assignments (4 at 20 points; final homework 40 points)
Students are expected to submit assignments by 2:30 pm on the date due.
If you experience a crisis that severely compromises your ability to submit your work on-time,
contact Ms. Lengerich prior to the due date to appeal for an extension. Otherwise, work
submitted one day late will receive half credit; work beyond one day late will not receive credit.
SAS:
SAS technical support: http://support.sas.com/techsup/
Stat software requirements and system requirements are here:
onlinecourses.science.psu.edu/statprogram/node/4
and onlinecourses.science.psu.edu/statprogram/node/3
SAS EG gives nice output and is more like Excel or Minitab with drop-downs under the Tasks
tab. However, the examples in this course provide programs that you can generally cut and paste
into the program screen for SAS EG or the Program Editor for SAS 9.2 and then modify as
needed to solve a homework problem. You will have examples of data entered in the program
itself.
Once a program is written, click the figure of the person 'running' or the tab 'run' to submit the
program and view the output. In SAS 9.3, you can save output to a file if you are in the output
window by clicking on the 'file' tab and 'save as'. If the program isn't working, you will want to
see the log window. The 'window' tab allows you to select the program editor, output or log or
graph windows (or tiling or cascading all 3). You can toggle between the screens you wish to
view.
In SAS EG, I can also paste a sample program in the program tab, modify, run (tab), look at
results and create (tab) a report which can be exported (another tab..means you save the report)
Once SAS is installed, for SAS coding problems...
1. Check for missing semicolons, check the log to see where it went bad. Use the Help
tab in SAS and check out examples for the PROC you using, also re-check examples in
the course notes.
2. We expect your homework submissions to be in your own words, representing
individual work. You may however discussion SAS coding problems with other students
and email the instructors if needed. I will also post a discussion space when homework
is assigned which you may use to post a SAS question or question on the assignment
…nights and weekends a fellow student may be quicker to see your post than the
instructor and provide an answer.
Tentative Course Schedule
Week 1
Aug 27
Week 2
Sept 3
Week 3
Sept 10
Week 4
Topics
Clinical Trials as
Research, Contexts
for Clinical Trials
(Ch 2 and 4)
Ethics, Clinical
Trial Design (Ch 6)
Random Error and
Bias, Objectives
and Outcomes (Ch
7-8)
Translational
Assignments
Discussion
Question Set 1:
Who am I and
why am I here?
Would you
participate in a
clinical trial?
Discussion
Question 2
Discussion
Question 3
Discussion
Completed by
In class
In class
In class
In class
Points
Sept 17
Clinical Trials,
Dose-Finding
Designs (Ch 9-10)
Sample Size and
Power (A) (Ch 11)
Sample Size and
Power: Noninferiority and
Equivalence Trials;
Study Cohort (Ch
12)
Treatment
Allocation;
Counting Subjects
and Events
(Ch 13 and 15)
Treatment Effects
Monitoring; Safety
Monitoring (Ch 14)
Question 4
Week 9
Oct 22
Week 10
Oct 29
Estimating Clinical
Effects (Ch 16)
Prognostic Factor
Analyses (Ch 17)
SAS programs
Homework 3
SAS programs;
11/11 2:30 pm
In class
Week 11
Nov 5
Reporting and
Authorship;
Factorial Design
(Ch 18-19)
Crossover Design
(Ch 20)
Meta-analysis (Ch
21)
No class…Give
thanks!
Medical Diagnostic
Testing; Correlation
and Agreement (Ch
22 -23)
Homework 5 review
Review factorial
study; SAS
program
In class
Homework 4
11/25 2:30 pm
20
Homework 5
SAS example
12/9 2:30 pm
In class
40
Week 5
Sept 24
Week 6
Oct 1
Week 7
Oct 8
Week 8
Oct 15
Week 12
Nov 12
Week 13
Nov 19
Nov 26
Week 14
Dec 3
Week 15
Dec 10
Homework 1
10/7 2:30 pm
20
(Homework 1)
Discussion
Question 5; SAS
program
In class
Discussion
Question 6
Homework 2
In class
20
10/28 2:30 pm
20
(Homework 5)
SAS examples
Academic Integrity Policy
Please review Penn State's tutorial on plagiarism and academic dishonesty.
120 total
All Penn State policies regarding ethics and honorable behavior apply to this course. Academic
integrity is the pursuit of scholarly activity free from fraud and deception and is an educational
objective of this institution. All University policies regarding academic integrity apply to this
course. Academic dishonesty includes, but is not limited to, cheating, plagiarizing, fabricating of
information or citations, facilitating acts of academic dishonesty by others, having unauthorized
possession of examinations, submitting work of another person or work previously used without
informing the instructor, or tampering with the academic work of other students.
For any material or ideas obtained from other sources, such as the text or things you see on the
web, in the library, etc., a source reference must be given. Direct quotes from any source must be
identified as such.
All exam answers must be your own, and you must not provide any assistance to other students
during exams. Any instances of academic dishonesty WILL be pursued under the University and
Eberly College of Science regulations concerning academic integrity.
Disabilities
It is Penn State's policy not to discriminate against qualified students with documented
disabilities in its educational programs. If you have a disability-related need for modifications in
this course, contact your instructor and the Office for Disability Services (located in 116 Boucke
Building). Instructors should be notified as early in the semester as possible. You may refer to
the Nondiscrimination Policy in the Student Guide to University Policies and Rules 1997. See
the website http://www.equity.psu.edu/ods/ for details.