United States
Environmental Protection
Agency
Environmental Monitoring
Systems Laboratory ;
Las Vegas, NV 89193-3478
Research and Development
EPA/600/S8-90/086 Mar. 1991
EPA Project Summary j
User's Guide: Chromosomal
Aberration Data Analysis and
Interpretation System
R. R. Tice, A. C. Pellom, and C. H. Nauman
This usar's manual provides guidance
to researchers and the regulatory com-
munity for interacting with a data analysis
and statistical interpretation system,
designated as CA. CA Is dedicated to the
in vivo chromosome aberration assay, a
routinely used genetic toxicology assay
for chemical compounds which may be
of health concern. The objective in de-
veloping this system has been to promote
consistency and intercomparability of
assay test results across laboratories,
thus providing researchers and govern-
ment decision makers with a means to
assure comparable analyses of test data.
The CA data analysis system has been
developed in consultation with a panel
of biostatisticians and experts in the
field of cytogenetics. Software for ex-
ecuting CA and two sets of test data,
contained on two 5.25 inch floppy disks,
accompany the user's guide.
This Project Summary was developed
by EPA's Environmental Monitoring
Systems Laboratory, Las Vegas, NV, to
announce key findings of the research
project that is fully documented in a
separate report of the same title (see
Project Report ordering Information at
back).
Introduction
CA is a data analysis and interpretation
system designed for chromosomal aberra-
tion and m italic index data collected using in
vivo test systems. The software consists of
a set of routines for 1) entering, editing and
storing experimental data and descriptive
information; 2) generating statistics appro-
priate to the analysis of chromosomal aber-
rations and m'rtotic index jdata; and 3) pre-
senting the results of these statistics through
graphs and tables. j
The user's guide consists of two parts.
The first describes the CA installation pro-
gram provided on the ptogram disk. The
second part describes how to use CA. This
description follows the organization of the
program, describing the main* menu first,
followed by the individual routines corre-
sponding to each of the rhenu entries.
Procedure '
CA is intended to run on an IBM PC
compatible with hard disk; under DOS. The
program-files take up approximately 360K
of storage on the hard disk[ while thesample
test data require about 85K.
The installation procedure creates two
directories, C:\CA and Q:\CA\HELP, and
copies executable and hejlp files into these
directories. Copying the two test data files
into the C:\CA directory simplifies recalling
these data when needed;|otherwise, these
files may be recalled from the second floppy
disk. ,
Operation ;
Each CA session maintains two distinct
data sets. The first is a multi-page fixed form
containing descriptive information relating
to the several aspects ofj the experiment.
The second is a spreadsheet for the experi-
mental data (entered from current experi-
ments or from one of the1 test data sets),
where the rows represent observations and
the columns represent fields. This spread-
sheet has a number of fixed fields and a
number of optional fields jthat may be se-
lected to tailor a session to(the nature of the
Printed on Recycled Paper
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experiment. Help screens are available
within each menu selection.
The main menu (Figure 1) is a single
selection menu. When a selection is made,
the menu closes and the selected operation
begins. All but one of the sixteen items of the
main menu are grouped into six classes:
Setup, Data Entry, Disk I/O, Analysis, Util-
ity, and Miscellaneous.
Leave CA
This is a special item outside the six
functional categories. Selecting this item
will prompt for disposition of any unsaved
changes and return to DOS.
Setup
The Setup routines (Endpoints and Op-
tional Fields) determine which of the
nondefaultfields will appearon the spread-
sheet. 'Endpoint' allows the selection of
either or both the chromosomal aberration
and the m'rtotic index endpoints. 'Optional
Fields' provides a way to define up to 15
additional data fields.
Data Entry
The Data Entry routines (Experiment
Description and Spreadsheet) are the means
by which data are entered into CA sessions
by keyboard. 'Experiment Description' con-
sists of a six-page form with which to enter
descriptive information pertaining to the
experiment, test article, solvent, positive
control, test system, and treatment. The
'Spreadsheet' allows access to the actual
data.
Disk I/O
'Recall' reads a CA file from disk and
makes H the current file. 'Save' writes the
current CA file to disk. 'Import' and 'Export'
being muftistep operations, are too compli-
cated to execute as a single menu selec-
tion. When selected as main menu items,
'Import' and 'Export' display text screens
describing the procedures.
Analysis
'Statistics' conducts specialized statisti-
cal analyses on selected endpoints and
presents the results via the screen with an
option to print as well. The CA software is
designed to analyze an in vivo experiment
involving either one or both sexes, from one
to five scorers, and a maximum of eight
dose groups and six sample times. 'Graph'
plots the means of selected response vari-
ables.
Utility
'List' produces a hard copy listing through
a printer connected to the serial port. There
are a number of parameters with which the
user can determine the form of the report.
'Sort' reorders the lines of the spreadsheet
(and optionally subsequent listings) ac-
cording to the values of any combination of
key fields, either ascending or descending.
'Clear Session' deletes all data and re-
moves all Set Up fields, in effect starting
over.
Miscellaneous
'Key Field Search' produces a report list-
ing either 1) the values of selected fields for
all CA files in the indicated search path, or
2) the names of all CA files in the indicated
search path whose valuesforselected fields
match key values entered here. 'GLP Log'
presents by screen or printer a record of all
accesses to the file and, after locking, all
new entries or changes to existing entries,
who made them and when.
Sample Data Sets
To assist the user in becoming familiar
with CA, data from two sample experiments
(CATEST01 .ILS and CATEST02.ILS) have
been included. Both experiments present
data in which male and female mice were
treated once with a test chemical, bone
marrow samples collected at 24,48 and 72
hours after treatment and the frequency
and distribution of chromosomal aberra-
tions and the mite-tic index were determined
by two scorers. In CATEST01, the chromo-
somal aberration data include cells contain-
ing 0, 1 or 2 aberrations. In CATEST02,
cells containing multiple aberrations were
detected among the treated mice. The same
outlier data are included in both data sets.
The statistical analyses of the chromosomal
aberration data are based on the assump-
tion that excluding the data at the highest
dose would always be considered and that
scorer differences would be evaluated. Hard
copies of the experimental information, the
chromosomal aberration and m'rtotic index
data and the results of the various statistical
analyses are provided in an Appendix. It is
suggested that the user recall the sample
test data files, page through the various
screens and invoke each of the subroutines
in orderto become familiar with the capabili-
ties of the software.
Software Availability
The Chromosomal Aberration Assay Data
Management and Analysis System soft-
Ware can be obtained by sending two for-
matted 5.25 inch 360KB diskstothefollowing
address: :
Dr. Charles H. Nauman
U.S. EPA, EMSL, MC-EAD
P. O. Box 93478
Las Vegas, NV 89193-3478
For further, information on the Chromo-
somal Aberration Assay Data Management
and Analysis System source code and pro-
grammer documentation, contact:
EPA Software Development Project
Integrated Laboratory Systems
P.O. Box 13501
Research Triangle Park, NC 27709
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Leave CA 1
— SetUp -
Endpoints
Optional
Fields
Data Entry
Experiment
Description
Spreadsheet
J— '
— Disk I/O ~
Recall
Save
Export
— Analysis —
Statistics
Graph
l_ Utility — .
List
Clear
session
Sort
jmrn^rn
4 »
Misc.
Key Field
Search
GLPLog
^— •
Figure 1. Main menu.
•&U. S. GOVERNMENT PRINTING OFFICE-. 1991/548-028/2Q175
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R R. TTce and A. C. Pelbm are with Integrated Laboratory Systems, Research Triangle
Park, NO 27709. The EPA author, C. H. Nauman (also the EPA Project Officer, see
below), Is with the Environmental Monitoring Systems Laboratory, Las Vegas, NV
89193-3478.
The complete report, entitled "User's Guide: Chromosomal Aberration Data Analysis
and Interpretation System," Order No. PB91-140 376/AS; Cost: $23.00, subject to
change) will be available only from:
National Technical Information Service
5285 Port Royal Road v
Springfield, VA 22161
Telephone: 703-487-4650 '
The EPA Project Off her can be contacted at:
Environmental Monitoring Systems Laboratory
U.S. Environmental Protection Agency
Las Vegas, NV 89193-3478
United States
Environmental Protection
Agency
Center for Environmental
Research Information
Cincinnati, OH 45268
BULK RATE
POSTAGE & FEES PAID
EPA
PERMIT No. G-35
Official Business
Penally for Private Use $300
EPA/600/S8-90/086
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