2018 CDISC U.S. InterchangeThe ADaM Universe of Mapping Specs, Datasets, Define.xml and BeyondPresented by Valerie WilliamsManager Statistical Reporting Standards, Systems and Processes, Biostatistics and Programming, ICON Clinical Research
10.10.2018
Agenda
1. Introduction
2. ADaM Content and Related Standards
3. ADaM Study Deliverables
4. Implementation Challenges
5. Solutions
The ADaM Universe
u·ni·verse /ˈyo͞onəˌvərs/
A particular sphere of activity, interest, or experience.
The ADaM universe is made up of CDISC standards content from which project/study ADaM deliverables are produced by users of those standards.
Introduction
The CDISC Analysis Data Model (ADaM), the ADaM Implementation Guide, ADaM Validation Checks, and Define.xml along with the associated TAUG standards, are the core of the ADaM universe and are surrounded by the ADaM Mapping Specifications, Data Sets, Analysis Data Reviewers Guide, and Define.xml files that are created by the implementers of the standards.
This presentation will discuss some of the challenges faced in ADaMimplementation and proposes a few solutions to improve productivity and quality metrics to utilize a standard approach across studies, facilitate code reusability and ease of code maintenance, while meeting this goal.
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ADaM Content and Related Standards
Core of the Universe
ADaM Core Content
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• The CDISC Analysis Data Model (ADaM),
surrounded by the ADaM Implementation Guide
(IG), Occurrence Data (OCCDS), Qualifying Rating
Scales (QRS), Therapeutic Areas (TA), and
Controlled Terminology (CT) are the core
components of the ADaM universe.
ADaM Peripheral Content
• ADaM Conformance Rules/Validation Checks
• ADaM Metadata: analysis dataset metadata, analysis variable
metadata (VLM), analysis parameter value level metadata,
and analysis results metadata (ARM.xml)
• Define.xml and XML Schema Definitions .xsd files for data
exchange. An XML schema defines the elements that an
XML file may contain. It provides a specific structure for XML
data, which is important when sharing XML files between
multiple systems. https://techterms.com/definition/schema
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ADaM Content Status
Standard Most Current Related Documentation Notes
ADaM v2.1
ADaM Implementation Guide v1.1 Version 1.2 ready for release
ADaM Basic Data Structure (BDS) for Time-to-Event (TTE)
Analyses v1.0
ADaM OCCDS (Occurrence Datasets) v1.0 Version 1.1 in progress
Works with ADaMIG 1.1
ADaM Conformance Rules v1.3
(Validation Checks) / ADaM Integration
Version 2.0 in public review
Comments due 12-Nov-2018
Analysis Results Metadata (ARM) v1.0 for Define-XML v2.0
ADRG Completion Guidelines
ADRG Template
ADaM Geriatric Depression Scale (GDS) Short Form
Questionnaire Supplement
Resolving Public Comments.
ADaM Medical Devices Preparing for Public Review.
ADaM Oncology In Progress
ADaM PK Analysis In Progress
ADaM Traceability Examples In Progress
Analysis Results Metadata (ARM) Conformance Rules In Progress
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ADaM Implementation Guide
ADaMIG v1.1 specifies ADaM standard dataset structures and variables, including naming conventions and specifies standard solutions to implementation issues.
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Significant IG v1.2 updates include:
• New Permissible variable within BDS: PARQUAL
• Nomenclature for Stratification variables within
ADSL
• Recommended approach for bi-directional toxicity
grades: laboratory tests that have separate CTC
grade criteria for both ends of the normal range
(one set of grades for low values and another for
high values)
ADaM Structure for Occurrence Data
ADaM OCCDS v1.0 is based on ADaM Version 2.1 and the
ADaMIG v1.1. Occurrence analysis is the counting of
subjects with a given record or term, and often includes a
structured hierarchy of dictionary coding categories.
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• Adverse Events
• Concomitant Medications
• Medical History
ADaM Conformance Rules
ADaM Conformance Rules v2.0 can be implemented with
software to test rules defined in the ADaM IG v1.0, ADaM IG v1.1,
and the ADaM OCCDS v1.0. First released on 20-Sep-2010 and
assists in traceability between SDTM and ADaM.
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Updates from the previous release include:
• Change to a Wiki-formatted document
• Check table includes one row per rule per ADaMIGversion
• A revised table format, including the addition of new cited guidance column(s) and removal of legacy columns which were no longer necessary
• Addition of Message Type which contains values of “Error”, “Warning”, and “Note” (defined in Section 3)
ADaM Related Content Status
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StandardMost Current Related
Documentation
Notes
Define.xml Define.xml Implementation
Guide v2.1
• Resolving public review comments
• Required by FDA and PMDA
Stylesheet In public review with PhUSE Optimizing
the Use of Data Standards Working
Group
StandardMost Current Related Documentation Notes
TAUGs Breast Cancer, COPD, Diabetes,
Diabetic Kidney Disease,
Dyslipidemia, Kidney Transplant, Major
Depressive Disorder, Prostate Cancer,
Rheumatoid Arthritis
Multiple TAUGs are in
development, including
Traditional Chinese Medicine -
Coronary Artery Disease/Angina
Therapeutic Area User Guide
v1.0 Comments Due by: 30 Oct
2018
Define.xml Documentation
Define.xml v2.1 - FDA is only supporting studies starting after Mar 15 2018 that use this. Define.xml is required standards for data submission to FDA (U.S.) and PMDA (Japan).
• The def:Class attribute on the ItemGroupDef element has been replaced by a def:Class element that includes a child element (def:SubClass)
• For Define-XML documents used for regulatory submissions, all dataset and codelist definitions where the corresponding ItemGroupDef or CodeList element represents a published CDISC standard or controlled terminology will be required to include a def:StandardOID attribute. Dataset and codelist definitions that do not follow a published CDISC standard or controlled terminology will be required to provide a def:IsNonStandard attribute.
• A new optional attribute def:HasNoData has been added to the ItemGroupDefand ItemRef elements. When the value of def:HasNoData is Yes, no data are available for the corresponding dataset or variable.
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ADaM Study Deliverables
Around the Core
ADaM Deliverables
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ADaM-related Study Artifacts Source Content
Documentation
SAP N/A
Specifications ADaMIG, OCCDS
Mocks for Tables, Listings, and
Figures
N/A
Analysis Data sets ADaM
Define.xml Define.xml
ARM.xml ADaM Conformance
Rules
Validation Checks (Pinnacle 21 and
supplemental programs) for .xpt or
datasets
ADaM, Define.xml
Analysis Data Reviewer’s Guide ADRG Package v1.1-
guidelines and template
SAP
A Statistical Analysis Plan (SAP) is required for each trial to
define guidelines for the analysis and presentation of data at
various stages of the trial. Statistical analysis is a clearly defined
section within the protocol and should be approved prior to the start
of the trial. https://warwick.ac.uk/fac/sci/med/research/ctu/conducting/setup/sap/
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ADaM Specifications
ADaM Specifications contain the requirements for each analysis
dataset and define.xml file, based on the analyses described in the
Statistical Analysis Plan (SAP).
• Provides traceability of a data element or metadata back to its source
SDTM (Study Data Tabulation Model) predecessor.
• Name, variable attributes, formats, and derivations required for the
analysis and reporting of clinical study data
• The specifications contain tabs for metadata, each dataset, controlled
terminology, and documentation
• The statistician reviews the draft ADaM specifications, once they have
been written by the programmer, and provides comments back to the
programmer.
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Sample ADaM Specifications
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ADaM details that will be included in the Define.xml are in yellow
Source information is in gray
ADSL
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ADAE
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ADaM Analysis Datasets
ADaM Analysis Datasets are created to support results presented in study reports, the Integrated Summary of Safety (ISS) and the Integrated Summary of Efficacy (ISE) and to support other analysis that enable a thorough regulatory review. They must facilitate unambiguous communication.
• Support traceability relationships between the analysis results and source data relationships across data types relationships within data types
• Be linked to machine-readable metadata (define.xml)
• Be analysis-ready allow for analysis with minimal additional processing
• Be usable with currently available tools SAS, Pinnacle21
Standard tools to create define.xml or check compliance
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ADaM Datasets
Analysis datasets must:
• include subject-level analysis dataset “ADSL”.
• comprise the optimum number of analysis datasets needed to allow analysis and review with little or no additional programming or data processing.
• be named using the convention “ADxxxxxx.”
• follow naming conventions for datasets and variables that are applied consistently across a given submission or multiple submissions for a product.
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ADaM Dataset Structures
• The Subject-Level Analysis Dataset (ADSL) Structureo One record per subject
o (Required for all CDISC based submissions)
• The ADaM Basic Data Structure (BDS) • One or more records per subject
o Per analysis parameter Per analysis timepoint (Conditional)
• ADLB, ADEG, ADVS, ADQS
• ADTTE
• The ADaM Structure for Occurrence Data (OCCDS)• Supports occurrence analysis, counting number of subjects with
given records or terms
• Often is there one record per record in SDTM domain
• ADAE, ADCM, ADMH
• ADaM Other (does not fit in the above data structures but adheres to ADaM basic guidelines)
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ADaM Dataset Usage
• ADaM Dataset Validation Checks
• Input= .xpt or ADaM data set shells
• Output= .xls files
Pinnacle 21
Supplemental ADaM Dataset Validation Checks for
compliance not covered in Pinnacle 21 ADaM v1.3 Data
Validation Checks
• Report Generation
• Generate Define.xml with ARM
Input= validated ADaM datasets
Output= define.xml
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ADaM Variables
• Any SDTM variable name in ADaM:
“same name, same meaning, same values”
• When ADaM column has an SDTM name, values must be copied and not altered
• If a standard ADaM variable exists, then one must use the ADaM variable name for that concept
• Obey SAS V5 transport file naming and labeling conventions
• Core Definitions are in the ADaM Mapping Specification
• Req- Required
• Cond- Required if applicable; conditionally required
• Perm- Permissible
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ADaM Variable Name Fragments
*N – a numeric version of a variable named *
*GRP – a grouping of a variable named *
*GRPN – a numeric version of a grouping of a variable named *
RACE, RACEN, RACEGRP, RACEGRPN
*FL – character flag
*FN – numeric version of character flag
TRT* – a treatment variable
*DY – a relative day (no day 0)
*DT, *TM, *DTM – numeric date, time, datetime
*DTF – date imputation flag (Y, M, D, null)
*TMF – time imputation flag (H, M, S, null)
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ADaM Variables
# Variable Type Len Format Label
1STUDYID Char 15 Study Identifier
2USUBJID Char 25 Unique Subject Identifier
3SUBJID Char 25 Subject Identifier for the Study
4SITEID Char 25 Study Site Identifier
5AGE Num 8 Age
6SEX Char 2 Sex
7SEXN Num 8 Sex (N)
8RACE Char 41 Race
9RACEN Num 8 Race (N)
10RACEOTH Char 100 Race Other
11ENRLFL Char 1 Enrolled Population Flag
12RANDFL Char 1 Randomized Population Flag
13SAFFL Char 1 Safety Population Flag
14 ITTFL Char 1 Intent-To-Treat Population Flag
15TRT01PN Num 8 Planned Treatment for Period 01 (N)
16TRT01P Char 100 Planned Treatment for Period 01
17TRT01AN Num 8 Actual Treatment for Period 01 (N)
18TRT01A Char 100 Actual Treatment for Period 01
19TRTSDT Num 8 DATE9. Date of First Exposure to Treatment
20TRTEDT Num 8 DATE9. Date of Last Exposure to Treatment
21RANDDT Num 8 DATE9. Date of Randomization
22TRTP Char 100 Planned Treatment
23TRTPN Num 8 Planned Treatment (N)
24TRTA Char 100 Actual Treatment
25TRTAN Num 8 Actual Treatment (N)
26AESEQ Num 8 Sequence Number
27AESTDTC Char 19 Start Date/Time of Adverse Event
28AEENDTC Char 19 End Date/Time of Adverse Event
29ASTDT Num 8 DATE9. Analysis Start Date
# Variable Type Len Format Label
30 ASTDTF Char 1 Analysis Start Date Imputation Flag
31 ASTDY Num 8 Analysis Start Relative Day
32 AENDT Num 8DATE9. Analysis End Date
33 AENDY Num 8 Analysis End Relative Day
34 AENDTF Char 1 Analysis End Date Imputation Flag
35 ADURN Num 8 Analysis Duration (N)
36 ADURU Char 20 Analysis Duration Units
37 AETERM Char 200 Reported Term for the Adverse Event
38 AEDECOD Char 200 Dictionary-Derived Term
39 AEBODSYS Char 67 Body System or Organ Class
40 AELLT Char 200 Lowest Level Term
41 AEHLGT Char 200 High Level Group Term
42 AEREL Char 20 Causality
43 AERELN Num 8 Causality (N)
44 AERELNST Char 200 Relationship to Non-Study Treatment
45 AESCONG Char 2 Congenital Anomaly or Birth Defect
46 AESDISAB Char 2 Persist or Signif Disability/Incapacity
47 AEACN Char 16 Action Taken with Study Treatment
48 AEOUT Char 32 Outcome of Adverse Event
49 AESDTH Char 2 Results in Death
50 AEDDTC Char 19 Date and Time of Death
51 AESHOSP Char 2 Requires or Prolongs Hospitalization
52 AESLIFE Char 2 Is Life Threatening
53 AEDIS Char 1 Study Discontinuation Due to AE
54 AESMIE Char 2 Other Medically Important Serious Event
55 AESEV Char 8 Severity/Intensity
56 AESEVN Num 8 Severity/Intensity (N)
57 AETOXGR Char 1 Standard Toxicity Grade
58 AETOXGRN Num 8 Standard Toxicity Grade (N)
59 AESER Char 2 Serious Event
60 TRTEMFL Char 1 Treatment Emergent Analysis Flag
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Define.xml and Schema
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ARM.xml
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ADaM Validation Checks
• Pinnacle 21
• Supplemental Checks
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Analysis Data Reviewer’s Guide
The ADRG provides context for the analysis datasets and
terminology that benefit from additional explanation beyond the
Data Definition document (define.xml). In addition, this document
provides a summary of ADaM conformance findings.
https://www.phusewiki.org/wiki/index.php?title=Analysis_Data_Reviewer%27s_Guide
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ADRG_Completion_Guidelines_2015-01-26.pdf
1. Introduction
1.1. Purpose
1.2. Acronyms
1.3. Study Data Standards and Dictionary Inventory
1.4. Source Data Used for Analysis Dataset Creation
2. Protocol Description
2.1. Protocol Number and Title
2.2. Protocol Design in Relation to ADaM Concepts
3. Analysis Considerations Related to Multiple Analysis Datasets
3.1. Comparison of SDTM and ADaM Content
3.2. Core Variables
3.3. Treatment Variables
3.4. Subject Issues that Require Special Analysis Rules
3.5. Use of Visit Windowing, Unscheduled Visits, and Record Selection
3.6. Imputation/Derivation Methods
4. Analysis Data Creation and Processing Issues
4.1. Split Datasets
4.2. Data Dependencies
4.3. Intermediate Datasets
4.4. Variable Conventions
5. Analysis Dataset Descriptions
5.1. Overview
5.2. Analysis Datasets
5.2.1 ADSL – Subject Level Analysis Dataset
5.2.x Dataset – Dataset Label
6. Data Conformance Summary
6.1. Conformance Inputs
6.2. Issues Summary
7. Submission of Programs
8. Appendix
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Implementation Challenges
Traceability
The main challenges are maintaining traceability of each data element
and correctly following the ADaM documentation:
Statistical Outputs (TFLs) => Analysis Data sets ADaM => ARM.xml =>
ADaM Define.xml => ADaM Mapping Specifications => SDTM Define.xml
=> CRF (see https://www.lexjansen.com/phuse/2014/dh/DH01.pdf)
Pinnacle 21 does not include the most current version of the ADaM
Validation Checks.
Over 1.2 million non-critical errors/warnings
Issues related to:
o Updating dataset code lists
o Study Design
o Propcase vs upcase for character variable values as per ADaM
Standards
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ADaM Specifications
• ADAE specification tab in not in desired format
• Metadata tab is not in desired format
• Metadata and spec tab column names are not in desired format
• ADSL, ADDS and ADEG specification tabs not in desired format
• Specification file extension is not in desired format
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Non-Compliant Analysis Datasets
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illegal variable name: y is not in
[1-9] for PARCATy(N)
Define.xml
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• Links for attached documents not working.
• Keys column for datasets needed updates (added AVISITNM
and QSGRPID to USUBJID, PARAMCD, ADT, ATM)
• Unwanted notes in derivation of variables
• Code list with parameters not up-to-date
ADRG
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• Incorrect study number
• Typos or grammatical errors
• Number of subject screened vs enrolled
• Site name vs center name
• Correct number of sites
• Inconsistent fonts
• Insufficient information; i.e., which ADaM domains have screen failure
subjects; imputations/derivations - specifying which analyses were
used for unscheduled visits
• Renaming datasets mentioned in ADRG but not updating the TLF
programs to output those dataset names.
Solutions
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Ways to Address ADaM Implementation Challenges
Develop Standard Tools and Processes:
• Specifications
• TLF Mocks
• Validation Checks
• ADaM Template Code
• Define.xml
• ARM.xml Code
• ADRG QC
• Compliance Metrics
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Solutions
• Develop/utilize the following items:
• Standard ADaM Specifications template and process
• Standard TLF Mocks
• Pinnacle 21 and supplemental user-written validation checked, based on ADaM Validation Checks 1.3.
• Validation checks to supplement P21
• ADaM Template Code, based on standard safety TFL mocks
• Standard Define.xml- use ADaM Specifications, ADaM Datasets and TFL annotation, Pinnacle 21, SHARE API, or develop a custom generic program to generate define.xml version and ARM.xml
• Standard ARM.xml code
• ADRG review process for accuracy and consistency
• Compliance metrics to track use and effectiveness
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Standard Code to Produce ADaM Datasets, Define.xml, and ARM.xml
• Develop ADaM Template Code that would need <20% modification
from study to study for creation of “analysis-ready” datasets, to
improve efficiency.
• Allows programmers to meet aggressive timelines and robust coding
with clear logical program flow and follow ADaM standards for all
studies for regulatory authority submissions.
• In the future, ADaM datasets may be generated from SDTM data sets
via machine learning.
• Improves Productivity & Quality metrics; Utilize a standard approach
across studies
• Code reusability; easy maintenance; represent high standards for
coding structure, defensive coding, commenting and cleanup of work
library.
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ADaM Template Code
• Base on ADaM V2.1, ADaM IG V1.1 and ADaM OCCDS V1.0.
• Include Safety datasets: ADSL, ADAE, ADCM, ADMH, ADEG, ADLB, ADVS, ADPE, etc.; include additional domains such as Oncology datasets.
• Include all ADaM required variables and standard TLF mock variables at minimum
• Assume a parallel study design
• Add study specific variables, drop extraneous variables, update existing derivation as per study need, etc.), in the respective study folder by the Study team, per study requirements
• Simple derived variables, e.g., TRTSDTM derived with Datetime of first exposure to treatment for a subject in a study
• Is not source code but a TEMPLATE so will not work without modification in studies.
• In lieu of validation, perform code review and User Acceptance Testing
• Helps to avoid code redundancy and unforeseeable issues
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Validate Define.xml
• Run Pinnacle 21• All the issues/errors/warnings identified should be resolved prior
to final package or a valid explanation should be provided explaining why these errors can’t be resolved.
• Check define.xml Source/Derivation/Comment section
• Check ALL the external documentation hyper-links
• Perform all the checks given in ADaM Electronic Submission
• Material Checklist
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Compliance Metrics
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Conclusion- Balance the ADaM Universe
• Establishing a team of ADaM subject matter experts to use standard tools and processes around ADaM standards and project deliverables improves quality and efficiency
• Next step for users of the standards- align project/study deliverables with ADAMIG v1.2
Acknowledgements
Thanks to ICON Programming
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