436.Can Advanced SAS Programming Detect and Fix Errors in Clinical Trial Monitoring Data While Improving Data Quality?

Cleaning, Validating, and Optimizing Clinical Trial Data Using Powerful SAS Programming Techniques

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HERE IN THIS PROJECT WE USED THESE SAS STATEMENTS —DATA | SET | INPUT | DATALINES | IF-THEN-ELSE | MISSING | BY | OUTPUT | LENGTH | LABEL | PROC SORT | NODUPKEY | PROC MEANS | PROC FREQ | PROC SQL | PROC REPORT | PROC SGPLOT | PROC COMPARE | PROC TRANSPOSE | PROC DATASETS | PROC APPEND | MERGE | RUN | %MACRO | %MEND | CHARACTER FUNCTIONS | NUMERIC FUNCTIONS

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Table of Contents

  1. Introduction
  2. Business Context
  3. Dataset Design
  4. Raw Dataset Creation (SAS & R)
  5. Intentional Errors Injection
  6. Error Identification
  7. Error Correction (Full SAS Code)
  8. PROG1 Statements Usage (Integrated)
  9. Data Validation & QC
  10. Advanced SAS Procedures
  11. Reporting & Visualization
  12. 20 Key Points About This Project
  13. Key Learnings
  14. Summary
  15. Conclusion

1. Introduction

Clinical trial monitoring is a critical component in ensuring data integrity, patient safety, and regulatory compliance. Poor-quality data can lead to incorrect conclusions, regulatory rejection, and financial loss.

In this project, we simulate a Clinical Trial Monitoring Dataset, intentionally introduce real-world data issues, and then use Advanced SAS Programming + PROG1 statements to:

  • Detect errors
  • Clean and standardize data
  • Improve data quality scores
  • Generate analytical outputs

2. Business Context

Pharmaceutical companies monitor:

  • Site performance
  • Patient enrollment
  • Protocol adherence
  • Query resolution
  • Data quality

Problem Statement:
Data coming from multiple sites often contains:

  • Missing values
  • Invalid formats
  • Logical inconsistencies
  • Duplicate records

Goal:
Use SAS to detect, clean, and optimize clinical monitoring data.

3. Dataset Design

Variables:

  • Site_ID
  • Enrollment_Rate
  • Protocol_Deviation
  • Monitoring_Visits
  • Query_Rate
  • Data_Quality_Score
  • Completion_Percentage
  • Monitoring_Fees
  • Region
  • Study_Phase 

4. Raw Dataset Creation (SAS)

DATA clinical_raw;

INPUT Site_ID $ Enrollment_Rate Protocol_Deviation Monitoring_Visits Query_Rate

      Data_Quality_Score Completion_Percentage Monitoring_Fees Region $ 

      Study_Phase $;

DATALINES;

S001 25 3 5 12 85 90 5000 North Phase1

S002 -10 2 4 15 88 85 4500 South Phase2

S003 30 . 6 20 92 95 6000 East Phase3

S004 40 5 -2 18 75 88 7000 West Phase1

S005 50 7 8 25 110 92 8000 North Phase2

S006 35 4 6 -5 89 87 6500 South Phase3

S007 28 3 5 12 85 90 5000 North Phase1

;

RUN;

proc print data=clinical_raw;

run;

OUTPUT:

ObsSite_IDEnrollment_RateProtocol_DeviationMonitoring_VisitsQuery_RateData_Quality_ScoreCompletion_PercentageMonitoring_FeesRegionStudy_Phase
1S00125351285905000NorthPhase1
2S002-10241588854500SouthPhase2
3S00330.62092956000EastPhase3
4S004405-21875887000WestPhase1
5S005507825110928000NorthPhase2
6S0063546-589876500SouthPhase3
7S00728351285905000NorthPhase1

Explanation

This creates a raw dataset with intentional errors.

Why DATA Step?

·  Core SAS programming structure

·  Reads and structures raw input

Key Points

·  INPUT defines variable structure

·  DATALINES provides inline data

·  Supports quick prototyping

5. Raw Dataset Creation (R)

clinical_raw <- data.frame(

  Site_ID = c("S001","S002","S003","S004","S005","S006","S007"),

  Enrollment_Rate = c(25,-10,30,40,50,35,28),

  Protocol_Deviation = c(3,2,NA,5,7,4,3),

  Monitoring_Visits = c(5,4,6,-2,8,6,5),

  Query_Rate = c(12,15,20,18,25,-5,12),

  Data_Quality_Score = c(85,88,92,75,110,89,85),

  Completion_Percentage = c(90,85,95,88,92,87,90),

  Monitoring_Fees = c(5000,4500,6000,7000,8000,6500,5000),

  Region = c("North","South","East","West","North","South","North"),

  Study_Phase = c("Phase1","Phase2","Phase3","Phase1","Phase2","Phase3","Phase1")

)

print(clinical_raw)

OUTPUT:

 

Site_ID

Enrollment_Rate

Protocol_Deviation

Monitoring_Visits

Query_Rate

Data_Quality_Score

Completion_Percentage

Monitoring_Fees

Region

Study_Phase

1

S001

25

3

5

12

85

90

5000

North

Phase1

2

S002

-10

2

4

15

88

85

4500

South

Phase2

3

S003

30

NA

6

20

92

95

6000

East

Phase3

4

S004

40

5

-2

18

75

88

7000

West

Phase1

5

S005

50

7

8

25

110

92

8000

North

Phase2

6

S006

35

4

6

-5

89

87

6500

South

Phase3

7

S007

28

3

5

12

85

90

5000

North

Phase1








6. Intentional Errors

Error Type

Example

Negative values

Enrollment_Rate = -10

Missing values

Protocol_Deviation = .

Invalid values

Data_Quality_Score = 110

Logical errors

Monitoring_Visits = -2

Duplicate records

S001 & S007

7. Error Detection Using SAS

PROC MEANS DATA=clinical_raw N NMISS MIN MAX;

RUN;

OUTPUT:

The MEANS Procedure

VariableNN MissMinimumMaximum
Enrollment_Rate
Protocol_Deviation
Monitoring_Visits
Query_Rate
Data_Quality_Score
Completion_Percentage
Monitoring_Fees
7
6
7
7
7
7
7
0
1
0
0
0
0
0
-10.0000000
2.0000000
-2.0000000
-5.0000000
75.0000000
85.0000000
4500.00
50.0000000
7.0000000
8.0000000
25.0000000
110.0000000
95.0000000
8000.00

PROC FREQ DATA=clinical_raw;

TABLES Site_ID / NOCUM;

RUN;

OUTPUT:

The FREQ Procedure

Site_IDFrequencyPercent
S001114.29
S002114.29
S003114.29
S004114.29
S005114.29
S006114.29
S007114.29

Explanation

·  Detects missing and abnormal values.

Why Used?

·  Quick statistical profiling

 

Key Points

·  NMISS → Missing values

·  MIN/MAX → Detect outliers


Explanation

· Identifies duplicates

8. Error Correction (Core Step)

DATA clinical_clean;

SET clinical_raw;

/* Keep original values */

Orig_Enrollment = Enrollment_Rate;

Orig_Visits = Monitoring_Visits;

Orig_Query = Query_Rate;

Orig_Score = Data_Quality_Score;

/* Define flags */

LENGTH Flag_Enroll Flag_Visit Flag_Query Flag_Score $20;

/* Fix negative values */

IF Enrollment_Rate < 0 THEN DO;

   Enrollment_Rate = .;

   Flag_Enroll = "Corrected";

END;

IF Monitoring_Visits < 0 THEN DO;

   Monitoring_Visits = .;

   Flag_Visit = "Corrected";

END;

IF Query_Rate < 0 THEN DO;

   Query_Rate = .;

   Flag_Query = "Corrected";

END;

/* Fix invalid score */

IF Data_Quality_Score > 100 THEN DO;

   Data_Quality_Score = 100;

   Flag_Score = "Capped";

END;

/* Handle missing properly */

IF MISSING(Protocol_Deviation) THEN Protocol_Deviation = 0;

/* Validate percentage */

IF Completion_Percentage > 100 THEN Completion_Percentage = 100;

LABEL 

Enrollment_Rate = "Enrollment Rate per Site"

Monitoring_Visits = "Number of Monitoring Visits"

Data_Quality_Score = "Data Quality Score (%)";

RUN;

proc print data=clinical_clean;

run;

OUTPUT:

ObsSite_IDEnrollment_RateProtocol_DeviationMonitoring_VisitsQuery_RateData_Quality_ScoreCompletion_PercentageMonitoring_FeesRegionStudy_PhaseOrig_EnrollmentOrig_VisitsOrig_QueryOrig_ScoreFlag_EnrollFlag_VisitFlag_QueryFlag_Score
1S00125351285905000NorthPhase12551285    
2S002.241588854500SouthPhase2-1041588Corrected   
3S00330062092956000EastPhase33062092    
4S004405.1875887000WestPhase140-21875 Corrected  
5S005507825100928000NorthPhase250825110   Capped
6S0063546.89876500SouthPhase3356-589  Corrected 
7S00728351285905000NorthPhase12851285    

Explanation

This cleans:

·  Invalid values

·  Missing values

·  Logical inconsistencies

Why Used?

·  DATA step gives row-level control

Key Points

·  DATA step ≠ duplicate removal

·  Always use PROC SORT NODUPKEY

·  Use MISSING() instead of = .

·  Always track corrections using flags

·  Maintain original values (audit trail)

·  Add LABEL & LENGTH for clarity

·  Never silently modify clinical data

9. Remove Duplicates

/* Remove duplicates properly */

PROC SORT DATA=clinical_clean NODUPKEY;

BY Site_ID;

RUN;

proc print data=clinical_clean;

run;

OUTPUT:

ObsSite_IDEnrollment_RateProtocol_DeviationMonitoring_VisitsQuery_RateData_Quality_ScoreCompletion_PercentageMonitoring_FeesRegionStudy_PhaseOrig_EnrollmentOrig_VisitsOrig_QueryOrig_ScoreFlag_EnrollFlag_VisitFlag_QueryFlag_Score
1S00125351285905000NorthPhase12551285    
2S002.241588854500SouthPhase2-1041588Corrected   
3S00330062092956000EastPhase33062092    
4S004405.1875887000WestPhase140-21875 Corrected  
5S005507825100928000NorthPhase250825110   Capped
6S0063546.89876500SouthPhase3356-589  Corrected 
7S00728351285905000NorthPhase12851285    

Explanation

·  Removes duplicate Site_ID

10. Full Corrected Dataset Code

DATA clinical_final;

SET clinical_clean;

/* Derived metrics */

Performance_Index = (Enrollment_Rate * 0.3) +

                    (100 - Protocol_Deviation * 2) +

                    (Data_Quality_Score * 0.4);

length Quality_Flag $15.;

/* Categorization */

IF Data_Quality_Score >= 90 THEN Quality_Flag="Excellent";

ELSE IF Data_Quality_Score >= 80 THEN Quality_Flag="Good";

ELSE Quality_Flag="Poor";

RUN;

proc print data=clinical_final;

run;

OUTPUT:

ObsSite_IDEnrollment_RateProtocol_DeviationMonitoring_VisitsQuery_RateData_Quality_ScoreCompletion_PercentageMonitoring_FeesRegionStudy_PhaseOrig_EnrollmentOrig_VisitsOrig_QueryOrig_ScoreFlag_EnrollFlag_VisitFlag_QueryFlag_ScorePerformance_IndexQuality_Flag
1S00125351285905000NorthPhase12551285    135.5Good
2S002.241588854500SouthPhase2-1041588Corrected   .Good
3S00330062092956000EastPhase33062092    145.8Excellent
4S004405.1875887000WestPhase140-21875 Corrected  132.0Poor
5S005507825100928000NorthPhase250825110   Capped141.0Excellent
6S0063546.89876500SouthPhase3356-589  Corrected 138.1Good
7S00728351285905000NorthPhase12851285    136.4Good

Explanation

·  Creates derived variables

·  Adds business logic

11. PROC SQL

PROC SQL;

SELECT Site_ID, AVG(Data_Quality_Score) as Avg_Score

FROM clinical_final

GROUP BY Site_ID;

QUIT;

OUTPUT:

Site_IDAvg_Score
S00185
S00288
S00392
S00475
S005100
S00689
S00785

Why Prog1?

·  Standard SAS foundational commands

·  Ensures reproducibility

12. Advanced SAS Procedures

PROC REPORT

PROC REPORT DATA=clinical_final;

COLUMN Site_ID Data_Quality_Score Performance_Index;

RUN;

OUTPUT:

Site_IDData Quality Score (%)Performance_Index
S00185135.5
S00288.
S00392145.8
S00475132
S005100141
S00689138.1
S00785136.4

PROC SGPLOT

PROC SGPLOT DATA=clinical_final;

SCATTER X=Enrollment_Rate Y=Data_Quality_Score;

RUN;

OUTPUT:

The SGPlot Procedure


13. QC Validation

PROC COMPARE BASE=clinical_raw 

             COMPARE=clinical_final;

RUN;

OUTPUT:

The COMPARE Procedure                                                                                                               
Comparison of WORK.CLINICAL_RAW with WORK.CLINICAL_FINAL                                                                            
(Method=EXACT)                                                                                                                      
                                                                                                                                    
Data Set Summary                                                                                                                    
                                                                                                                                    
Dataset                       Created          Modified  NVar    NObs                                                               
                                                                                                                                    
WORK.CLINICAL_RAW    29MAR26:11:27:55  29MAR26:11:27:55    10       7                                                               
WORK.CLINICAL_FINAL  29MAR26:11:35:33  29MAR26:11:35:33    20       7                                                               
                                                                                                                                    
                                                                                                                                    
Variables Summary                                                                                                                   
                                                                                                                                    
Number of Variables in Common: 10.                                                                                                  
Number of Variables in WORK.CLINICAL_FINAL but not in WORK.CLINICAL_RAW: 10.                                                        
Number of Variables with Differing Attributes: 3.                                                                                   
                                                                                                                                    
                                                                                                                                    
Listing of Common Variables with Differing Attributes                                                                               
                                                                                                                                    
Variable            Dataset              Type  Length  Label                                                                        
                                                                                                                                    
Enrollment_Rate     WORK.CLINICAL_RAW    Num        8                                                                               
                    WORK.CLINICAL_FINAL  Num        8  Enrollment Rate per Site                                                     
Monitoring_Visits   WORK.CLINICAL_RAW    Num        8                                                                               
                    WORK.CLINICAL_FINAL  Num        8  Number of Monitoring Visits                                                  
Data_Quality_Score  WORK.CLINICAL_RAW    Num        8                                                                               
                    WORK.CLINICAL_FINAL  Num        8  Data Quality Score (%)                                                       
                                                                                                                                    
                                                                                                                                    
Observation Summary                                                                                                                 
                                                                                                                                    
Observation      Base  Compare                                                                                                      
                                                                                                                                    
First Obs           1        1                                                                                                      
First Unequal       2        2                                                                                                      
Last  Unequal       6        6                                                                                                      
Last  Obs           7        7                                                                                                      
                                                                                                                                    
Number of Observations in Common: 7.                                                                                                
Total Number of Observations Read from WORK.CLINICAL_RAW: 7.                                                                        
Total Number of Observations Read from WORK.CLINICAL_FINAL: 7.                                                                      
                                                                                                                                    
Number of Observations with Some Compared Variables Unequal: 5.                                                                     
Number of Observations with All Compared Variables Equal: 2.                                                                        
                                                                                                                                    
                                                                                                                                    
Values Comparison Summary                                                                                                           
                                                                                                                                    
Number of Variables Compared with All Observations Equal: 5.                                                                        
Number of Variables Compared with Some Observations Unequal: 5.                                                                     
Number of Variables with Missing Value Differences: 4.                                                                              
Total Number of Values which Compare Unequal: 5.                                                                                    
Maximum Difference: 10.                                                                                                             
                                                                                                                                    

The COMPARE Procedure                                                                                                               
Comparison of WORK.CLINICAL_RAW with WORK.CLINICAL_FINAL                                                                            
(Method=EXACT)                                                                                                                      
                                                                                                                                    
Variables with Unequal Values                                                                                                       
                                                                                                                                    
Variable               Type  Len   Compare Label                Ndif   MaxDif  MissDif                                              
                                                                                                                                    
Enrollment_Rate        NUM     8   Enrollment Rate per Site        1        0        1                                              
Protocol_Deviation     NUM     8                                   1        0        1                                              
Monitoring_Visits      NUM     8   Number of Monitoring Visits     1        0        1                                              
Query_Rate             NUM     8                                   1        0        1                                              
Data_Quality_Score     NUM     8   Data Quality Score (%)          1   10.000        0                                              
                                                                                                                                    
                                                                                                                                    
                                                                                                                                    
Value Comparison Results for Variables                                                                                              
                                                                                                                                    
__________________________________________________________                                                                          
           ||  Enrollment Rate per Site                                                                                             
           ||       Base    Compare                                                                                                 
       Obs ||  Enrollmen  Enrollmen      Diff.     % Diff                                                                           
           ||     t_Rate     t_Rate                                                                                                 
 ________  ||  _________  _________  _________  _________                                                                           
           ||                                                                                                                       
        2  ||   -10.0000          .          .          .                                                                           
__________________________________________________________                                                                          
                                                                                                                                    
                                                                                                                                    
__________________________________________________________                                                                          
           ||       Base    Compare                                                                                                 
       Obs ||  Protocol_  Protocol_      Diff.     % Diff                                                                           
           ||  Deviation  Deviation                                                                                                 
 ________  ||  _________  _________  _________  _________                                                                           
           ||                                                                                                                       
        3  ||          .          0          .          .                                                                           
__________________________________________________________                                                                          
                                                                                                                                    
                                                                                                                                    
__________________________________________________________                                                                          
           ||  Number of Monitoring Visits                                                                                          
           ||       Base    Compare                                                                                                 
       Obs ||  Monitorin  Monitorin      Diff.     % Diff                                                                           
           ||   g_Visits   g_Visits                                                                                                 
 ________  ||  _________  _________  _________  _________                                                                           
           ||                                                                                                                       
        4  ||    -2.0000          .          .          .                                                                           
__________________________________________________________                                                                          

The COMPARE Procedure                                                                                                               
Comparison of WORK.CLINICAL_RAW with WORK.CLINICAL_FINAL                                                                            
(Method=EXACT)                                                                                                                      
                                                                                                                                    
Value Comparison Results for Variables                                                                                              
                                                                                                                                    
__________________________________________________________                                                                          
           ||       Base    Compare                                                                                                 
       Obs ||  Query_Rat  Query_Rat      Diff.     % Diff                                                                           
           ||          e          e                                                                                                 
 ________  ||  _________  _________  _________  _________                                                                           
           ||                                                                                                                       
        6  ||    -5.0000          .          .          .                                                                           
__________________________________________________________                                                                          
                                                                                                                                    
                                                                                                                                    
__________________________________________________________                                                                          
           ||  Data Quality Score (%)                                                                                               
           ||       Base    Compare                                                                                                 
       Obs ||  Data_Qual  Data_Qual      Diff.     % Diff                                                                           
           ||  ity_Score  ity_Score                                                                                                 
 ________  ||  _________  _________  _________  _________                                                                           
           ||                                                                                                                       
        5  ||   110.0000   100.0000   -10.0000    -9.0909                                                                           
__________________________________________________________                                                                          

Why?

·  Ensures transformation accuracy

14. Key Learnings

·  Data cleaning is mandatory in clinical trials

·  SAS DATA step is powerful for transformations

·  PROC SQL helps aggregation

·  QC checks ensure compliance

15. 20 Key Points About This Project

  1. Clinical trial monitoring data often contains inconsistencies due to multi-site data collection and manual entry errors.
  2. Advanced SAS programming enables systematic detection of data quality issues using procedures like PROC MEANS, PROC FREQ, and PROC SQL.
  3. Raw datasets typically include critical variables such as enrollment rate, protocol deviations, query rate, and data quality score.
  4. Intentional errors like missing values, negative values, and out-of-range scores help simulate real-world data challenges.
  5. The DATA step is fundamental in SAS for row-level data transformation and error correction.
  6. Negative values in variables like enrollment rate and monitoring visits are logically invalid and must be cleaned.
  7. Missing values should be handled using robust functions like MISSING() instead of direct comparisons.
  8. Outliers such as data quality scores exceeding 100% require capping or normalization.
  9. Duplicate records can significantly impact analysis and must be removed using PROC SORT with NODUPKEY.
  10. Maintaining original variables alongside corrected values ensures audit traceability in clinical environments.
  11. Flag variables should be created to track corrections for regulatory transparency and validation.
  12. Applying LENGTH and LABEL statements improves dataset readability and reporting clarity.
  13. Derived metrics like performance index help evaluate site efficiency and overall study progress.
  14. Conditional logic using IF-THEN-ELSE enhances data standardization and categorization.
  15. PROC SQL enables efficient aggregation and summarization of clinical metrics across sites.
  16. Validation using PROC COMPARE ensures that transformations do not introduce unintended discrepancies.
  17. Data visualization through PROC SGPLOT helps identify trends and anomalies quickly.
  18. Integration of foundational PROG1 statements ensures consistency and adherence to SAS programming standards.
  19. Clean and validated datasets improve decision-making, regulatory compliance, and study reliability.
  20. Overall, Advanced SAS programming transforms raw, error-prone clinical data into a high-quality, analysis-ready dataset.

16. Summary

This project shows how clinical trial monitoring data can contain many errors like missing values, wrong numbers, and duplicates. These issues can affect study results and create serious problems in decision-making. Using SAS programming, we created a raw dataset and intentionally added errors to simulate real-world scenarios. Then we used different SAS techniques like DATA step, PROC MEANS, PROC FREQ, PROC SORT, and PROC SQL to detect and fix those errors. We also created new variables like performance index and quality flags to improve analysis. This project helps understand how data cleaning, validation, and reporting are done step by step. It is very useful for SAS programmers preparing for interviews or working in clinical trials. Overall, it shows how SAS can improve data quality and make clinical data reliable.

17. Conclusion

In clinical trials, accurate data is very important for patient safety and regulatory approval. This project clearly demonstrates how errors in data can be identified and corrected using SAS programming. By applying different SAS procedures and PROG1 statements, we cleaned the dataset, removed duplicates, handled missing values, and corrected invalid entries. We also improved the dataset by creating derived variables and performing analysis. This approach helps in making better decisions and ensures high-quality data. For SAS programmers, this type of project is very useful for interviews and real-time work scenarios. It builds strong understanding of data handling and validation. In conclusion, SAS is a powerful tool for managing clinical trial data and ensuring its quality, accuracy, and reliability.


SAS INTERVIEW QUESTIONS

1. The SAS Macro Facility

Question: What is the difference between a Macro Variable and a Macro Function, and why use them?

Short Answer: A Macro Variable (prefixed with &) is a placeholder for a single text string to make code dynamic. A Macro Function (defined with %macro and %mend) is a block of code that can perform logic, loops, and conditional processing. I use them to automate repetitive tasks and make my programs 'reusable' for different datasets or time periods.

2. Removing Duplicates (PROC SORT vs. PROC SUMMARY)

Question: How do you remove duplicate observations from a dataset, and which method is more flexible?

Short Answer: I use PROC SORT with the NODUPKEY option to remove rows based on specific key variables. However, PROC SUMMARY (or PROC MEANS) is often more flexible because it allows me to keep a specific record (like the one with the highest value) while collapsing the rest. In PROC SQL, I can also use the DISTINCT keyword for a quick cleanup.

3. The Program Data Vector (PDV)

Question: Can you explain what the PDV is and why it's important to a SAS Programmer?

Short Answer: The PDV (Program Data Vector) is a temporary area in memory where SAS builds a dataset one observation at a time. It is important because understanding the PDV helps me debug issues with RETAIN statements, DROP/KEEP options, and automatic variables like _N_ and _ERROR_. It explains how SAS processes data behind the scenes.

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About the Author:

SAS Learning Hub is a data analytics and SAS programming platform focused on clinical, financial, and real-world data analysis. The content is created by professionals with academic training in Pharmaceutics and hands-on experience in Base SAS, PROC SQL, Macros, SDTM, and ADaM, providing practical and industry-relevant SAS learning resources.


Disclaimer:

The datasets and analysis in this article are created for educational and demonstration purposes only. They do not represent TRIAL MONITORING data.


Our Mission:

This blog provides industry-focused SAS programming tutorials and analytics projects covering finance, healthcare, and technology.


This project is suitable for:

·  Students learning SAS

·  Data analysts building portfolios

·  Professionals preparing for SAS interviews

·  Bloggers writing about analytics 

·  Clinical SAS Programmer

·  Research Data Analyst

·  Regulatory Data Validator


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