Biostatistics V – special topic: Bioinformatics for clinical re

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Oct 1, 2013 (4 years and 13 days ago)

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Biostat 226 / TICR V
-

Winter 2006


Classes: 1/3
-
3/7, Tuesdays 10:30 A.M.
-
noon, China Basin Landing, Room 6704

Course website:

http://www.epibiostat.ucsf.edu/courses/schedule/biost
atv.html


In the health
-
care setting, randomized controlled trials (RCTs) are experiments in which
investigators randomly assign eligible patients into intervention groups, then compare
the outcomes of the groups to determine the relative effect of the in
terventions. The
primary outcome variable in such trials is typically a direct measure of change in
ultimate clinical status, such as disease progression. In this course, we will examine
methods that have been developed to ensure the validity of the result
s of RCTs.


Recently, high
-
throughput molecular technology


genomics and proteomics, for
example


have revolutionized the way biology and diseases are studied, and begin to
pave the way towards personalized medicine. RCTs that use molecular data as
pred
ictors, outcomes, or patient inclusion criteria also face special challenges in study
design and data analysis. Statistical and bioinformatics methods are essential to reduce
the sea of data to manageable components with biological interpretation. In this
course,
we will discuss methods for analyzing
omics

data using examples from published
clinical research literatures.


The goals of this course are

1.

To understand the importance and pitfalls of bioinformatics in clinical research
and the methods commonl
y used for the design and analysis of
omics

studies

(Topic I: Statistical Methods in Bioinformatics; weeks 1
-
5).

2.

To understand methods that ensure the validity of RCTs

(Topic II: Current Issues in RCTs; weeks 6
-
10).


To achieve these goals,



The profe
ssors will present 3 methodological lectures on each Course Topic.



Lectures will be followed by presentations of student project, with students
working in pairs on projects of their interest. Ideally, the students will propose a
RCT that incorporates a bi
oinformatics component.



For each Course Topic students will

o

Select for review one or more publications that extend the material
presented in the lectures, and

o

Indicate in written and oral reports how the methods discussed in the
lectures and selected p
ublications apply to their project.


Grading
:
25% classroom participation; 25% oral presentation; 50% written reports



Papers for review will be chosen with input from the instructors from among (i)
methodological publications, (ii) applied publications, a
nd (iii) student projects
that substantially address course topics.

o

Proposals for student projects (selection of paper/topic) must be submitted
to the instructor via e
-
mail by 5 P.M. on Jan 16 for Topic I; Feb 20 for
Topic II.




Students will submit

two wr
itten reviews (each 2 pages minimum),

one per
Course Topic. Reviews may be jointly written by the student
-
pair or individually
written.

o

Written reviews must be submitted to the instructor via e
-
mail by 5 P.M. on
Feb 6 for Topic I; Mar 6 for Topic II.




Ea
ch team will present
two oral reviews
, one for each topic
(15 minutes
including discussion; no more than 15 slides)
. The quality and length of oral
reports should typify those made to professional societies.

o

Oral presentations: Jan 24
-
31 for Topic I; Feb

28
-
Mar7 for Topic II.



Schedule & Instructors:


Course Topic I:

Statistical Methods in Bioinformatics


Jan 3:


Lecture 1
-

Introduction to bioinformatics

Jan 10:

Lecture 2
-

Statistical methods for microarray expression data analysis

Jan 17:

Lecture
3
-

Statistical data
-
mining

Jan 24:

Student presentation session I
-
1

Jan 31:

Student presentation session I
-
2


Instructor
:

Ru
-
Fang Yeh, Assistant Professor of Biostatistics




Email:
rufang@biostat.ucsf.edu


Phone: (415) 514
-
8033, Office: CBL
-
5731



Course Topic II:

Current Issues in the Design & Analysis of Randomized Clinical Trials


Feb 7:


Lecture 1
-

Endpoints in RCTs: Clinical outcomes and surrogate markers

Feb 14:

Lecture 2
-

Study designs: Non
inferiority
versus

superiority trials

Feb 21:

Lecture 3
-

Monitoring: Group sequential designs for randomized clinical trials

Feb 28:

Student presentation session II
-
1

Mar 7:


Student presentation session II
-
2


Instructor
:

Joan F. Hilton, Associate Prof
essor of Biostatistics




Email:
joan@biostat.ucsf.edu

Phone: (415) 514
-
8029, Office: CBL
-
5727