JOB SUBMISSION MENU (JSM):
A PROGRAMMING TOOL
TO STANDARDIZE CLINICAL TRIAL SUMMARIZATION
Iraj Mohebalian, Parke-Davis Pharmaceutical Research
Mark Becker, STATPROBE, Inc.
Lora H. Schwab, STATPROBE, Inc.
The standardized SAS programs within JSM do not
include batch Job Control Language (JCl), TSO
commands, or any SAS code specific to a given drug.
Instead unique information about each drug is stored
wtthin the JSM environment. During submission of
reports, JCl, CLlST, or SAS codes are dynamically
constructed and passed to programs for execution.
ABSTRACT
A Job Submission Menu (JSM) is described which
aids in standardizing the SAS programming that lists,
summarizes, and analyzes the data from clinical trials.
Design objectives of the system include:
selfdocumentation of clinical trial programming, simplified
batch and interactive job submission of SAS
programs within the IBM/MVS operating system, a
library system to document all clinical drug projects,
minimization of duplicate programs across clinical
studies, potential Computer-Assisted New Drug
Application (CANDA) uses. The system was designed
wtth flexibiltty to handle both standardized and nonstandardized programming. After over six years of
use the system has gained dramatically in users and
is credited with facilitating the evolution of
standardization. JSM is compared to one other
approach to standardization.
STANDARDIZATION OF CLINICAL TRIAL
MANAGEMENT
Standardization of clinical trials is the process of
making efficient use of similarities and repetition in
any aspect of clinical trials. Aspects of clinical trial
management where standardization can occur are:
•
•
•
•
•
INTRODUCTION
protocols
case report forms (CRFs)
database design and variable names
format decodes and dictionaries
computer programs to list and summarize data
• research reports
The Job Submission Menu (JSM) system aids in
standardizing clinical trail summarization. It is written
in SAS, IBM ISPF Dialog Manager, and TSO CLlST,
and tt works wtthin the IBM/MVS operating system in
conjunction wtth the CA-LiBRARIAf118 program source
code management system and the CA-'!'" automated
scheduling system. After approximately 200 pages of
programming code and four different releases over
the past six years of use, JSM has gained
dramatically in users and is credited with facilttating
standardization of programming.
Advantages of standardization include reduced time
spent reinventing methods and systems already
developed; consistent handling of data and
presentations, more easily understood because users
and readers are accustomed to the methods; ability
to quickly absorb a mass of data and provide timely
reporting of results; and promotion of good scientific
research by demanding careful planning across a
series of stUdies.
However, there are problems in implementing
standardization. Time and effort are required to
achieve and to maintain standard programs.
Insufficient foresight combined with a lack of flexibiltty
can quickly ruin a system of standardization. The
necessary cooperation from the various groups
involved in each clinical trial can be difficult to obtain.
Presently the JSM system allows data processors,
statisticians, and programmers to work wtthin an
integrated environment in the preparation of reports
for clinical trials. Users can locate and process any
SAS programs assigned to an investigational drug.
954
APPENDIX B.2
(PAGE 1 OF 1)
DOUBLE-BLIND, MULTICENTER" PLACEBO-CONTROLLED STUDY OF TEST DRUG
VERSUS CONTROL DRUG IN PATIENTS WITH DISEASE X
PROTOCOL 9999-135-OVERALL
N
SEX
MALE
FEMALE
PLACEBO
TEST DRUG
7S
••
52
23
(69.3"10)
(30.7%)
38
31
7.
(55.1%)
(44.9%)
AGE (VRS) MEDIAN (RANGE)
34.0 12l-53}
35.0 (19-50)
RACE:
57
,.
(78.0%)
(18.7%)
(5.3%)
(0.0%)
57
(52.2%)
(30.-4%)
(13.0'%)
(4.3%)
15
(76.0%)
(9.3%)
(14.7%)
59
CAUCASIAN
BLACK
OTHER
NOT STATED
•
0
REPRODUCTIVE POTENTIAL (FEMALE):
BIRTH CONTROL
HYSTERECTOMY
INFERTILEITUBAL
MENOPAUSE/POST
GRADE OF DISEASE:
STAGE 1
STAGE 2
STAGE 3
12
7
57
7
11
,.
2
•
11
•
,.
TREATMENT GROUP
CONTROL
DRUG
TOTAL
.,
2'
21.
(58.6%)
(41.4%)
34.5 (21-49)
,.
(82.6%)
(14.5%)
56
(2.9"10)
3
(0.0%)
(48.-4%)
(35.5%)
(12.9%)
(3.2%)
"8
(78.3%)
(7.2%)
(14.5%)
52
8
5
2
,.
(80.0"10)
(14.3%)
(4.3%)
(1.4%)
(48.3%)
(27.6%)
(17.2"10)
(6.9%)
(74.3"0)
(11.4%)
(14.3%)
131
83
(61.2%)
(38.8%)
34.5 (2l-53)
17.
3'
•
"2.
•
12
163
2.
31
(79.4%)
(15.9%)
(4.2%)
(0.5%)
(49.9%)
(31.3%)
(19.5%)
(9.8%)
(76.2%)
(9.3%)
(14.5%)
FIGURE 1. AN EXAMPLE OF A CLINICAL TRIAL REPORT
A LOGICAL APPROACH TO
STANDARDIZATION
• a time-saving system which "self-documents" the
computer programs which list, summarize, and
analyze the results of a clinical trial.
JSM was originally developed to facilitate
standardization of clinical trial report generation. The
task of standardizing all aspects of clinical trial data
management and reporting was overwhelming so the
JSM system began with one part of the process and
expanded standardization from this base. The part
selected was the generation of reports Oisting and
summary tables) of clinical trial results.
As it
developed, JSM provided a logical approach to
standardization.
• a time-saving system which provides for easy
submission of SAS computer programs in the
environment of an unfriendly operating system
(e.g., JCL requirements of TSO).
• a system which has the potential to assist in
achieving a currently popular result, ComputerAssisted New Drug Applications (CANDA).
EXAMPLE: STANDARDIZING A
"REPORT"
To be readily accepted, a system for standardizing
programs across stUdies must be capable of evolving
over time. The system must be flexible to handle
both standard and non·standard input. A system
which handles subgroups of standard input will
provide the seed offuture widespread standardization.
Finally, to be more readily accepted, the system
should offer an advantage which is of interest to users
who don't care about standardization. JSM satisfied
this last ideal by providing the following:
An example ·report· is given in Figure 1 for a
·Summary of Patient Characteristics". The report
shown is typical of a clinical trial in which there are
three treatment groups (placebo, test drug, and
control drug). The report is a summary of patient
characteristics over all investigative sites or centers in
a multicenter study; a similar summary would also be
generated for each center. Assume that the same
report is wanted for many clinical trials and assume
955
that the databases for these clinical trials are
"standard" wtth respect to variable names and codes
for patient characteristics.
special PROe FORMAT statements). Table 1 is a
sample of how JSM handles some non-standard
ttems.
Non-standard items, that is, ttems which change from
one clinical trial to the next, in the text of the report in
Figure 1 include the following:
TABLE 1. How JSM Handles Non-Standard
Items
•
•
•
•
•
•
•
•
the source of data
the study tftle(s)
the test drug identffication
the protocol identification
the study center identifications
the report numbers (e.g., Table 4)
the treatment group names
the number of treatment groups
Method
C
B
B
B
A
B
E
D
Non-Standard Items
The source of data
The study tttle(s)
The test drug identffication
The protocol identffication
The study center identffications
The report ttties (tablenames & numbers)
The treatment group names
The number of treatment groups
Non-standard ttems in processing the report include
the following:
JSM PROFILES
• computer system user to notffy
where to route job
job priortty on the computer system
The study profile, saved in a portion of JSM called
JSM Profile, is the aggregate of non-standard ttems
and default job submission (i.e., JCL) options
available when requesting reports for a specffic study.
In addttion to constructing JCL or a CLiST based on
each user profile, JSM passes 131 SAS macro
variables to each selected SAS program based on a
user profile and the user-constructed study profile.
Table 2 shows a few selected SAS macro variables
which are passed to each program.
• submtt to print or to held queue
number of copies
• choice of paper (3-hole, no punch, portratt,
landscape)
• choice of printer Qaser or not)
• SAS mode (batch, interactive)
program name and location
Standard items in the report include:
TABLE 2. Some JSM Macro Variables
• the form of data (names of variables, codes)
the format of the report
Variable Name Purpose
• the title of the report itself
&JSMBASE
&JSMDDBAS
&JSMDECOD
&JSMDDECO
&JSMEXEC
There are at least five methods for providing standard
treatment of non-standard ttems. Method A is to
include non-standard items as variables in the
database. Method B is to treat non-standard items as
macro variables passed to the SAS report program at
the time of job submission. Method C is to treat nonstandard ttems as variables passed to job control at
the time of job submission. Method D is to handle
the ttem through programming (perhaps keying on a
variable passed at the time of job submission or
computed from data within the same program, or by
providing two or three versions of the "standard"
program). Method E is to treat non-standard items as
source code statements to be inserted in the SAS
report program at the time of job submission (such as
&JSMTITLl
&JSMOPT1
&JSMTRIAL
&JSMLlBRA
&JSMNUM1
956
Dataset name of primary SAS library
DDname of primary SAS library
Dataset name of SAS decode file
DDname of primary SAS decode file
Specifies which SAS catalog
procedure to execute
First line of title wtthin a report
Used to specffy optional SAS logic
wtthin report source code
Used to specify the subset of trial
numbers (Le., various study
centers)
Name of LIBRARIAN file containing
report SAS source code
Name/number of table used within
title
8UBJOB MENU
COMMAND
~
,---- JCL
Drug.ID
=:::::::::>
eon
8tudr-1D
c:::::::::::>
0&
JOBNAMEI REPORT
NOTIFY, JDOW
COPIE8. 1
M8GCLAS9. iii.
CLASSI U
BINI 124
SiloS MODE -==c> lATCH
LASER: Y (YIN)
Option.
CONTROLI 8U.MIT
0:;::::::(>
IF 8TArUS - 2 I
<==<>
Tableb) SpeCllloatlon:
1. R9iGA.Oll Appendix E.1 /I LIST OF ADVERSE EVENTS
2. Rg90A12 I Table B.20 /I SUMMARY OF I.E SEVERITY
..
..
8. RSl911H02 I Appendix F.2 1/ LIST MEDICAL HISTORY
5.
7.
FIGURE 2. EXAMPLE OF JSM REPORT SUBMISSION SCREEN
Then, at the time of job submission (as seen in
Figure 3), JSM will prompt the user with a complete
list of programs assigned to the specific clinical trial
project. One can see at a glance which programs
generate which report numbers, and one can quickly
change report numbers by modifying the area in JSM
Profile rather than the individual programs. JSM has
security features which allow only authorized
personnel to change a profile.
The information in JSM Profile is passed to the SAS
report program at the time of job submission. For an
example of the JSM job submission screens, see
Figures 2 and 3. Figure 2 shows the screen used to
submit a report using JSM. The screen permits the
user to choose a specific study ("Drug-ID" and
"Study-ID") and various JCL options (default values
appear so that the set-up may not need to be
changed). The user fills in the 'Table(s) Specification"
lines with specific report requests. If the user prefers
to select from a list of reports, the screen illustrated
in Figure 3 appears if no request is entered on the
"Table(s) Specification" lines. The user then selects
reports by entering "S" to the left of all reports
desired.
COMPARISON TO ANOTHER
APPROACH TO STANDARDIZATION
There are other approaches to standardization. In the
AUTO REPORT GENERATOR system, non-standard
information is fed to a standard program which in turn
generates non-standard SAS programs to report a
specific clinical trial. In contrast, in the JSM system,
standard SAS programs are written with macros
which receive non-standard information from the
profile set up for each clinical trial. Table 3 compares
these two systems briefly.
The features of JSM encourage users to document
the programs used to generate reports for a dinical
trial. First, a special area in the JSM Profile is
reserved for listing program names, passwords
(assigned when programs are permanently stored in
the LIBRARIAN system), and report numbers which
are passed as macro variables (e.g., APPENDIX B.2).
957
REPORT 8ELECTION MENU
COMM"ND
-==<>
SOROLL
~ PAGr:
Drug_to: 8908
8tudy.IDI DB
LINE
CMO
Table(a} epecltlcatlon
A"'A01 I Appel\dlx E.1 II LlaT OF ADVERSE EVENTS
R8IUIA11 I Tabl. B.18 1/ SUMMARY RELEATED AE·.ODY BY8TEM
RaSUtAtl I TABLE 8.20 /I 8UMMARY OF AE SEVERITY
RoaaAiS J APpendix E.7 /I LIST PTa DISCONTINUED
. s ..
RIIDD10 I rable E.10 II aUMWARY OF PATIENTS DISCONTINUED
RIgIE10 I rabl. B •• "
SUMMARY OF ETT BY WEEK
RlltlaHat I Appendl:a F.1 /I LIST PATIENT CHARACTERISTICS
AI.GH02 I Ap,endlx F.2 II LlaT MEDICAL HI8TORY
RIShlH03 I App.ndlx F.3 II LlaT PRIOR MEDICATION
R9UH04 I Tabl. B.1 1/ SUMMARY PATIENT CHARACTERlaTICa
FIGURE 3. EXAMPLE OF JSM REPORT SELECTION SCREEN
TABLE 3. Comparison of Two Standardization
Systems
JSM
Easy to set-up
Easy to modify
Handles non-standard
Promotes gradual standard
Promotes documentation
NO
YES
YES
YES
YES
ACKNOWLEDGEMENTS
SAS is a registered trademark of SAS Institute Inc.
Cary, NC.
AUTO
REPORT
IBM is a registered trademark of International
Business Machines Corporation.
NO
NO
NO
NO
CA-UBRARIAN and CA-7 are trademarks of Computer
Associates International., Inc., Garden City, NY.
?
For further Information regarding this paper, please
contact:
CONCLUSION
Mark Becker. PhD
STATPROBE. Inc.
5340 Plymoulh Road
Ann Arbor. Michigan 48105
leI. (313) 769-5000
The Job Submission Menu (JSM) has been successful
in simplifying submission of report requests (SAS
programs) for clinical trials, facilitating standardization
of report requests, handling both standard and nonstandard reports, and improving documentation of
reports of clinical trials.
STATPROBE, Inc. is a contract research organization
serving the pharmaceutical industry.
958