SAS Life Science Analytics Framework · (SAS® Visual Analytics, ...) ADAPTIVE DESIGN AUTOMATION ( Life Science Analytics Framework Extension/App ) Internal system(s) / customers

Copyr i g ht © 2015, SAS Ins t i tu t e Inc . A l l r ights reser ve d .

STIJN ROGIERS - SAS SENIOR INDUSTRY CONSULTANT

GLOBAL PRACTICE, HEALTH & LIFE SCIENCES

CDISC Italian User Network Day – 21Oct2016

(Data standard e loro applicazione)

SAS Life Science Analytics Framework


AGENDACDISC ITALIAN

USER NETWORK DAY

1. Introduction to SAS Life Science Analytics Framework (LSAF)

2. CDISC Standards & Study Metadata

Demo - Generation of Empty Datasets & Define.XML

3. End-2-End flow

SAS LSAF + Extensions through LSAF API

SDTM transformation

Cross-functional Review (structural & content checks, visualizations)

4. Use Cases


QUIZCDISC ITALIAN

USER NETWORK DAY


INTRODUCTION

LIFE SCIENCE ANALYTICS FRAMEWORK


CDISC ITALIAN

USER NETWORK DAY

SAS LIFE SCIENCE ANALYTICS FRAMEWORK

KEY FACTS (1/3)

Managing, analyzing, reporting, and reviewing (clinical) research information in the same analytical environment

Repository provides seamless integration with the SAS program development (authoring environment)

and execution environment, along with workflow capabilities

-- NEW Authoring Environment compared to SAS DRUG DEVELOPMENT (SDD)

-- NEW Business Process Model and Notation (BPMN) 2.0 standard support compared to SAS DRUG DEVELOPMENT (SDD)

Cloud based

Provides more flexibility, lower costs, greater scalability, ease of use and, if done correctly,

increased security and disaster recovery

IT seen as an ‘Innovator’ supporting the rest of the company to achieve its goals


CDISC ITALIAN

USER NETWORK DAY


PROGRAM AUTHORING & EXECUTION


CDISC ITALIAN

USER NETWORK DAY


WORKFLOW (SUPPORT BPMN STANDARD)



KEY FACTS (2/3)

Collaboration & Accessibility

internally and externally (geographically remote)

direct access to research content, clearly organized and searchable

Configurable User Interface

Highly flexible (configurable) permission model privileges & permissions

High-performance (Remote) Application Programming Interface (extend & automate)

Java API and SAS Macro API, moving to RESTful API

Complete audit history and robust version control system managing change history of all files

Job concept and Manifest file

Job Concept reproducibility and usability (for non-technical savvy users)

Manifest File transparency and traceability

CDISC ITALIAN

USER NETWORK DAY


REPOSITORY AND CREATION OF JOB

EXAMPLECDISC ITALIAN

USER NETWORK DAY

Create Job from existing SAS files + Run and Populate


REPOSITORY AND CREATION OF JOB

EXAMPLE

CDISC ITALIAN

USER NETWORK DAY

Create Job from existing SAS files + Run and Populate

“Run and Populate” scans all SAS programs to produce “Input & Outputs” automatically (example of Inputs/Outputs on next slide).


JOB MANIFEST FILE

EXAMPLECDISC ITALIAN

USER NETWORK DAY



KEY FACTS (3/3)

Standards metadata management (driving automation) -- NEW compared to SAS DRUG DEVELOPMENT (SDD)

Standard (Global) Level (SDTM & SEND) “ Data Standards ” Module

Study Level Study Specification: Empty Datasets + Define XML 2.0 creation “ Studies ” Module

Support Visual Analytics (integration) -- NEW compared to SAS DRUG DEVELOPMENT (SDD)

Expanding Suite of Extensions (optional modules build on robust LSAF API)

E.g. ‘Templates’ extension to automate creation of folder structure

within repository incl. administration/security.

Note: See also additional extensions slides related to end-2-end flow.

CDISC ITALIAN

USER NETWORK DAY


CLINICAL STUDIES VISUALIZATION

EXAMPLE

32

1

1. Direct link to Patient Profile

2. Drop down list showing

# of subjects in a site

3. Drop down list showing #

of subjects who died in study

Aggregate Panel Review

CDISC ITALIAN

USER NETWORK DAY


1

2

3

4

5

5

6

7

8

9

101. DM domain view

2. SV domain view

3. SE domain view

4. DS domain view

5. CM domain view

6. AE domain view

7. MH domain view

8. LB domain view

9. VS domain view

10. Visits view

11. Link back to

Demographic view

11

CLINICAL STUDIES VISUALIZATION

EXAMPLE

Patient Profile

CDISC ITALIAN

USER NETWORK DAY


CDISC STANDARDS AND STUDY METADATA


GLOBAL STANDARDS

STANDARDS MANAGEMENT – STUDY METADATA – DATA PROCESSING – REVIEW – ANALYSIS

External /

Other Data

eSHARE

Standards

IMPORT eSHARE CDISC

STANDARDS

CREATE CUSTOMER STANDARDS

Global Standards

DEFINE

STUDY LEVEL METADATA

CREATE SUBMISSION

READY SDTM DEFINE.XML

SHARE WITH INTERNAL & EXTERNAL

STAKEHOLDERS

Study Metadata

Sensors/

Wearables

Protocol

EDC DATA EXTRACTION

(Life Science Analytics Framework

Extension/App)

Other DATA EXTRACTION


Extension/App)

Event Streaming

(SAS® Event Stream Process

Engine)

Extraction & Transformation

Specifications

EDC

SDTM

Transformation(Life Science Analytics

Framework

Extension/App)

Specifications

Cross-Functional Review

Final Deliverables

Deliverables (Internal sharing of SDTM data after Structure ‘automated’ verification)

Automated + Manual Review Activities

(Life Science Analytics Framework Programs/Jobs + SAS® Visual

Analytics + Pinnacle 21 (~Open CDISC), ...)

1 2

3

3

3

45

Cross-Functional Review Tracking

(Life Science Analytics Framework Extension/App)

Review Input

PROGRAMS-JOBS

DEVELOPMENT

* CREATION, QC & USAGE

(INCL. VERSION

CONTROL)

* SIGN-OFF

* AUTOMATION VIA

WORKFLOW

• RUNNING “R” CODE

THROUGH PROC IML

VISUALIZATIONS

(SAS® Visual Analytics, ...)

ADAPTIVE DESIGN

AUTOMATION

( Life Science Analytics

Framework Extension/App )

Internal

system(s) /

customersOutbound data

( Life Science Analytics Framework Extension/App )

7

8

6

CDISC ITALIAN

USER NETWORK DAY

Analysis Activities

PROGRAMMING

TRACKING & PROGRESS

( Life Science Analytics Framework

Extension/App )


STUDY METADATA


External /

Other Data

eSHARE

Standards

IMPORT eSHARE CDISC

STANDARDS


Global Standards

DEFINE


CREATE SUBMISSION



STAKEHOLDERS

Study Metadata

Sensors/

Wearables

Protocol

EDC DATA EXTRACTION


Extension/App)



Extension/App)

Event Streaming


Engine)


Specifications

EDC

SDTM


Framework

Extension/App)

Specifications


Final Deliverables





1 2

3

3

3

45



Review Input

PROGRAMS-JOBS

DEVELOPMENT


(INCL. VERSION

CONTROL)

* SIGN-OFF

* AUTOMATION VIA

WORKFLOW

• RUNNING “R” CODE

THROUGH PROC IML

VISUALIZATIONS


ADAPTIVE DESIGN

AUTOMATION

( Life Science Analytics

Framework Extension/App )

Internal

system(s) /

customersOutbound data

( Life Science Analytics Framework Extension/App )

7

8

6

CDISC ITALIAN

USER NETWORK DAY

Analysis Activities

PROGRAMMING

TRACKING & PROGRESS

( Life Science Analytics Framework

Extension/App )



STANDARDS MANAGEMENT

CDISC ITALIAN

USER NETWORK DAY



STUDY METADATA MANAGEMENT

CDISC ITALIAN

USER NETWORK DAY



END-2-END FLOW (LSAF + EXTENSIONS)


END-TO-END FLOWCDISC ITALIAN

USER NETWORK DAY


Analysis Activities

SDTM TRANSFORMATION


External /

Other Data

eSHARE

Standards

IMPORT eSHARE CDISC

STANDARDS


Global Standards

DEFINE


CREATE SUBMISSION



STAKEHOLDERS

Study Metadata

Sensors/

Wearables

Protocol

EDC DATA EXTRACTION


Extension/App)



Extension/App)

Event Streaming


Engine)


Specifications

EDC

SDTM


Framework

Extension/App)

Specifications


Final Deliverables





1 2

3

3

3

45



Review Input

ANALYSIS PROGRAMS-

JOBS


(INCL. VERSION CONTROL)

* SIGN-OFF

* AUTOMATION THROUGH

WORKFLOW

* RUNNING “R” CODE THROUGH

PROC IML

VISUALIZATIONS


ADAPTIVE DESIGN

AUTOMATION


Extension/App)

Internal

system /

PartnerOutbound data

7

8

6

CDISC ITALIAN

USER NETWORK DAY


END-2-END FLOW:

SDTM TRANSFORMATION (LSAF EXTENSION)

Supported by SAS Solutions On Demand

Current Flow Overview (all details can be provided during a demo)

Publish manual mapping to Auto-mapping definitions for future (~ machine learning).

Over time this will reduce manual mapping efforts significantly.

Generate Program Templates with Pre-Code, Mapping information and Post-Code

CDISC ITALIAN

USER NETWORK DAY

Define StudyIdentify CDISC

Mapping Standard

Identify Data Sources

Understand / browse

through raw data

Table to Domain mapping

Variable Mapping

(Auto-mapping and manual +

Progress)

Publish Mappings

Transformation Program

‘Templates’


CDISC ITALIAN

USER NETWORK DAY

END-2-END FLOW:

SDTM TRANSFORMATION (LSAF EXTENSION)

Define StudyIdentify CDISC

Mapping Standard

Identify Data Sources

Understand / browse through

raw data

Table to Domain mapping

Variable Mapping

(Auto-mapping and manual +

Progress)

Publish Mappings

Transformation Program

‘Templates’

• Generate Program Templates with Pre-Code, Mapping information and Post-Code


Analysis Activities

CROSS-FUNCTIONAL REVIEW


External /

Other Data

eSHARE

Standards

IMPORT eSHARE CDISC

STANDARDS


Global Standards

DEFINE


CREATE SUBMISSION



STAKEHOLDERS

Study Metadata

Sensors/

Wearables

Protocol

EDC DATA EXTRACTION


Extension/App)



Extension/App)

Event Streaming


Engine)


Specifications

EDC

SDTM


Framework

Extension/App)

Specifications


Final Deliverables





1 2

3

3

3

45



Review Input

ANALYSIS PROGRAMS-

JOBS


(INCL. VERSION CONTROL)

* SIGN-OFF

* AUTOMATION THROUGH

WORKFLOW

* RUNNING “R” CODE THROUGH

PROC IML

VISUALIZATIONS


ADAPTIVE DESIGN

AUTOMATION


Extension/App)

Internal

system /

PartnerOutbound data

7

8

6

CDISC ITALIAN

USER NETWORK DAY


CDISC ITALIAN

USER NETWORK DAY

CROSS-FUNCTIONAL REVIEW:

AUTOMATED (1/4)

Review Tracking Rules

(= Compliance Rule(s) ~Structural , Global Content Rule(s), Trial Specific Content Rule(s))


CDISC ITALIAN

USER NETWORK DAYCROSS-FUNCTIONAL REVIEW: AUTOMATED (3/4)

Review Tracking Output (Follow-Up)


CDISC ITALIAN

USER NETWORK DAYCROSS-FUNCTIONAL REVIEW: AUTOMATED (4/4)

Review Tracking Output (Follow-Up) - Details including History, Attached Files.


CDISC ITALIAN

USER NETWORK DAYCROSS-FUNCTIONAL REVIEW: MANUAL

Opportunity to raise Manual findings

e.g. Visualizations (medical review); looking at output, listings; etc. …


USE CASES


QUIZCDISC ITALIAN

USER NETWORK DAY

Tip: 2760 m ?


MAJOR PHARMACEUTICAL

PROCESS IMPROVEMENT

2010 - 2016

BUSINESS ISSUE(S)

• Needed better Quality Control on Data Management CROs

• ability to handle changing CDISC data standards (standards management)

• be able to create Study Level Metadata (Define.XML) and provide to DM-CRO as clear specifications

• wanted automated review process of DM CROs deliverables (SDTM data + Define.XML) prior to data

being given to data management

• Needed new Data Management platform (in the Cloud) to facilitate new DM processes

• clean the data (focusing on Primary & Secondary endpoints; Standard work done by DM-CRO)

• be able to run CDISC Compliance Checks on the data received from the DM-CRO

• be able to explore the datasets within the same platform

• Transfer data from/to other stakeholders - systems (e.g. External Data such as but not limited to

Central ECG or Central Lab; DM-CRO’s end deliverables; Feeds of data into DWH of sponsor; etc.)

• Repository for all their Clinical Trial Data (incl. Audit Trail, Version Control, Part 11 compliant,

Workflow Management)

• handle growth to allow other areas of clinical R&D to access information and do their analysis in same

platform/environment.

USE CASE 1 (PAGE 1/3)



PROCESS IMPROVEMENT

2010 - 2016

SOLUTION

• SAS Drug Development + Custom Application Development by 3rd party

[ Java UI + Oracle DB using SDD API’s ]

RESULTS

PHASE I (2010-2014)

• Automated DM-CRO review process (less time and review cycles by customer)

• Quality increase of DM-CRO deliverables (through clear specifications)

• Increase of Traceability (Job Manifests) & Reproducibility (Jobs)

PHASE II (2015-2016)

• Scalable environment has allowed them to provide access to new teams (Statistical Programmers &

Statisticians) for new clinical trials with no new investment in hardware

• Increase collaboration (partnering) between DM and Stats Programmers/Statisticians

• Migration of all ongoing clinical trials to LSAF (from own internal Servers / SAS environment) = Recently

Started.

FUTURE STEPS

• Provide access to other teams (scale up)

• As more standards functionalities become available in LSAF (compared to SDD), transition from

the Custom Application to LSAF Build-in (standard) functionalities started




PROCESS IMPROVEMENT

2010 - 2016

SOME FIGURES

• Users on SDD

• Current Status (including external company users): +1000

• By End 2016: +1500

[ Data Management & Statistical Programming/stats ]



VACCINES SUBSIDIARY OF


COMPANY

SOLUTION

• SAS Drug Development

RESULTS

• All data management and statistical programming

• Strict hierarchy set up to complete separate DM (Data Standards Programming and Study-

Specific) and statistical work

• Data transferred from EDC system (Inform) to SAS solution

• Using Spotfire to help out with clinical data management review process, SAS to clean data

• Integration with safety system

• Integrations with Oracle user management database (trial access) and program lifecycle

management database

• SAS solution is also being used by trial operations and clinicians as central and operational-

critical hub for accessing clinical trial data and support trial analytics

About +/- 1500 users in total, of which about 300 concurrent in the environment

USE CASE 2


AS A

REFERENCE


THANK YOU !

EMAIL:

[email protected]

TWITTER:

@STIJNROGIERS

LINKEDIN:

HTTPS://WWW.LINKEDIN.COM/IN/STIJNROGIERS

Documents

SAS Life Science Analytics Framework · (SAS® Visual Analytics, ...) ADAPTIVE DESIGN AUTOMATION ( Life Science Analytics Framework Extension/App ) Internal system(s) / customers