Sample_Example_Sentinel_Task_Order.docx

Core Sentinel Activities Task Order

SAMPLE/EXAMPLE

(NOT FOR EVALUATION PURPOSES)

Core Sentinel Activities Task Order Performance Period – September 22, 2014 – September 21, 2016

Table of ContentS

DATA INFRASTRUCTURE

Data Infrastructure Governance In addition to the governance developed in the Base contract[footnoteRef:1] (C2. Coordinating Center Activities), the Contractor shall develop governance to address data specific issues and the interaction between the Sentinel Coordinating Center (SCC) and the Data Partners. The distributed data network governance shall allow for the creation of policies, procedures, and processes that ensure scientific rigor, data integrity, and protection of privacy. This governance shall enable active medical product surveillance, including near real-time assessment of medical products used during public health emergencies. The Contractor shall use the Mini-Sentinel (MS) Principles and Policies document developed during the MS Pilot as a reference.[footnoteRef:2] Specific requirements include: [1: RFP #FDA-14-RFP-1127332] [2: See MS Principles and Policies, November 2013. Available at: http://mini-sentinel.org/work_products/About_Us/Mini-Sentinel-Principles-and-Policies.pdf. ]

Deliverable(s):

· Create a board or workgroup to ensure multi-stakeholder representation in the creation and implementation of the governance structure

· Create policies and procedures that are not already in place as a part of governance created in the Base contract.

Create the SCDM for De-identified Electronic Health Care Data The Contractor shall use the latest version of the Mini-Sentinel Common Data Model (MSCDM)[footnoteRef:3] specifications to develop the Sentinel Common Data Model (SCDM). The format of the SCDM should allow the development of new analytical tools containing additional types of information from other sources. [3: The MSCDM is a standard data structure that enables Data Partners to run standardized programs against data stored locally at their sites. Details and specifications of the MSCDM can be found at http://www.mini-sentinel.org/data_activities/distributed_db_and_data/default.aspx ]

Deliverable(s):

· Finalize and implement SCDM specifications

Data Partners - Create and Maintain the Sentinel Distributed Database The Contractor shall ensure that Data Partners representing the electronic healthcare data of at least 100 million patients will extract, transform and load (ETL) all or part of their data into the SCDM format and execute data checking programs (see Section A.4.2) for review by the SCC. This set of transformed data holdings will be known as the Sentinel Distributed Database (SDD). The SCC will work closely with Data Partners to create the SDD.

Deliverable(s):

· Contractor shall ensure that Data Partners test and implement SCDM

· Contractor shall ensure that Data Partners use ETL process developed by SCC to create SDD (see Section A.4.1)

· Contractor shall ensure that Data Partners use ETL process developed by SCC to update SDD per identified schedule (see Section A.4.1)

· Contractor shall ensure that Data Partners implement data quality review activities described in Section A.4.2 and respond to problems identified during this process

· Contractor shall ensure that Data Partners have the SDD ready to accept queries: Ongoing throughout the performance period of task order

SDD - Facilitate Creation and Update of the Sentinel Distributed Database (SDD) Data Conversion and Refresh The Contractor will work with Data Partners to maintain and update all data components of the SDD throughout the period of performance. Activities will include creation of an ETL process, clarifying and revising the SCDM (see Section A.3 and A.5), iterative data checking via distributed programs, and identification of problems with completeness or characteristics of the data (see Section A.4.2). Data will be updated periodically. Updates of Data Partners’ entire datasets will occur at a minimum of two times per year; however, quarterly updates are preferred. If a data partner site is to refresh their data on a less frequent schedule, justification should be provided and approved by FDA. The exact frequency and schedule of updates will be determined in consultation with FDA and the Data Partners, and will depend on needs and available resources. Although preferred, it is not necessary for all updates to occur at the same time.

For some active surveillance activities, updates for some data fields may need to occur as often as weekly or require access to the freshest feasible data. If more frequent updates are needed for a specific activity, this will be accounted for as a part of the task order. For example, in the case of semi-automated routine surveillance, Data Partners may also be required to do “ad-hoc updates” of specific data elements within the SDD to facilitate real-time surveillance. This will be determined on a case by case basis and be determined based on the medical product under evaluation and the need for assessments on accumulating data on a more frequent basis than the currently planned SDD updates. Data refresh results should be included in the quarterly reports (see Section A.4.3)

Deliverables:

· Contractor to develop ETL process for Data Partners to create the SDD

· Contractor to develop and finalize workplan and data refresh schedule to perform regular updates of the SDD

· Contractor to implement workplan: Ongoing throughout the performance period of task order

Data Checks - Develop, Document, Implement Data Quality Review and Data Characterization Procedures To ensure Data Partners are ready to evaluate queries, on an ongoing basis, the Contractor shall develop data quality protocol and related programs that will be implemented at each Data Partner site. Additionally, the Contractor shall regularly update these programs to capture new data elements (i.e., administrative and clinical data) that have been added to the SCDM. These programs will be used in data quality checking activities, to be implemented by each Data Partner following transformation of their data into the SCDM format. The data quality checking process will also collect information about the time period covered, the number of individuals included in the SDD at each participating data partner, basic population demographics, and summary information on selected data elements available in the SCDM. This activity will include resolution of missing data, anomalies, and inconsistencies.

A programming environment using synthetic data based on the CDM will be created by the Contractor to allow development and testing of data quality checking and analytic programs.

Deliverables:

· The Contractor shall design the specifications and create the testing environment

· The Contractor shall ensure data quality checking programs are complete and ready for implementation

· The Contractor shall conduct the initial assessment of Data Partners implementation of the SCDM specifications: within 15 days of receiving results of data checking program.

· The Contractor shall ensure data quality checking programs are updated regularly and ready for implementation: 60 days after new data elements incorporated into SCDM Inventory Updates Describing SDD Following implementation of the SCDM, the Contractor will describe the data available through the SDD for each Data Partner. These reports (e.g., tables) shall include information on data available for surveillance activities, including but not limited to; time period covered, the number of individuals (i.e., enrollments), date of last and next data refresh, basic population demographics, and summary information on selected data elements (e.g., clinical data) available in the SCDM. Inventory reports shall be updated and available for FDA review within 30 days after each quarter.

Deliverables:

· The Contractor shall design and finalize template report.

· The Contractor shall update the inventory reports: Quarterly(fiscal year), throughout the performance period of task order

Enhance and Augment the SCDM Incorporating National Data Standards in the SCDM During the MS Pilot, the Contractor and FDA worked to identify potentially relevant national medical coding standards and controlled terminologies. A workplan was developed to evaluate the appropriateness of identified standards, describe the use of standards within the CDM, and develop a strategy for incorporating appropriate, national standards in the SCDM. The evaluation included an assessment of the strengths and weaknesses of relevant standards and controlled terminologies in the context of the MSCDM, medical product safety surveillance, and the data capture environment of current and potential future Data Partners.

Leveraging the work done during the MS Pilot, the Contractor shall continue to incorporate national data standards for data elements incorporated within the SCDM and engage with any national data standards bodies as appropriate. As new data elements (e.g., clinical data) are added, continued attention will need to be maintained to ensure that newly incorporated data elements also conform to national standards and new developments in the area of data standards implementation and adoption are incorporated into Sentinel activities.

Deliverables:

· The Contractor shall develop policies and procedures to ensure national data standards are addressed: Ongoing throughout the performance period of task order Expansion of the SCDM The Contractor shall review the MS Expansion Plan[footnoteRef:4] developed during the MS Pilot and assess current needs and identify additional priorities. The Contractor will assess the costs and added value of identified priorities and determine whether these new data elements should be made available either through integration into the SCDM or through an alternative mechanism. As part of this assessment, the Contractor should determine the granularity of available data elements, the frequency of potential data refreshes, determine whether existing modular programs may be executed on these data streams, and assess the capacity to link this data (e.g., individual hospitalizations to outpatient data streams) among the Data Partners. [4: MS Expansion Plan is available upon request from FDA.]

Further expansion of the SCDM will need to consider needs for medical product routine surveillance, and other variables, including available data resources within the Sentinel Data Partners and other Sentinel collaborating institutions and any identified gaps. Once priorities have been identified, the SCC will expand the SCDM to incorporate the new elements (e.g., additional clinical data) and the SDD will be refreshed to reflect this change. This process will include the Contractor writing, testing, and revising specifications for updates to the SCDM, incorporation of such revisions to the ETL process, and revisions of data checking programs and performing data quality and characterization activities to incorporate any expanded data elements.

If the identified elements require standardization in order to be used in MS assessments, the Contractor will work with Data Partners contributing those elements to ensure that the transformed data are able to be used for Sentinel activities (e.g., evaluating the completeness, ranges of values, and frequencies of these clinical data elements). At a minimum, a sufficient sample will be extracted to allow thorough evaluation of each participating data resource. After new elements have been incorporated into the SDD, Data Partners will need to have the capacity to accept queries utilizing all data elements in the SCDM.

Deliverables:

· The Contractor shall review the MS Expansion Plan to assess current needs and identify additional priorities for SCDM expansion

· The Contractor shall develop workplan to implement expansion of SCDM

· The Contractor shall implement expansion of SCDM priorities as described in workplan and incorporate into Data Partner’s SDD updates (see Section A.4): Ongoing throughout the performance period of task order

Write an Annual Report Analyzing the SCDM, SDD and other Data Activities The Contractor shall write a report to FDA will summarize the status of the SCDM and SDD. It should also include any lessons learned with the implementation and update of the SCDM, identify plans to adapt it to leverage other CDMs in related projects, and create plans for identifying and conforming to recognized and evolving national data standards (see Section A.5.1). Finally, it shall also address how other types of healthcare data (e.g., inpatient EHR, registry data) will be incorporated into the existing CDM, characteristics, availability, completeness, advantages and disadvantages of specific elements for inclusion based on identified priorities and gaps (see Section A.5.2). The report should be inclusive of all the subprojects conducted in support of data infrastructure activities and Data Partners.

Deliverables:

· The Contractor shall develop outline for review and approval to FDA

· The Contractor shall draft and finalize report by the end of each performance year of task order

SURVEILLANCE ACTIVITES

Develop, Maintain and Enhance Standardized Analytical Tools The Contractor shall develop, maintain and enhance standardized analytical tools (e.g., distributed menu-driven query infrastructure, modular programs, and summary tables for surveillance activities. These tools will allow rapid interrogations of the SDD to facilitate routine surveillance. The Contractor shall leverage the infrastructure and analytical tools developed during the FDA’s Mini-Sentinel Pilot.

The Contractor shall:

· Develop menu interface for queries to quantify exposures or outcomes.

· Develop programs for Data Partners to create summary tables and a schedule for updating.

· Adapt existing MS modular programs to conduct rapid response surveillance queries in the SDD.

· Enhance existing modular programs[footnoteRef:5] to allow for new features (e.g., modifications to include new study designs, enhanced exclusion/inclusion criteria including dispensings, procedures and/or diagnoses).) [5: Details and specifications of MS modular programs can be found at: http://mini-sentinel.org/data_activities/modular_programs/default.aspx ]

· Develop programs to incorporate all standardized clinical elements into standardized tools (e.g., modular programs, summary tables) to allow rapid characterization of exposures and outcomes in the SDD.

Deliverables:

· The Contractor shall develop and finalize workplan

· The Contractor shall implement workplan (i.e., tools should be ready to use and enhance tools): Ongoing throughout the performance period of the task order.

Prepare and Update Summary Tables to Support Queries The Contractor shall ensure Data Partners whose data are a part of the SDD will create summary tables for use with the Sentinel distributed querying tool (see Section B.1). These summary tables will be used to address initial feasibility queries through the distributed querying tool. Creation of these tables involves execution of a series of distributed programs designed by the SCC to run against the SDD. The Data Partners will retain possession of these data tables in a database format compatible with the query tool.

Deliverables:

· The Contractor shall ensure that Data Partners create and update summary tables in accordance with Section B.1

Expand Semi-Automated Prospective Routine Observational Monitoring Tools (PROMPT) Surveillance Capabilities Using work completed during the MS Pilot, the Contractor shall expand development of a semi-automated prospective surveillance system (i.e., PROMPT), which will be used to conduct surveillance of newly approved and existing medical products. The activities for this system consist of supporting and strengthening the existing infrastructure and include, but not limited to, the following:

· Expand operational and methodological capabilities of the system

· Develop new methods modules (i.e., semi-automated routine surveillance modular programs) that include other epidemiologic study designs and statistical analytic methods

· Build sufficient capability into the system to routinely evaluate 20-25 medical products each with up to 10-15 HOIs per year

· Evaluate performance of new modules against several pairs of exposures and outcomes whose epidemiologic association is already known (including both known positive and negative association).

· Prioritize the development and implementation (i.e., programming, testing, executing) of identified algorithms (e.g., HOIs, cohorts, confounders)

· Develop algorithms for additional health outcomes of interest, potential confounders, and cohorts of interest.

· Prepare report evaluating the strengths and limitations of the current methods modules should be prepared. The report should include recommendations and a workplan for improvements/revisions to the existing processes, procedures, and modules performance.

Deliverables:

· The Contractor shall meet with FDA to discuss objectives and goals and develop a draft workplan to implement future activities as listed above

· The Contractor shall finalize and implement the workplan: Ongoing throughout the performance period of the task order

Establish Capability to Implement Medical Product Routine Surveillance (e.g., summary tables, modular programs, and PROMPT)

The Contractor shall ensure the following requirements related to capacity and timeliness are established by the SCC and Data Partners.

quarter

3(SCC)

12(SCC)

Establish SCC capability to implement PROMPT medical product routine surveillance, (e.g., summary tables, modular program and PROMPT) The Contractor shall ensure that the SCC establish the capability to implement modular programs, summary tables, and PROMPT tools for routine surveillance in collaboration with Data Partners. The SCC will be required to complete query requests in accordance with capacity and timeline requirements summarized in Section B.4. See Section B.4.2 for Data Partner implementation capability.

Deliverables:

· The Contractor shall ensure that the SCC is able to provide queries to Data Partners within established timelines: Ongoing throughout the performance period of the task order.

· The Contractor shall ensure that the SCC is able to provide reports to FDA within established timelines: Ongoing throughout the performance period of the task order.

Establish Data Partner administrative and technical capability to respond to PROMPT medical product routine surveillance, (e.g., summary tables, modular program and PROMPT) Then Contractor shall ensure that Data Partners establish, maintain, and implement the administrative and technical capability to accept and respond to queries using the tools described in Section B.4. This will involve maintaining the local querying infrastructure and having the necessary personnel available to respond to queries and potential secondary questions regarding their results. The following requirements related to capacity and timeliness is required by the Data Partners. See Section B.4.1 for SCC implementation capability.

Deliverables:

· The Contractor to ensure that the Data Partners are able to respond to queries within established timelines: Ongoing throughout the performance period of the task order

Methods Development Activities

Method Development Taking into consideration key gaps identified during the MS Pilot and through consultation with FDA, identify three to six specific projects per performance period year where methodological development to support active surveillance evaluations in SDD is needed. Development will include testing using sample questions, where appropriate. In addition, the report should include a description of how each method will be used for active surveillance evaluations, including optimal situations for use, strengths, and limitations.

The methods selected for development should address the most pressing methods priorities for Sentinel. Methods will also be selected based on their ability to be implemented in a distributed system.

This Task Order activity will require creation of three to six teams that will be responsible for development and testing of the new methodological approaches for active surveillance in a distributed data environment. Each team will work with FDA to create and finalize the study specifications, develop and test the methods, and manage the project in accordance with the requirements listed in this Task Order. The teams will actively engage with the Contractor and Data Partners to ensure the proposed methods are viable within the SDD and to identify any future implementation barriers. Work must ensure coordination of methods development across task orders.

· Methods development will use the SDD. If this is not feasible for some reason and a test data set is more appropriate, adequate justification and alternative data source(s) will be provided for FDA review and concurrence.

· The task order deliverable will validate new methods that are able to be implemented for routine use in active surveillance evaluations conducted on the SDD. These methods will be tested with appropriate known safety questions so as to test their performance within the SDD.

This activity is not limited to epidemiological and statistical methods development. Methods projects could also include development of approaches to facilitate real-time active surveillance capabilities within a distributed database. Lastly, the methods taxonomy decision tool[footnoteRef:6] shall be maintained and further expanded as new research methods are developed and implemented in the Sentinel distributed database environment. [6: See MS Taxonomy of Observational Study Designs – Phase 3. Available at: http://mini-sentinel.org/methods/methods_development/details.aspx?ID=1044

Deliverables:

· Contractor to meet with FDA to identify topic for evaluation

· Contractor shall develop and implement workplan: Ongoing throughout the performance period

· Contractor shall conduct training on methods development: Ongoing throughout the performance period of task order

Last Updated: 26 June 2014