THE INTRICATE ORGANIZATION AND MANAGEMENT OF CLINICAL RESEARCH LABORATORY SAMPLES USING SAS/AF"

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1 THE INTRICATE ORGANIZATION AND MANAGEMENT OF CLINICAL RESEARCH LABORATORY SAMPLES USING SAS/AF" Jacqueline A. Wendel, M.S., University of Rochester Daniel A. Nosek, University of Rochester ABSTRACT: The Core Laboratory of the General Clinical Research Center at the University of Rochester processes thousands of blood and urine samples to obtain data for different research studies. A system is needed to label, organize and track these samples in order to facilitate data analysis. The linkage of the three tasks allows for the most efficient means of data entry and analysis. The system must be able to fulfill the needs of the nursing personnel obtaining the samples, the lab personnel running tests on the samples and the investigators using the data to analyze and publish the results of their studies. An application was developed that mainly utilizes SAS/ AF", but is supplemented by SAS Screen Control Language and Macro Variables. It consists of three main subunits. The first generates the labels for the sample tubes. The second enters a record of these tubes into the lab log. The third subunit generates reports used to analyze the data. The system features reduced duplicate entry time, increased quality control and direct transfer of data to the investigator. INTRODUCTION: The General Clinical Research Center (GCRC) is a multidisciplinary unit funded by the National Institutes of Health (NIH) which provides inpatient and outpatient beds, nursing staff, a metabolic kitchen, a computing facility and a core laboratory to facilitate NIH sponsored research in our institution. Due to the large number of protocols which utilize the services of the Core Laboratory annually, a mechanism was required to handle the labelling of acquired samples and the further reporting and analysis of these samples. SAS/AF is used in conjunction with SAS/FSP" to provide a complete data management system for all samples processed by the GCRC Core Laboratory. The services provided by both nursing staff and laboratory technicians were assessed to define areas where duplication of effort existed and to streamline the collection process, the processing of specimens and distribution of results to GCRC investigators. LABEL GENERATION & MANAGEMENT The entry point of a sample is determined at the time the protocol is set up by the investigator. Each research protocol has a well defmed collection process which is outlined for the nursing staff in advance through a Protocol Flowsheet. The flow sheet shows the time, amount of sample, type of test to be processed and tube type used for each collection period. From this document the nursing staff ascertains which samples are to be sent to the GCRC Core Laboratory. The flowsheet identifies other samples which may be sent to the Hospital laboratories or to outside laboratories. When the application in SAS/ AF begins, the following menu is displayed: WELCOME TO THE GCRC TUBE LABEL SYSTEM You have the following options: 1130

2 0 Quit 1... Enter Protocol Data for Labels 2 Enter Patient Data & Print Labels Please Enter an Option Number: Option 0 exits the labelling system completely and returns you to the VMS "$" prompt. PROTOCOL DATA The Protocol Worksheet described previously is the basis for the Protocol Data Base included in this portion of the system. SAS/FSP was used to create user friendly data entry screens which include information for each tube label to be prepared for each study. The study type and the protocol number are key fields to this data set because many protocols may have more than one study type. Option I opens the SAS/FSP data entry screen to enter the information for individual labels based on the Protocol Flow Sheet. Each observation in the SAS dataset corresponds to a tube label for the study to be performed. Variables in each observation include the GCRC assigned protocol number, time point for the sample, a description of the label (ie. grey top, red top etc.), the type of study (ie. clamp, leucine, etc.) and a coded variable to indicate the destination of the tube. A" I" in this field indicates that it is a tube destined for the Core Laboratory and is a blood specimen. A "2" indicates a urine sample. Labels are created for all tubes used in the study including backups. A specific protocol may have more than one type of study in the protocol dataset. The observations for each type of study are entered once and become part of the permanent dataset until such time as a protocol or study type are terminated by the investigator. ENTER PATIENT DATAl PRINT LABELS When a patient is scheduled for a specific study on the patient unit, Option 2 is used to enter the patient and study information necessary to create labels. Macro variables are used in the AF screen for the patient last and first name, date of the study, protocol number and type of study to be performed. Once this information is entered and the END command is entered, the data are match merged with the protocol data base to create all labels for samples to be collected during the study. Initially, the program checks for invalid entries to the screen. For example, if any field on the screen is blank, the program will not process the label and the user is returned to the main menu. In the case of a valid entry, a PROC SORT is used on the data set containing the protocol information with the BY variables protocol number and type. It is then match merged with the single observation data set created from the data entry screen which contains patient and protocol information, using the same BY variables. Once the label file has been created, samples which will be processed by the Core Laboratory are assigned sequential log numbers and placed in a temporary log file for later placement in the permanent sample log data base. Assignment of the sequential log number is a complex process. Because samples may be entered to the permanent log file manually, it is necessary to ensure that log numbers are not duplicated in the temporary log file. Therefore, both the temporary and the permanent log files are reviewed to find the largest existing log number. This number is stored and used as a seed for the subsequent log numbers. Labels are created using PROC FORMAT and 1131

3 are printed on the laser printer in the computing facility. LAB DATA MANAGEMENT SYSTEM The Laboratory Data System contains all processes for logging samples received, entering results obtained from the assays, and reporting the results to the investigator for later analysis. In addition it provides statistical analysis for NllI utilization reporting. The Laboratory Director made the decision early to maintain separate log and results files for urines and bloods, rather than using a code variable to distinguish between sample types. Therefore, a menu selection at different points in the system asks whether the specimen is blood or urine. The main menu of this system includes the following options: 1. Enter log data 2. Enter test data 3. Generate reports 4. Create data set for investigator 5. Modify temporary files 6. Exit application MANAGING TEMPORARY FILES The process of creating tube labels places log numbers on samples to be sent to the core lab and stores observations in a temporary log file which correspond to those samples. Samples which are to be processed by the core laboratory are placed into a temporary log file because circumstances during the actual conduct of the study may reduce the number of samples to be collected. Because of the large number of studies and the large number of tubes which must be labelled for each study, most labels are created prior to the actual study date. In some cases, the study may be cancelled or the patient may not show up for the study. Observations of this type placed in the temporary file should not become part of the permanent log data set. Option 5 of the main menu leads to a sub-menu which contains the following log file maintenance options: 1. Print labels in temporary me 2. Delete labels from temporary me 3. Enter labels into the lab log PRINTING LOGGED SAMPLES Option I prints the contents of the temporary log file for review by the Core Laboratory staff. This report allows verification that the tubes received by laboratory personnel match what has been entered to the log. This tool can be used by both nursing and technical staff. DELETING OBSERVATIONS FROM THE TEMPORARY FILE Once the temporary log file has been reviewed, incorrect observations are deleted through Option 2. Macro variables are used to provide a range of log numbers to be deleted from the log file. A single sample which was not collected or an entire study can be deleted with this option. This eliminates unnecessary entries in the log file and reduces storage requirements. The program checks to be sure that the beginning log number is less than the second log number when records are deleted. If the beginning and ending log numbers are the same, then only one observation is to be deleted. CONVERTING DATA FROM THE TEMPORARY LOG TO THE PERMANENT LOG FILE Once a study has been completed, the log numbers included in the temporary log file may be merged into the permanent blood or urine log 1132

4 file for further processing and reporting by the laboratory technicians. Option 3 prompts for the beginning and ending log number which should be merged to the permanent log file. The appropriate range tests are included in the process to check that data entry at this point is correct and to avoid unnecessary additions to the permanent log. Again, one or many samples may be moved to the permanent file. MANUAL LOG DATA ENTRY From time to time the Core Laboratory will process samples which were not obtained at the GCRC of the University of Rochester. Manual data entry is required to incorporate these samples into the permanent log. SAS/FSP has been used to create user friendly data entry screens for these samples. Sequential log numbers for these samples will be assigned manually after reviewing both the temporary and permanent log files to ascertain the next number to be assigned. If this step is ignored, inappropriate reporting will occur due to duplicate log numbers in the file. TEST DATA ENTRY A SAS/FSP data entry screen is available for each test which the core laboratory performs. The log number is the key field which links the permanent log file to these test result files. Tests are also distinguished by the type of sample which is used. For example the Core Laboratory performs creatinine determinations on both urine and blood. A separate data set and FSP screen is used for the results of each type of test. Many of the result data sets include calculations which are made from the raw data generated by the assay. These calculations are performed at the time the variables required are entered and return is pressed. These values are part of the permanent data set and are reported to the investigator. REPORT GENERATION A variety of reports are available which include: reporting data from the permanent log file and reporting test results in hard copy and file transfer format. Macro variables are used in a report screen to store report requests. Reports may be sorted by specific patient (name or identifier), protocol, range of dates, assigned log number or type of test. A specific value for any of the options listed above may also be entered. Choice lists are provided for the type of test, variables to sort by, and levels of sorting. The number of tests run and not run can be reported to plan and schedule assay runs at any given time. End of the year reporting to NIH is performed through these functions. INVESTIGATOR DATA SET CREATION AND TRANSFER A number of investigators utilizing the services of the Core Laboratory also utilize the GCRC Computing Facility for data management and analysis. A procedure was established which allows the technician to transfer directly test result data from the Core Laboratory account to a SAS data set in the investigator's account on the V AX: system. Option 4 from the main menu leads to the following data entry screen : Please enter protocol number: &PROT 1133

5 Please enter the desired test: &TEST Please enter directory: &DRECTRY Do you wish to obtain a printed copy?: &C EXIT: &E The first variable "&PROT" refers to the specific CRC protocol to be transferred. The test name must be a specific test which the laboratory performs. If the test name is in doubt, enter a "7" and a choice list will appear. The directory is a VMS user directory where result data sets and catalogs are to be moved. This must be entered without the brackets "0" normally used in a VMS directory specification. The directory must have appropriate VMS protections to allow the lab account to write to it. The results being sent to the user directory can also be printed locally. At the exit prompt answer either Y to leave and return to the previous menu, or N to remain in the screen and perform another file transfer. This capability has decreased data entry time for investigators and improved quality control by eliminating duplicate data entry. Investigators who utilize PC SAS in their own department may also utilize this facility. CONCLUSION/BENEFITS The development of a comprehensive data management system for the core laboratory has provided an electronic environment for labelling, logging and reporting laboratory results. The institution of the system has had varying effects on the departments within the General Clinical Research Center. Nursing Impact: When initially introduced to Nursing staff, the SAS system was in the form of an independent label system. That system reduced manual tube label generation time significantly. In an effort to decrease data entry time for the laboratory staff, the new label system was incorporated into the Lab Data Management software. The result of this merger has been a slower system for label production when the temporary log file is not properly maintained. Nursing must be more acutely aware of the needs of the core laboratory and keep informed of the change in procedures in the laboratory. Data entry for a protocol occurs only one time at this point. This reduces errors when compared to producing manual labels for studies which sometimes include over 100 labels. Core Laboratory Impact: The computerized approach to data management has improved the reporting capabilities significantly. Handwritten logs which were part of the previous manual system no longer exist. Reporting formats are consistent and contain information valuable to both the laboratory and the investigator. The laboratory must report the number and type of samples analyzed on an annual basis. This system provides a prompt and accurate means of reporting utilization to the funding agency. Manually logging of GCRC acquired samples is no longer performed by technical staff. According to a Core Laboratory Director, this has resulted in a 5 to 8 hour a week reduction in data entry time. 1134

6 Investigator Impact: Once samples have been analyzed and results entered into the system, the investigator can receive reports from the system. Investigators can receive reports as paper hard copy, file transfers or both. Investigators are provided concisely formatted reports and a SAS file ready for data analysis. Overall Impact: The overall impact is a reduction in duplication of effort at all levels. Quality control has significantly increased by eliminating duplicate data entry. FUTUREDIRECTIONS/ENHANCEMENTS Of major concern is what to do with protocol data once a study is complete. A mechanism for archiving and deleting all log and result data for a specific protocol number should be developed to reduce the hardware requirements of the software. SAS, SAS/AF, and SAS/FSP are registered trademarks or trademarks of SAS Institute Inc. in the USA and other countries. ~ indicates USA registration. Other brand and product names are registered trademarks or trademarks of their respective companies. VAX and VMS are registered trademarks of Digital Equipment Corporation. 1135