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GENFILES A computerized medical genetics information network. III. CHROMO The cytogenetics database

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American Journal of Medical Genetics 7:267-278 (1980)
GENFILES A Computerized Medical
Genetics Information Network.
111. CHROMO: The Cytogenetics Database
William D. Loughman, Douglas C. Mosher, and Charles J. Epstein
Department of Pediatrics, and the Computer Center, University of California, San
Francisco
The computer database CHROMO is the cytogenetic branch of the GENFILES
medical genetics information system. Complete cytogenetic laboratory data are
maintained in a format that allows detailed searches of client records. Both
the standard and extended Paris nomenclature are used.
Key words: cytogenetics, medical genetics, CHROMO, information storage and retrieval, database
systems, CENFILES
INTRODUCTION
Karyotype analyses, even from normal persons, can produce very complex data.
A complete analysis should contain some notation both of normal variation and of those
atypical findings with as yet unknown significance. It is generally quite cumbersome to
sift such information-rich records for evidence of a time-dependent incidence of abnormalities or for correlations with phenotypes. Addditionally, manual searching and tabulation are prone to error. Therefore, the computer database named CHROMO has been
designed to perform storage, search, and correlation tasks. All of the cytogenetic data
obtained in a large prenatal diagnosis program [Golbus et al, 19791 are stored in CHROMO,
as well as the analyses performed for a large genetic counseling clinic. CHROMO now contains the cytogenetic results from over 5,500 prenatal analyses and over 2,600 clinical
analyses.
DATABASE DESCRIPTION
CHROMO is a hierarchical archive file with 26 data fields containing both karyotype descriptions and related laboratory data. About half of the fields are used for patient identification, clinic information, laboratory quality control, or database interconnection. The remaining fields are devoted to a segmented description of the patient’s
karyotype, along with any comments or information not accommodated in a specific data
Received for publication April 21, 1980; revision received July 30, 1980.
Address reprint requests to Dr. William D. Loughman, Cytogenetics Laboratory, AC-28, University
of California, San Francisco, CA 94143.
0148-7299/80/0703-0267$02.000 1980 Alan
R. Liss, Inc.
Loughman, Mosher, and Epstein
268
field. Paris cytogenetic nomenclature is fully utilized in the stored karyotype descriptions.
The new analyses that may require updating or correction are stored temporarily in an
identically structured input file, the content of which is peridocally incorporated into
CHROMO.
Table I shows the data structure of CHROMO, with its field names and a short description of the type of data each contains. In this description, LEVEL is a hierarchical
branch-point where multiple entries may be appended to existing data. Fields may be identified for data entry or reports by number (not shown), fieldname, or synonym. TYPE
and LENGTH dictate the format of a field’s content. For example, the alphabetic field
SURNAME may contain up to 16 characters of any kind. The BIRTHDATE field, however, contains only six integers, arranged to provide two digits each for the year, month,
and day (YYMMDD).
The definitions for the 26 fields in CHROMO shown in Table I are those stored
within the computer, but a fuller explanation of certain fields follows. RF’RT is the date
that a Birth Defects Center physician examined the laboratory results. STORAGE is a
room number in the University, showing where the medical record is kept. INDICATION
is the reason the study was performed. This is a field with a closely controlled but
expandable vocabulary. SOURCE and PHYSICIAN help keep track of where reports
TABLE 1. Brief Description of File CHROMO
LEVEL FIELDNAME
SYNONYM
1
2
LAST
FIRST
BIRTHDATE
FAMNUM
IN
HARVEST
OUT
ENTER
LOC
WHY
CLINIC
MD
LABN
RAMPASS
LINE
CNUM
SEXC
SIGN
TRIPLET
(:SOME1
CSOME2
PARENT
BAND1
BAND2lSTAIN
COM
QD
3
4
5
SURNAME
GIVEN
DOB
FAMILY
INTAKE
HRVST
RPRT
FILED
STORAGE
INDICATION
SOURCE
PHYSICIAN
LAB NUM
RAMPASS
M
CN
sx
6
7
S
TRI
c1
C2
PRNT
B1
B2S
COMMENT
BRIEFLY
TYPE
A
A
I
A
I
I
LENGTH
16
14
6
8
A
6
6
6
6
10
18
12
16
10
8
I
2
3
I
6
4
4
A
A
A
A
A
4
6
42
12
1
I
A
A
A
A
A
A
A
I
A
A
A
A
5
DEFINITION
FAMILY NAME O F SUBJECT
FIRST NAME OF SUBJECT
BIRTHDATE OF SUBJECT: YYMMDD
KEY FOR LINKING FAMILY MEMBERS
DATE O F SAMPLE RECEIPT: YYMMDD
DATE O F CULTURE HARVEST: YYMMDD
DATE MD CERTIFIED RESULTS
DATE RECORD ENTERED TO COMPUTER
STORAGE LOCATION OF LAB RECORD
REASON FOR KARYOTYPE
ORIGINATING CLINIC
REFERRING PHYSICIAN
AC28 ACCESSION NUMBER
. . . A SECURITY DEVICE
CELL LINE NUMBER IF MOSAIC KARYOTYPE
NUMBER O F CHROMOSOMES IN KARYOTYPE
SEX CHROMOSOMES. QUOTE: SEE TO RIGHT
PLUS/MINUS SPECIFIED CHROMOSOME
“PARIS CONFERENCE” TRIPLET CODE
IST (OR ONLY) CHROMOSOME 1NVOLVF.D
2ND (IF ANY) CHROMOSOME INVOLVED
CONTRIBUTOR PARENT (OR) NUMBER ALIKE
AFFECTED BAND OF C1
AFFECTED BAND O F C2 (OR) STAIN CODF
ADDITIONAL INFORMATION
SIGNIFICANT FEATURE OF KARYOTYPE
GENFILES: The Cytogenetics Database
269
must be sent. LAB NUM is the number assigned to each sample entering the laboratory.
Every sample gets a unique number consisting of a letter (A, B, G, etc) designating the
type of sample (amniotic fluid, blood, gonad, etc), and a number that is sequential within
years. For example: B80201 is the 201st blood sample in 1980.
RAMPASS is a field whose contents, normally blank, become an additional password. M or LINE is the number of the cell line in a mosaic patient. This may be 1 , 2 , 3 , etc.
If 0, no mosaicism was detected. COMMENT allows entry of anything not covered in
the record format. Usually, ratios of abnormal count to total count (in an analysis), stains
used, and similar information are stored here. The remaining fields are a part of the
karyotype itself.
KARYOTYPE REPRESENTATION IN CHROMO
The karyotype begins at level 5, with field “M” (LINE). In order to see how the
data are structured within CHROMO, consider the following karyotype:
mos 46,XX,-S,+der(5)t(5;16) (q35;q23)pat,var(16)(qll ,CBG43)mat,var(l3)
(s,GTG44)*2/46,XX, var(l6) (41 1,CBG43)mat, var(13)(s,CTG44)*2
Ignoring the chromosome number and sex designation, it is possible to consider all
elements between commas (except within parentheses) as karyotpe units that refer uniquely
to a single structure. Inspection shows that each such unit, in principle, contains five
major parts. These are a sign (+/-), a leading triplet code, two sets of parenthetical expressions, and a trailing qualifier. If anything to the right of the sex designation exists, then
at least some of the content of the first set of parentheses exists. This content always is
preceded by either or both of a sign and a triplet. The parenthetical expressions contain at
least two elements each, but in degnerate cases one or more elements may be blank, as
may be the trailing qualifier. The content of the first parenthetical expression always refers
to at least one chromosome. That of the second always refers either to at least one breakpoint or to a band number and a code describing how the band behaved under a particular
stain.
If the derivative-5 chromosome in the example were to be written in the conventional way, but incorporating these concepts, it would look like this:
+der(5 ;. . .)(. . .;. . .) . . .
. . .t(5 ;16)(q35 ;q23)pat
In this representation, an ellipsis is a place holder indicating an unused element. This is the
karyotype representation used in CHROMO, producing the configuration shown in Table
11. The distinct subdivisions are arranged one above the other. Corresponding parts are
aligned vertically in an orderly repetition of fields TRI, C1, C2, B1, B2S, and PARENT.
Visually, the arrangement suggests a matrix, and it might be treated as such. But CHROMO
is a hierarchically structured file that uses three levels for the karyotype. Thus, in CHROMO
the matrix does not exist. The representation is useful though, and it is retained in the
data input form used by the Cytogenetics Laboratory (Fig. 1).
It is possible to descibe almost every chromosome abnormality in this format, even
those involving more than two chromosomes and more than two breakpoints. For example,
this hypothetical fourchromosome translocation:
270
Loughman, Mosher, and Epstein
Fig. 1. Form used for recording input data for CHROMO. The regions contained within the heavy
lines are filled o u t by the referring professional.
t(l;2;3;4)(q 1 1;q 12;ql3,14)
becomes, for entry to CHROMO:
TRI C1 C2
B1 B2S
t
(1 ;2) (qll
( ;3) (
;q13)
( ;4) (
;c114)
The one-line karyotype becomes three branches of a hierarchical "tree," uniquely tied
to each other by at least one common node. In this case, the node is the SIGN field, on
which the t h e e records depend. The absence of C1 for the records pertaining to chromosomes 3 and 4 is a convention used in CHROMO to indicate multichromosome aberrations.
If there were more than one such aberration in a karyotype, and possible ambiguity as to
which chromosome was in which translocation, a qualifier would be added.
GENFILES: The Cytogenetics Database
271
Some very complex karyotypes might resist unambiguous description. These would
be “flagged” in the TRI field, and the karyotype would be written conventionally in the
COMMENT field. We have not encountered a need to do this, although CHROMO has
over 11,000 entries.
There are some problems with the Paris nomenclature itself. For example, the
standard designation for a Robertsonian translocation may not make clear which chromosome arms are actually present in the karyotype. This and related ambiguities are resolved
in CHROMO by using the field name BRIEFLY. In practice, the most common application of this field has been in rapid searching for broad categories of chromosome aberration - eg, 5 q t , TRI21, and the like.
REPORTING FROM THE DATABASE
Two related methods are available to obtain reports from CHROMO. The most
general is to use the standard RAMIS report language, typing a series of instructions at
the terminal, l i e by line. The easier method is to use GENFILES preprogrammed procedures. The list of these has become quite large. Included are commands that provide complete karyotypes and other data over a range of group selection criteria, compute and
tabulate duration of culture for selected sample types, and graph the frequencies of
occurence of a field’s content. Most routines are quite general and require the addition of
a few parameters. If the parameters are neglected, the computer prompts for their entry.
In many cases the parameters permit restriction of a search range or permit conditional
search. Three examples of GENFILES routines that address CHROMO follow.
An example of a special Cytogenetics Laboratory summary is shown in Table 111. The
report in Table 111 contains results of amniotic fluid cell analyses sequenced by laboratory
number. Amniotic cell karyotype A5025, from a 38-year-old woman, is of a male fetus
with variants of chromosomes 13,15, 19, and 21; an inversion of chromosome 9 between
p12 and q12; and a reciprocal balanced translocation between chromosomes 1 8 and 21.
Ariother type of report provides information about the technical aspects of the
laboratory procedures. A summary of the duration in culture of amniotic fluid cells
calculated from the intake dates and the harvest dates for all months in 1979 is shown in
Table IV. Minimum, average, and maximum values are displayed, and “no growth” results
are ignored in order to show true minima.
Procedures are also available for extracting various types of demographic data from
CHROMO. An example of this is the table and graph of the number of mothers in yearly
age categories of fetuses prenatally diagnosed as having simple non-mosaic trisomy 21
shown in Figure 2. The women’s ages were calculated by subtracting birthdates from the
date of amniocentesis.
The examples given above are straightforward and uncomplicated uses of GENFILES.
Much more complex search and reporting methods are possible. One involves the concept of virtual files. These are not data files in the usual sense. Rather, they are empty
files that contain instructions for obtaining real data from one or more real files. They
can be used for many quite different purposes. For example, a single low-level selector
(ie, BRIEFLY) can be used to obtain the complete karyotype, which is the whole hierarchical patient record, without an expensive file inversion. Results of such a search to
obtain from CHROMO complete karyotypes for all patients having “partial trisomy of 5q”
are shown in Table V.
272
Loughman, Mosher, and Epstein
TABLE 11. A Karyotype Arranged for Entry to CHROMO
M
CN
1
46
sx
xx
S
-
+
2
46
xx
TRI
der
t
var
var
var
var
C1
5
5
5
16
13
16
13
C2
B1
B2S
PRNT
COM
BRIEFLY
12/30
mon5q part.
tril6q part.
18/30
5q+ mos
Pat
16
q35
q23
q l l CBG43
GTC44
s
CBG43
s
CTG44
qll
mat
*2
mat
*2
AGE COUNT
--- -----
20
35
36
37
39
40
41
42
43
48
AGE
1
6
5
5
10
3
5
2
4
1
COUNT C
20
22
24
26
26
30
32
34
36
36
40
42
44
46
48
C
C
C
C
FROM DATA IN COMPUTER ON ( 1 4 / 0 7 / 8 0
AT 6.05.21
Fig. 2. Ages of women found to have fetuses with trisomy 21 at time of receipt of amniotic fluid
sample in laboratory. The age frequency above age 15 years is tabulated and plotted.
AS026
JE
AS032
YO
38
46XY
1
VAR
VAR
VAR
VAR
VAR
19
VAR
S
21
H
S
Q12
PI1
012
012
PI3
PI2
S
Q12
21
GTC43
CBC23
B2S
GTG43
GTGO2
GTG43
CBG43
GTG43
GTG02
412
CTGO2
GTGO2
GTC43
Q12
P I 3 CTG43
P I 3 GTG43
P116 Q112
PI3
H
B1
14
19
22
9
INV
19
19
21
9
VAR
VAR
INV
VAR
1s
18
C2
PRNT
UCSF-PRENATL MSG
UCSF-PRENATL MSC
PHYSICIAN
GTG/CBG/RHG
GTG/CBG/RHG
RHG1CBG:DlTTO
CTG/CBG/RHG
G r c ONLY SEE ~ 2 2 9 3
GTG/CBC/RIIG
GTG/CBG/RHG
UCSF-PRENATL MSG
UCSF-PRENATL MSG
UCSF-PRENATL MSG
UCSF-PRENATL MSG
UCSF-PRENATL MSC
UCSF-PRENATL MSG
UCSF-PRENATL MSG
UCSF-PRENATL MSG
33/33 CELLS (2 FLASKS)
GTC/RHC/NOR/QFQ/CBG
ON PREPONDERANCE OF
EVIDENCE
CTGIRHG SEE A2748
GTG:DITTO
COMMENT
SOURCE
*Names in the report have been coded by the computer for publication. The normal report contains the patients’ full names.
LU
AS027
MO
DO
A5028
NO
PH
AS029
RE
MA
AS030
BE
CO
AS031
LA
13
VAR
VA R
RCP
36
40XX
36
46XX
38
46XX
37
46XY
35
46XY
36
46XY
21
VAR
EL
GO
9
C1
VAR
3s
2 41XY”
40
46XY
38
46XY
PA
AS023
DA
YO
AS024
FR
KA
AS025
CO
M CNSX S TRI
LABNUM
LASTNAME FlRSTNAME INDICATION
UNIVERSITY O F CALIFORNIA, SAN FRANCISCO
CYTOGENETICS LABORATORY, AC-28
(415) 666-3121
CYTOCENETIC ANALYSES REPORTED BY FIELD LABN FROM AS000 TO A6000.
FILE: NEWSTUFF 02/28/80 15.48.27
TABLE 111. Portion of Weekly Cytogenetia Laboratory Report of Amniotic Fluid Cell Karyotypes*
INV9
lNV9
T(18;21) BAL
BRIEFLY
274
Loughman, Mosher, and Epstein
TABLE IV. Average, Minimum, and Maximum Times in Days Required to Culture
Amniotic Fluid Cells for the Cited Year (1979) and Months*
YR
MN
AVE
TH
MIN
TH
MAX
TH
79
1
2
3
4
5
6
7
8
9
10
11
12
15.65
14.42
14.15
15.69
15.54
16.27
16.43
17.55
16.05
15.44
14.98
15.09
9.00
10.00
10.00
10.00
11.00
12.00
10.00
7.00
10.00
11.00
11.00
10.00
43.00
20.00
28.00
24.00
27.00
49.00
50.00
43.00
25.00
21.00
20.00
21.00
*“No-growths” are ignored in order t o show true minima.
TABLE V. Part of a Report of A Search of CHROMO for all Patients With Partial Trisomy of 5q
VIRKARYO RAMEXEC
REPORTED ON FIELD BRIEFLY=TRISQ-PART.
FROM DATA IN COMPUTER ON 04/07/80 AT 10.46.20
SURNAME GIVEN DOB
c1
C2
5
9
16
16
16
16
RCP
5
9
16
16
5
T
+DER
-
5
16
16
16
LABNUM
M CNSX
STRI
DE
s799
FE
790509
T
VAR
+DER
46XY
-
SA
46XY
A4 184
550119
T
VAR
+DER
-
H76204
DO
876301
BL
DE
876309
RI
B78350
46XX
0
46XY
0
46XX
DA
46XY
T
+DER
7 10320
T
VAR
+DER
-
5
16
16
2
13
15
19
22
2
2
PKNT
B1
b25
Q34
H
Q24
GTG23
TRI5q-PART.
MONl6Q-PART.
MAT
MAT?
MAT
16
MAT
434
H
Q24
RHG23
Q34
~ 2 4
Q34
Q24
Q34
Q 24
TRISQ-PART.
MON 16Q-PART.
MAT
5?
P24
S
S
Q12
PI 2
NEW
TRISQ-PART.
MON16Q-PART.
T (5;16) BAL
TR15Q-PART.
MON 16Q-PART.
MAT
16
BRlEFLY
4 31
CTC43
CTG43
GTG 32
GTG43
T (2;5?)
TRISQ-PART.
MON2P-PART.
CENFILES: The Cytogenetics Database
275
PASSWORDS, CON F IDENTI ALI TY, A N D DATA SECU R IT Y
Although standarized procedures are used for data transfers, mistakes can compromise the integrity of the database. Consequently, such maneuvers are performed only
by a small number of well-trained personnel who have been provided with the proper
password. A second password is used to allow staff members (clinicians, counselors) the
privilege of searching the database and reporting from it, without the capability to make
changes.
The confidential nature of the data is assured through two devices. The “secure”
version for CHROMO is called CHROMOS. Patient identification fields are not available
to persons who access CHROMOS, no matter what password is issued. Attempts to obtain
the patient identifiers cause complete failure of the report request.
The second device assuring confidentiality is the RAMPASS field shown in the
fde description of CHROMO (Table I). For most patients records this field has no content;
it is blank. If an entry exists, it becomes a password which can block access to all data
below it in the file structure, namely the complete karyotype. Typically, this method is used
to protect employee’s test results from inspection by co-workers, but it has applications
as well for cooperative databases.
DISCUSS ION
There are only a handful of computerized information systems the major emphasis
of which is the handling of cytogenetic data. Most of these employ the older computer
technology current when they were designed [Human Cytogenetic Registers, 19771. To
emphasize the use of a modern computer database management system (DBMS) and the
flexibility and ease of use that can be obtained through use of a DBMS as a cytogenetic
register, we shall compare CHROMO with only one of these existing systems, the Interregional Cytogenetic Register System (ICRS) [Prescott et al, 19781.
The ICRS stores chromosome data in a well-defined matrix, each row of which
records two chromosomes and corresponding band numbers or breakpoints. There is no
limit on the number of rows that might be used to code a complete karyotype. An
“Aberration Code” in each row records the general class of each aberration. Generally,
as is the case for sex chromosome descriptions, this is a fwed code with limited possibilities
for expansion. It would appear to be cumbersome to code and then retrieve the more
complex chromosome aberrations involving three or more chromosomes, or to provide
unambigous descriptions of multiple aberrations within the same chromosome. When
these occur, the lCRS stores complete karyotypes in a subsidiary field. Direct search for
subunits within this format would be awkward.
The approach in CHROMO is generally similar, but the d e f i e d matrix is replaced
by a hierarchical data structure. Instead of one chromosome aberration per row, as in the
ICRS matrix, CHROMO stores each element of an aberration in a “row,” with no limit t o
the number of rows per aberration. This, in addition to easily defined subfields for any
entry, affords great specificity for data searching. The “Aberration Code” used in the
ICRS is most closely represented in CHROMO by the field BRIEFLY. But BRIEFLY contains a standard description of the effect, not the form, of each element in the chromosome
aberration. Data entries are not coded in CHROMO, except insofar as the standard cytogenetic nomenclature is a code. Insomuch as the standard nomenclature is hugely expansible, so also are the “standard” entries to CHROMO. There is no obvious limit to the
276
Loughman, Mosher, and Epstein
growth of the database lexicon. There is also no need to refer to code equivalences. Knowledge of cytogenetic nomenclature generally is sufficient, and recourse to written-out
karyotypes has not been necessary.
The batch processing ICRS system is written in COBOL, and it is therefore relatively difficult to alter either fde formats or procedures used to report from files. CHROMO
is interactive with an on-line database. It is very easy to reprogram the system, at least
for obtaining reports, and this is done often by genetics staff. An on-line computer system
will be more expensive, at least in memory costs, than a system utilizing magnetic tape or
card deck storage of data. CHROMO is no exception to this principle, and as it grows
some aged data undoubtedly will be stored off-line.
FUTURE PLANS
The RAMIS database management system was designed for use in a multiple subsidiary large corporation environme,it, and these design provisions influence the potential
for growth and adaptation of CHROMO. Like the other GENFILES subsystems, CHROMO
should be very easy to use as part of a distributed information network. This concept is
implemented at present using a laboratory affiliated with our own institution. Our experience to date has provided no serious problems of a technical nature. We plan expansion
to four additional laboratories in a trial of the distributed network structure. As a necessary part of this expansion, CHROMO will be modified to enhance further the strict
confidentiality of patient records. One step will be division of CHROMO into two parts,
isolating patient identification data into separate files under the sole control of the
individual cooperating laboratories. The remaining large archive file, with no patient
identification at all, will be accessible to all laboratories in the network. The two parts
are easily linked, permitting the retrieval of complete patient records only by the laboratory possessing the necessary linkage information.
Management of different laboratories’ conflicting needs and goals, and file adaptations to meet these conflicts, are expected to be important problems. These growing pains
are expected to include problems common to all distributed or cooperative computer
ventures [Bernard, 19791.
ACKNOWLEDGMENTS
The authors wish to acknowledge the assistance of Ms Karen Michalski for aid in the
production of figures and tables from CHROMO, and Ms Mary Joan Fredette for typing the
manuscripts.
This work was supported in part by PHS grant T32GM07085-03, by a grant from
The National Foundation - March of Dimes, and by a contract with the California State
Council on Developmental Disabilities. Dr. Epstein is an Investigator of the Howard
Hughes Medical Institute.
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