Measuring LVEF regularly can show the rate of decline in left ventricle function for a patient with DMD. Therefore, it was selected as an endpoint for this example to measure whether a course of therapy may slow the progression of heart failure for the patient. The second endpoint chosen, NT-proBNP, is a biomarker that may be used to predict or diagnose heart failure.
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Ejection Fraction
NTproBNP
SDTM Examples: Basic Systolic Function |
This section illustrates example analysis datasets for the following endpoints:
- Percent change in ejection fraction over time (1 year)
- Decline in ejection fraction over time (1 year) grouped by a decline greater than 5%-5.0%
- Percent change in NTproBNP NT-proBNP over time (1 year)
Source Data
The SDTM examples used as the source data are from Section 2.1, Basic Systolic Function. The records in the CV dataset contains 16 rows, 1-8 for visit 1 and 9-16 for visit 6. Of these rows, the for which CVTESTCD = "LVEF_C" and CVTESTCD = "RVEF_C" representing the Ventricular Ejection Fraction, Calculated (%) for left and right were selected for the analysis. The records in the LB dataset test where LBTESTCD = "BNPPRONT" was were used to add the value of BNPPRONT to compute the percent change over time , and then it was added as a potential covariate in each row for the last analysis. Both SDTM domains are used in one analysis dataset to demonstrate the flexibility of ADaM and to show that the various SDTM domains can be combined into one dataset both as rows and also as covariates.
Example Analysis Datasets
The following tables below show the analysis dataset metadata and metadata and parameters used for this example.
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ADSL
The ADSL contains subject characteristics and covariates that are important for analyses. Stratification variables can be created in the ADSL to subset the dataThe ADSL was combined with other SDTM datasets to create the analysis datasets. More than one SDTM dataset can be combined in this way. Also, stratification variables can be created in the ADSL to subset by, or to add variables needed in the analyses. For example, a flag (ACEMEDFL) could be added for ACE inhibitors. Another variable, body surface area (BSABL), was derived from the LB dataset at the baseline visit and added to ADSL.
The ADCVNTP dataset includes tests pertinent to these analyses. The records from CV where CVTESTCD = "LVEF_C" and "RVEF_C" and the records from LB where LBTESTCD = "BNPPRONT" were selected. Many lab draws may occur throughout the year, but only those linked to a specific visit were included. By subsetting the LB dataset by LBLNKID not missing, laboratory data that aligns with CV data can be filtered out and sorted using USUBJID and VISIT. If LBLNKID is not available, a windowing strategy could be used to select the laboratory draw closest to that visit for merging with CV, computed in AVISIT.
ADCVMR is an efficacy analysis dataset with only a few records for more complex modeling of changes in ejection fraction, plus the ProB-type test results. It is an ADaM Basic Data Structure (BDS) dataset, with additional variables added from ADCVNTP.
ADSL Analysis Dataset
This is a simplified example ADSL dataset; it is expected that additional variables for stratification, or of interest for analysis, would be included.
may be used as input to the ADSL. This is a simplified example ADSL dataset; the ADaMIG should be referenced for additional variables.
For this example:
- Analysis age (AAGE) was included to provide age with more precision.
- A flag indicating the use of ACE inhibitors (ACEINHFL) is shown with example derivation from the CM dataset.
- Body surface area at screening (BSASC) was derived from the VS dataset using height and weight at the screening visit. There are many possible calculations for BSA; for this example, the Du Bois method was used.[11] Note that the screening visit and visit 1 occurred at the same time in this example.
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Variable Name | Variable Label | Type | Codelist/Controlled Terms/Format | Source |
Convert BRTHDTC from ISO 8601 format to numeric date. (Note that if exact date is not found then use two variables to capture year and month.) | AGE | Num | DM.AGE AGEU | Char | YEARS | DM.AGEU SEX Num | M, F | DM.SEX RACE Num | (RACE) | DM.RACE TRTSDT | Date of First Exposure to Treatment | Num | date9. |
TRT01P | Planned Treatment for Period 01 Char | Drug A, Drug B | Predecessor; DM.ARM. May be changed to lower case or more descriptive term for use in tables and listings. | ITTFL Intent-To-Treat Population Flag Char Y; N Derive the intent-to-treat population as per the protocol and SAP. | ACEINHFL ACE Inhibitor Medications Flag Char Y; N Select a list of ACE inhibitor medications from concomitant medications (CM) domain, and from treatment (EX or EC) domains as per Statistical Analysis Plan or Protocol. Code "Y" if the medication was taken during the study. Can be used to subset or to exclude the population who took ACE inhibitors. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1 | DMD-EFLGE | DMD-EF-01-101 | 07FEB2010 | 15FEB2022 | Drug A | Y | 0.65 | Y | 2 | DMD-EFLGE | 3 | DMD-EFLGE | 4 | DMD-EFLGE |
ADCVNTP Analysis Dataset
In this example, columns for derived variables BASE, CHG, PCHG and CHGCAT1 have been added to facilitate analyses of the efficacy endpoints. Specifically, example demographic data for ADSL were created for an 8 year old male. Also, a custom variable for BSA at baseline (BSABL), and an example of a stratification variable for subjects with was added from ADSL.
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ADEFNTP
The ADEFNTP includes tests pertinent to analyses. The records from CV (CVTESTCD = "LVEF_C" and "RVEF_C") and the records from LB (LBTESTCD = "BNPPRONT") were selected. Many lab draws may occur throughout the year, but only those linked to a specific visit were included. By subsetting the LB dataset by LBLNKID not missing, laboratory data that aligns with CV data can be filtered out and sorted using USUBJID and VISIT. If LBLNKID is not available or the LB dataset does not contain VISIT, a windowing strategy could be used to select the laboratory draw closest to that visit using date of lab draw (LB.LBDTC.).
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In this example, variables BASE, CHG, PCHG, and CHGCAT1 were added to facilitate analyses of the efficacy endpoints. the variables SRCDOM, SRCVAR, and SRCSEQ provide traceability to the combined source datasets. The tables below represent parameter value level lists for applicable variables.
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ADCVNTP | AVAL | PARAMCD in ("LVEF_C", "RVEF_C") | Num | Predecessor | Set to CV.CVSTRESN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ADCVNTP | AVAL | PARAMCD = "BNPPRONT" | Num | Predecessor | Set to LB.LBSTRESN where LB.LBTESTCD = "BNPPRONT" | ADCVNTP | CHGCAT1 | PARAMCD = "LVEF_C" | Char | Categorize the value of CHG as follows: If CHG >= 5.00 THEN CHGCAT1 = "Decline >=5%". Else if CHG not missing and CHG < 5.00 THEN CHGCAT1 = "Decline <5%" | ADCVNTP | CHGCAT1 | PARAMCD = "RVEF_C" | Char | Categorize the value of CHG as follows: If CHG >= 5.00 THEN CHGCAT1 = "Decline >=5%". Else if CHG not missing and CHG < 5.00 THEN CHGCAT1 = "Decline <5%" | ADCVNTP | CHGCAT1 | PARAMCD = "BNPPRONT" | "Increase GT 100 pg/mL" | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Variable Name | Variable Label | Type | Codelist/Controlled Terms/Format | Source | Derivation/Comment | STUDYID | Study Identifier | Char | CV.STUDYID USUBJID | Unique Subject Identifier | Char | CV.USUBJID Select for records with RE data. | BRTHDT | Date of Birth | Num | Date9. | ADSL.BRTHDT TRT01P | Planned Treatment for Period 01 Char | Drug A, Drug B | ADSL.TRT01P | ITTFL Intent-To-Treat Population Flag Char Y; N ADSL.ITTFL HEIGHT Height (cm) Num Set to VS.VSSTRESN where VS.VSTEST = "HEIGHT" and merge by visit. WEIGHT Weight (kg) Num Set to VS.VSSTRESN where VS.VSTEST = "WEIGHT" and merge by visit. BSA | Body Surface Area (m2) | Num | Compute from HEIGHT and WEIGHT by visit, using the Du Bois method. BSA = 0.007184 × W0.425 × H0.725 Note that there are multiple methods and the study protocol should describe which one to use (e.g., Mosteller, Haycock, Gehan & George, Boyd, Fujimoto, Takahira, and Schlich). ACEINHFL ACE Inhibitor Medications Flag Char Y; N ADSL.ACEINHFL PARAM | Parameter | Char | Left Ventricular Ejection Fraction, Calculated (%); Right Ventricular Ejection Fraction, Calculated (%);
For tests from CV, set to the values of CV.CVTEST plus CV.CVTESTU with spaces and parentheses as shown. For tests from LB, set to the value of LB.LBTEST plus LB.LBTESTU with spaces and parentheses as shown. PARAMCD | Parameter Code | Char | LVEF_C; RVEF_C; BNPPRONT If CV.CVTESTCD = "LVEF_C" then PARAMCD = "LVEF_C" If CV.CVTESTCD = "RVEF_C" then PARAMCD = "RVEF_C" If LB.LBTESTDC = "BNPPRONT" then PARAMCD = "BNPPRONT Note: for this example dataset, select the records where the test values shown above are included. PARAMN | Parameter (N) | Num | Number PARAMCD as follows: LVEF_C = "1" RVEF_C = "2" BNPPRONT = "3" AVAL | Analysis Value | Num | See Parameter Value List AVISIT | Analysis Visit | Char | If CV.VISIT = "VISIT 1" then AVISIT = "Visit 1 (Baseline)". Else if CV.VISIT = "VISIT 6" then AVISIT = "Visit 6 (1 Year)". AVISITN | Analysis Visit (N) | Num | CV.VISITNUM LB.VISITNUM VISIT | Visit | Num | CV.VISIT LB.VISIT ADT | Analysis Date | Num | date9. | Date portion of CV.CVDTC or LB.LBDTC converted to numeric and displayed in a format such as date9. | ABLFL | Baseline Record Flag | Char | Y | If CV.VISIT = "VISIT 1" then ABLFL = "Y". BASE | Baseline Value | Num | Set BASE to AVAL from the record for that subject and parameter where ABLFL = "Y". Populate BASE for additional visits by merging the value of BASE in the baseline record by USUBJID and PARAMCD. CHG | Change from Baseline | Num | Compute CHG = AVAL - BASE for that record. Only compute for post-baseline records. | PCHG | Percent Change from Baseline | Num | Compute PCHG = (CHG / BASE) * 100. Only compute for post-baseline records. | CHGCAT1 | Change from Baseline Category 1 | Char | Decline >=5% ; Decline <5% Increase GT 100 pg/mL See PVLM table. | SRCDOM | Source Data | Char | CV; LB Set to the SDTM domain name that relates to the analysis value. | SRCVAR | Source Variable | Char | Set to the SDTM variable that relates to the analysis value. | SRCSEQ | Source Sequence Number | Num | CV.CVSEQ LB.LBSEQ Set to the SDTM domain sequence number that relates to the analysis value. | |
Example 1
This example dataset shows the findings and additional analysis variables associated with:
- Left Ventricular Ejection Fraction, Calculated (%)
- Right Ventricular Ejection Fraction, Calculated (%)
- N-Terminal ProB-type Natriuretic Peptide (pg/mL)
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In this table the ADaM parameters are used rather than the source SDTM data.
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ADCVCMR Analysis Dataset
Example 2
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ADEFMRI
The ADEFMRI is an efficacy analysis dataset with only a few records for more complex modeling of changes in ejection fraction, plus the proB-type test results. It is an ADaM Basic Data Structure (BDS) dataset
, with additional variables added from ADEFNTP dataset. Jira showSummary false server Issue Tracker (JIRA) serverId 85506ce4-3cb3-3d91-85ee-f633aaaf4a45 key TAUGDMDCIS-15
The dataset can can be used for analyses with multiple covariates
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ADCVCMR | AVAL | PARAMCD = "BNPPRONT" | BNPPRONT | N-Terminal ProB-type Natriuretic Peptide (IU/L) | ||||||||||||||||||||
ADCVCMR | CHG | PARAMCD = "BNPPRONT" | BNPCHG | N-Term ProB-type N Pep Change Category | ||||||||||||||||||||
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Row | STUDYID | USUBJID | ASEQ | BRTHDT | TRT01P | ITTFL | BSA | ACEINHFL | BNPPRONT | BNPCHG | PARAM | PARAMCD | PARAMN | AVAL | AVISIT | AVISITN | VISIT | ADT | ABLFL | BASE | CHG | PCHG | SRCDOM | SRCSEQ | 1 | DMD-EFLGE | DMD-EF-01-101 | 1 | 07FEB2010 | Drug A | Y | 1.09 | Y | 40 | Left Ventricular Ejection Fraction, Calculated (%) | LVEF_C | 1 | 70 | Visit 1 (Baseline) | 1 | VISIT 1 | 16MAY2022 | Y | 70 | CV | 3 | 2 | DMD-EFLGE | DMD-EF-01-101 | 2 | 07FEB2010 | Drug A | Y | 1.09 | Y | 40 | Right Ventricular Ejection Fraction, Calculated (%) | RVEF_C | 2 | 75 | Visit 1 (Baseline) | 1 | VISIT 1 | 16MAY2022 | Y | 75 | CV | 7 | 3 | DMD-EFLGE | DMD-EF-01-101 | 3 | 07FEB2010 | Drug A | Y | 1.33 | Y | 900 | 2150 | Left Ventricular Ejection Fraction, Calculated (%) | LVEF_C | 1 | 65 | Visit 6 (1 Year) | 6 | VISIT 6 | 06APR2023 | 70 | -5 | -10.447761 | CV | 11 | 4 | DMD-EFLGE | DMD-EF-01-101 | 4 | 07FEB2010 | Drug A | Y | 1.33 | Y | 900 | 2150 | Right Ventricular Ejection Fraction, Calculated (%) | RVEF_C | 2 | 70 | Visit 6 (1 Year) | 6 | VISIT 6 | 06APR2023 | 75 | -5 | -17.567568 | CV | 15 |
Example Analysis Results Metadata (ARM) Tables
For more details on ARM, see the ADaMIG and the Analysis Results Metadata (ARM) v1.0 for Define-XML v2.0 (https://www.cdisc.org/standards/foundational/adam).
Table 1. A simple comparison of change by treatment groups over one year.
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Table 14.xx.xx Change in Left Ventricular Ejection Fraction Percent Over 1 Year
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Data References
(incl. selection criteria)
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PARAMCD = "LVEF_C"
Where ITTFL = "Y" and AVISITN = 6;
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Comparison of Means with 95% confidence interval
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Programming Statements
(Add programming language statements here: SAS, R, etc.)
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/* Subset the data. Can run again selecting for paramcd="RVEF_C"*/
DATA ONE;
SET ADCVCMR;
Where ITTFL = "Y" and AVISITN = 6 and PARAMCD = 'LVEF_C';
RUN;
PROC MEANS DATA=ONE N MEAN clm STDERR;
CLASS TRT01P;
VAR CHG;
RUN;
Table 2. This table demonstrates a model over multiple time points, adding some of the covariates that were retained in the analysis dataset.
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Table 14.xx.xx Percent Change in Left Ventricular Ejection Fraction Percent Over Time (Yearly)
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PARAMCD = "LVEF_C"
Where ITTFL = "Y"
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The mixed model using lsmeans to compare treatment groups
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Programming Statements
(Add programming language statements here: SAS, R, etc.)
/* Note that CHG is only computed post-baseline, so subset for the yearly visits, i.e. 6, 12, 18 etc. */
DATA TWO;
SET ADCVCMR;
/* Subset by param, as there are two parameters with CHG calculated*/
Where ITTFL = "Y" and AVISITN IN(6,12,18,24,36,48) and PARAMCD = "LVEF_C";
RUN;
PROC MIXED DATA=ADCVNTP;
CLASS STUYDID TRT01P AVISITN;
MODEL PCHG=AVISITN*TRT01P/Solution;
RANDOM INTERCEPT / SUBJECT=STUYDID TYPE=UN;
LSMEANS TRT01P*AVISITN/ CL PDIFF;
RUN;
Table 3. This example uses the dataset ADCVNTP, selecting for the parameter "N-Terminal ProB-type Natriuretic Peptide (IU/L)".
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Display
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Table 14.xx.xx Percent change in NTproBNP over 1 Year
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Data References
(incl. selection criteria)
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PARAMCD = "BNPPRONT"
Where ITTFL = "Y" AND AVISIT GE 6;
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The mixed model using lsmeans to compare treatment groups
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Programming Statements
(Add programming language statements here: SAS, R, etc.)
/* NEEDS UPDATING*/
PROC MEANS DATA=ADCVCMR MEAN STD MEDIAN maxdec=3;
CLASS TRT01P;
BY VISIT;
VAR BNPPRONT;
...
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