Attachment_1-SOW-ExpertConsultant_101316.pdf

SOW Expert Consultant 1 10/12/2016

Attachment 1

Statement of Work – Expert Consultant

Background

The National Cancer Institute (NCI), Center for Cancer Genomics’ (CCG’s) goal is to integrate structural, functional, and computational tools with multiple cancer genomic datasets, which are then made broadly available via data commons to the research community. To this end, in June 2016, CCG launched the Genomics Data Commons (GDC), an integrated database to house multiple large-scale cancer genomics data sets with supporting analytical tools. The GDC is a growing, multi-petabyte collection of data generated by CCG Offices and other cancer genomic programs housed on a “big data” cloud-capable technology stack designed and built under contract to CCG. Recently, the GDC was named one of the ten initiatives highlighted under Vice President Biden’s Cancer Moonshot that supports the goal of making a decade’s worth of cancer research progress in five years.

GDC currently includes data from The Cancer Genome Atlas (TCGA) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) programs. Data from an additional ~10 NCI-sponsored programs are slated to enter GDC over the next 1.5 years. A key requirement of data entering the GDC is that they must be harmonized into a single standard for maintenance and eventual comparability during analyses. As more data is added to the GDC, the system’s value to the research community multiplies.

To support continued growth of the GDC, CCG Office of the Director requires the services of a Subject Matter Expert in bioinformatics in the clinical research field. Effort under this project will advise and assist CCG in the continuing development of the GDC which is in its pilot phase, among other bioinformatics projects.

The objectives of this procurement are to ensure the continued success of the GDC, a complex database and analytical software system that manages petabytes (and growing) of cancer genomic data. Much of success of the GDC to date is dependent on understanding the nature of the data going into it, the lessons learned from prior systems holding cancer genome data, and understanding modern architectures of system capable of managing such data.

Scope of Work

Support for CCG’s critical programs is provided in four task areas, briefly described below:

1. Task Area 1 - Center for Cancer Genomics (CCG): Provide expert guidance and support for with CCG’s oversight of the of the GDC to facilitate the continued development and utilization CCG’s Genomics Data Commons (GDC).

2. Task Area 2 – Office of Cancer Genomics (OCG): Provide support and expert technical guidance that facilitates policy and standards compliance and data normalization.

3. Task Area 3 – CCG Programs Office/TCGA:

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a. Clinical Data Center (CDC) and Biospecimen Core Resource (BCR) Support: provide expert technical support for clinical data and biospecimen service procurement efforts.

b. Cancer Characterization Programs: provide expert technical guidance and services to support the closure of completed programs and ongoing activities of new programs.

4. Task Area 4 – Division of Cancer Epidemiology and Genetics (DCEG):

a. DCEG Biorepository Inventory Management System Review: provide continued Subject Matter Expert support to DCEG Director’s Office for the implementation of the restructured biorepository system.

b. Next Gen Cohort: support the Deputy Director DCEG and the study’s Principal Investigator in procurement of data systems required for the Next Gen Cohort study.

c. DCEG-wide Operations Management and Reporting Platform: support the Deputy Director DCEG in developing a system to provide operational reporting data (a “dashboard”) to DCEG leadership that tracks the status of studies in DCEG from concept and inception through all stages ending in manuscript clearance.

d. Genomics Data Commons (GDC): support the Director and Deputy Director DCEG in developing a plan to pilot deposition of DCEG data sets into the GDC.

Objectives

The objectives of this acquisition are to ensure the continued success of the GDC, a complex database and analytical software system that manages petabytes (and growing) of cancer genomic data, and related programs that contribute data to the GDC. Much of success of the GDC to date is dependent on understanding the nature of the data going into it, the lessons learned from prior systems holding cancer genome data, and understanding modern architectures of system capable of managing such data.

Requirements

Task Area 1 – Center for Cancer Genomics (CCG) Background The CCG manages NCI's research activities in this domain by establishing pre-clinical research programs based on petabyte-sized molecular characterization studies. CCG is the umbrella for programs run from the Office of Cancer Genomics (OCG) and the CCG Program Office which ran TCGA and follow-on studies. CCG’s goal is to integrate structural, functional, and computational tools with multiple cancer genomic datasets, which are then made broadly available via data commons to the research community. A key tool in this set is the GDC, a growing collection of data generated by CCG Offices and other cancer genomic programs

SOW Expert Consultant 3 10/12/2016 housed on a “big data” cloud-capable technology stack designed and built under contract to

CCG.

Work Requirements

• Support the GDC and CCG’s oversight of the continued development and utilization of the GDC.

• Provide Subject Matter Expertise on the detailed technical requirements and provide expert input to support verification of the status of requirements. This may include working regularly with vendor technical teams.

• Provide Subject Matter Expertise on the implementations of systems architecture requirements, including data models, data processing pipeline, and polyglot / NoSQL databases / persistence systems. Specifically ensure that clinical data and models are harmonized as data are imported from diverse cancer genomic programs.

• Support CCG program data submission cutovers from existing Data Coordinating Center (DCC) to the GDC when that system goes live and the legacy program’s DCCs are closed down.

• Provide Subject Matter Expertise to the GDC committees and working groups, including the Project Team, Steering Committee, Engineering Review Board, Change Review Board, Clinical Data Working Group, Standard Operating Procedures (SOP) Working Group, and others as requested.

• Provide information / lessons learned on TCGA, TARGET/CGCI, BLGSP, HCMI, and other programs as related to data standards, data policies and technical specifications, including history, current example, and opportunities for improvement. Provide information on technical issues related to importation of legacy data from current CCG data systems into the new system.

• Present the GDC to 3rd parties considering deposition of their data therein. Establish communications and collaboration between those 3rd parties, CCG Director, and the GDC Program Manager, as requested.

Task Area 2 – Office of Cancer Genomics (OCG) Background The OCG, within CCG, supports translational programs generating petabyte-sized molecular characterization analyses linked to donor’s demographic and clinical data. These data sets will be deposited into CCG’s, and therefrom broadly shared to the investigator community. Data from OCG and other programs deposited into the GDC must use common data elements, data models, and formats to ensure integration and the ability to be cross-analyzed.

Work Requirements

• Provide Subject Matter Expertise on issues related to human subject enrollment and sample accrual for genomics programs, including human subjects’ protections, Material Transfer Agreements (MTA), HIPAA, and data access and use policies. Support includes drafting and editing of IRB protocols, informed consents, Data Use Agreements, and other materials and services as needed.

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• Provide expert technical advice and support during concept development and pre-procurement activities in compliance with study protocols for OCG projects. Specifically review data collection forms and data elements within those forms for NCI cancer Data Standards Registry (caDSR) compliance, element re-use and non-redundancy across OCG programs, and compliance with GDC requirements.

• Identify and recommend solutions to informatics data model details that will minimize differences between clinical and biospecimen data elements and content in OCG cancer genomics programs versus those being collected in other CCG cancer genomics programs whose data will be deposited in the GDC.

• Continually review OCG program data standards compliance with CBIIT with National Cancer Informatics Program (NCIP) cancer Data Standards Registry (caDSR) data specifications. Liaise NCIP on data standardization and data access issues as requested.

• Work with OCG cancer genomics collaborators and vendors to develop specifications and deploy systems for data normalization in preparation for sharing and distribution of those data to the GDC or other 3rd party cancer genomic data portals.

• Represent OCG needs in technical requirements during continued development of the

GDC.

• Liaise with the CCG Programs Office, to ensure harmonization of data elements collected on projects in the two offices when studying the same cancer.

• Participate, as requested by OCG Director, in International Cancer Genome Consortium (ICGC) activities in which relevant subject matter expertise is required.

Task Area 3 –CCG Programs Office/TCGA Background The CCG Programs Office implements programs the generate large-scale genomic characterization data derived from cancer patients donating their clinical data and tissue samples to research. The office ran TCGA project in conjunction with the National Human Genome Research Institute and has since leveraged the multi-institutional collaboration created for TCGA to characterize cancer from numerous higher-value projects, especially including studies whose donors participated in clinical trials.

Work Requirements Provide Subject Matter Expertise to CCG Programs Office Director, Clinical Data Collection (CDC) program, Biospecimen Core Resource (BCR) program, and other programs or initiatives as needed.

a. CCG Clinical Data Center (CDC) and Biospecimen Core Resource (BCR) support.

Support CCG clinical data and biospecimen service procurement efforts necessitated by the decision to split current Biospecimen Core Resource services into separate Clinical Data Collection and Biospecimen Core Resource contracts. Activities include:

• Provide technical expertise and guidance to assist in the development and/or review of Statements of Work requirements and deliverables to ensure that informatics requirements support data submission to GDC.

• Develop and support the presentation of technical materials describing service requirements to support procurements.

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• Provide Subject Matter Expertise on RFP proposals for use by review committees, as requested.

For the future CDC and current and future BCR vendors, provide support to ensure that from the perspective of bioinformatics, clinical informatics, and IT issues, all technical requirements are met. Activities include:

• Reviewing data submissions to ensure the BCR is receiving, processing and delivering annotated biospecimens / analytes that meet the scientific, technical and administrative needs of CCG characterization programs.

• Ensure CDC and BCR operations are adherent to relevant ethical, legal and technical requirements by performing in-depth data mining and analysis.

• Provide Subject Matter Expertise regarding data standards required for CCG compliant submissions to the GDC.

• Coordinate between the CDC, BCR and GDC to ensure that any modifications of CDC or BCR data models are cohesive with the developing GDC data models.

• Ensure communication between the CDC, BCR, and GDC to ensure that Tissue Source Site, Characterization Center, CDC, and BCR generated Case Notes are delivered to GDC as required.

• Regularly communicate with CDC and BCR to support their development of software systems and data standards to meet the goals and requirements of CCG cancer characterization programs. Specifically, ensure that clinical and biospecimens data are received, and analyte data are distributed according to the SOW requirements, GDC submission format requirement, and CCG needs.

• Provide CCG Programs Office Director and the individual service program managers with regular activity reports on CDC and BCR informatics processes and issues that arise. Activities will include weekly conference calls and written updates as requested.

• Provide Subject Matter Expert opinions on BCR and CDC vendor performance for consideration by the applicable COR(s) and Program Managers.

b. CCC Cancer Characterization Programs

The Cancer Genome Atlas (TCGA)

• Provide Subject Matter Expertise to the TCGA Project Team, committees, and working groups, as requested.

• Provide expert consultation on policies and operations related to patient privacy, HIPAA, data access and distribution, intellectual property, and human subjects’ issues, and ensuring these requirements are encoded and maintained with data.

Review evolving applicable technical standards to TCGA data, and ensure compliance with those standards, on clinical- and bio-informatics data generated by TCGA and submitted to GDC.

• Ensuring, as TCGA is closed-out over FY2017, that the GDC has a faithful copy of the entire data set, and that data elements collected in TCGA are correctly represented in the GDC enabling data model enabling query and retrieval.

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New Programs (e.g. CDDP, Alchemist, ER, CTSP, etc.)

• Support tissue procurement activities including, review of RFPs and Statements of Work. Specifically ensure clinical and biospecimen data collection requirements of CCG are complied with by sites contributing donor data and materials to CCG programs, and review detailed data dictionaries to ensure such compliance. Address issues arising around informed consents, MTA, data use agreements, intellectual property, and patient protection, as requested.

• Liaise with NCI CBIIT on informatics issues, primarily clinical and biospecimen data standards as they relate to CDC and BCR operations and CCG data requirements. Specifically participate in NCIP data standardization activities that directly support and impact CCG programs from both technical informatics and policy perspectives as related to Common Data Elements used by GDC and maintained in the CBIIT cancer Data Standards Registry (caDSR).

• Represent CCG Programs Office needs in technical requirements during continued development of the Genomics Data Commons (GDC).

• Liaise with programs in the Office of Cancer Genomics (OCG), to ensure harmonization of data elements collected on projects in the two offices when studying the same cancer.

• Participate, as requested by CCG Programs Office Director, in International Cancer Genome Consortium (ICGC) activities in which the required subject matter expertise overlaps with CCG work.

Task Area 4 – Division of Cancer Epidemiology and Genetics (DCEG) Background The Division of Cancer Epidemiology and Genetics (DCEG) at the National Cancer Institute (NCI) has a mission to conduct broad-based, high quality, high impact research to uncover the causes of cancer and the means of its prevention. DCEG studies operate both nationally and internationally, with priority given to emerging issues identified through epidemiologic, clinical, and laboratory observations. DCEG also addresses public health concerns identified by the NCI, Congress, regulatory agencies, and other appropriate bodies. The Division develops research resources and strategic partnerships in molecular epidemiology across NCI, NIH, and the global research community. Towards achieving this mission, DCEG, studies include as a primary objective the collection, annotation, storage, redistribution, processing and study of large numbers of biospecimens maintained in a system of biorepositories.

a. DCEG biorepository inventory management system review Provide Subject Matter Expert support to DCEG Director’s Office for the implementation of the restructured biorepository system, including:

• Discussions with DCEG leadership and investigators, to include:

o Face-to-face “debrief” with Deputy Director who will be overseeing biorepository operations.

o Additional discussions with DCEG leadership and research staff on implementation details contained in the recommendation plan.

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• Incorporate potential changes to the biorepository recommendation plan, if suggested and/or required by DCEG, and deliver the revised plan to the DCEG Director.

• Provide Subject Matter Expert guidance and input on any Statements of Work resulting from potential DCEG decisions to modify the work and deliverables provided by vendors delivering biorepository services to the division.

• Support the onboarding of new DCEG Program Manager for biorepository operations, by providing Subject Matter Expertise on the DCEG biorepository system, the recommendation plan, be available for Q&A, and provide other support as requested.

Review and provide expert opinion on the suitability of Information Management Services, Inc. (IMS) Biological Specimen Inventory (BSI) software to support DCEG’s new “Next Gen Cohort” and other studies coming online beginning in FY 2017 – 2018. Work will include:

• Interviews with DCEG staff to determine scale, timing, biospecimen type scope, and biospecimen annotation scope for large cohort study.

• Review of BSI software current and planned capabilities, which may include the following activities:

o Review of product literature and documentation.

o Review of product development roadmap, if provided by IMS.

o Accompany and advise DGEC personnel meeting with IMS product manager and developers, if possible, to determine BSI current and future capabilities.

o Gap analysis between version currently-used by DCEG and current version in production.

• Deliverable:

o Report providing expert yes/no opinion on continuing the use of BSI to support DCEG biospecimen inventory management for consideration by the DCEG Director.

If recommended, provide as part of the above deliverable a summary recommendation on whether or not legacy BSI data should be forward migrated into the version of BSI that will also house the new cohort studies.

If not recommended, provide as part of the above deliverable summary recommendations on alternatives.

b. Next Gen Cohort Support the Deputy Director DCEG and the study’s Principal Investigator in procurement of data systems required for the Next Gen Cohort study, including:

• Provide Subject Matter Expertise in support of the development of requirements for the study’s data systems infrastructure RFP.

• Provide expert feedback on responses to the sources sought notice received from interested providers of the data systems infrastructure for consideration by DCEG staff in the procurement process.

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• Upon issuance of a contract for the data systems infrastructure, provide Subject Matter Expertise on the contractor’s system design plans and iterative deliverables for consideration by DCEG staff.

c. DCEG-wide Operations Management and Reporting Platform Support the Deputy Director DCEG in developing a system to provide operational reporting data (a “dashboard”) to DCEG leadership that tracks the status of studies in DCEG from concept and inception through all stages ending in manuscript clearance.

Work will include:

• Provide expert input into the development of a Statement of Work for a vendor who will perform division-wide business analysis for this product and develop an implementation plan.

• Participate, as requested, on any DCEG groups that provide input into the business analysis process and provide expert opinion on the resulting implementation plan.

d. Genomics Data Commons

• Support the Director and Deputy Director DCEG in developing a plan to pilot deposition of DCEG data sets into the GDC.

• Act as a liaison for administrative and technical.

Deliverables

The following table contains a list of deliverables with notation of due dates. All days identified are intended to be normal business days unless otherwise specified. The Contractor may suggest an alternative due date for any or all deliverables in their offer. The final schedule will be agreed to by the NCI COR and the Contractor, based on the Contractor’s proposed delivery schedule.

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Task Area Deliverable Submitted To Due Date All Monthly Status and

Accomplishments Report COR First business day of each month for the duration of the period of performance

3 Service Requirements MaterialsE

CCG Programs Office/TCGA Director and COR

As defined by CCG Programs Office/TCGA Director and Contractor

3 Activity Reports on CDC and BCR Informatics Processes and Issues

CCG Programs Office/TCGA Director, Individual Service Program Managers, and

COR

Weekly phone conferences; weekly written updates as requested by CCG Programs Office/TCGA Director

4 Revised Biorepository Recommendation Plan

DCEG Director and COR

As defined by DCEG Director and Contractor

4 Report on Continuing Use of BSI to Support DCEG Biospecimen Inventory Management including Summary Recommendation

DCEG Director and COR

As defined by DCEG Director and Contractor

Period of Performance A severable base year plus two option years is anticipated for a period of performance of December 1, 2016 – September 30, 2019.