SOW-SME_5-30-19.pdf

SOW Expert Consultant 1

Attachment 1

Statement of Work – Expert Consultant

Background

The National Cancer Institute (NCI), Center for Cancer Genomics’ (CCG’s) unifies NCI's activities in cancer genomics by aiming to synthesize research in different fields of cancer genomics – structural, functional, and computational – to improve patient outcomes. CCG programs and collaborations generate cancer genomic and clinical data and make these data available for widespread use by the research community. To this end, in June 2016, CCG launched the Genomic Data Commons (GDC), an integrated database to house multiple large-scale cancer genomics datasets with supporting analytical tools. The GDC is a growing, multi-petabyte collection of data generated by NCI Offices and other internal and external cancer genomics programs housed on a “big data” cloud-capable technology stack designed and built under contract with Leidos Biomedical Research. .

The GDC currently includes data from The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Treatments (TARGET) programs, Human Cancer Models Initiative, Clinical Proteomic Tumor Analysis Consortium (CPTAC), and others. Data from an additional dozen internal and external programs are slated to enter GDC over the next three 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 and enhancement of the GDC, 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 the 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 genomic data and understanding modern architectures of systems capable of managing such data.

Scope of Work

Support for CCG’s critical programs is provided in three 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 for Cancer Moonshot and other OCG programs.

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3. Task Area 3 – TCGA Program Office:

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

Support: provide expert technical support for clinical data and biospecimen service ongoing operations.

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

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, including Cancer Moonshot programs. Much of the 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 systems 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 Cancer Genome Atlas Program Office which ran TCGA and now manages the NCI Genome Characterization Pipeline 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 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 implementation of systems architecture requirements, including data models, data processing pipeline, and polyglot / NoSQL

SOW Expert Consultant 3 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.

• 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.

• Inform GDC Project Team plans with relevant information gleaned from DCEG’s deployment of U Chicago’s Generation 3 Data Commons software within the context of CBIIT’s Cancer Research Data Commons (CRDC) environment.

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. OCG manages CCG’s Cancer Moonshot program, the Human Cancer Models Initiative (HCMI).

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.

• Provide expert technical advice and support during concept development and pre-procurement activities in compliance with study protocols for OCG projects.

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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 TCGA Program 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 support of the Cancer Models Development Centers (CMDC) comprising the NCI commitment to the Human Cancer Models Initiative (HCMI). Specifically, provide technical support (as described above) for CMDC clinical data submission from CDC to the GDC, biospecimen data submission from BPC the GDC, and population of data into the HCMI Searchable Catalog.

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Task Area 3 – TCGA Program Office

Background

The TCGA Program Office implements programs that 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 the TCGA Director, Clinical Data Collection (CDC) program, Biospecimen Processing Center (BPC) program, cancer characterization programs, participate in and travel to the international Cancer Genome Consortium (ICGC) meeting, and other programs or initiatives as requested.

a. CCG Clinical Data Center (CDC) and Biospecimen Processing Center (BPC) support.

As requested for the CDC and BPC vendors, provide Subject Matter Expertise to ensure that, from the perspective of bioinformatics, clinical informatics, and IT issues, all technical requirements for submission of data to the GDC are met. Activities may include facilitating communication regarding data standards between CDC, BPC, and GDC.

b. CCG Cancer Characterization Programs

The Cancer Genome Atlas (TCGA)

• As requested, support CCG Director’s office and TCGA Program Office with implementing the project to collect follow-up clinical data on the TCGA cohort.

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

• As requested, support the TCGA Program Office with technical expertise in the collection of clinical and biospecimen data, including providing guidance on semantics, standardization, and compliance with GDC submission requirements for all projects.

c. International Cancer Genome Consortium, ICGC ARGO

CCG may decide to participate in the next ICGC project, known as “ICGC-ARGO.”

ICGC-ARGO is a worldwide clinical sequencing project that will collect more extensive

SOW Expert Consultant 6 clinical data than the original ICGC. The new project’s requirements include more uniformly standardized clinical data than the first project.

As requested by the TCGA Program Office Director in support of ICGC-ARGO, the Contractor shall:

• Serve as the CCG representative to the ICGC Data Coordination and Management Working Group.

• Serve as the CCG representative to the ICGC ARGO Clinical Data and Biospecimen Annotation Standards working group.

• In support of direct transmission of GDC data to ICGC ARGO, specify and review CCG clinical data standards mapping into international standards.

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

2 Service Requirements Materials

TCGA Director and COR

As defined by TCGA Director and Contractor

3 Activity Reports on CDC and BCR Informatics Processes and Issues

TCGA Director, Individual Service Program Managers, and

COR

Weekly phone conferences; weekly written updates as requested by TCGA Director

All Accessibility Checklist COR Annually per deliverable format type

All Roster of Employee(s) Requiring Suitability Investigations

COR Within 30 calendar days of award and updated annually

All Non-Disclosure Agreement

COR Prior to beginning work on the contract.

All IT Security Awareness Training

COR Prior to beginning work on the contract and annually thereafter.

Period of Performance A severable base year plus three option years is anticipated for a period of performance of December 1, 2019 – August 20, 2023.

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Base Period of Performance: December 1, 2019- November 30, 2020

Option One: December 1, 2020- November 30, 2021

Option Two: December 1, 2021- November 30, 2022

Option Three: December 1, 2022- August 20, 2023

Attendance at conferences

Contractor will be required to participate in the below meetings:

1. AACR (Tasks 1, 2, 3)

• Sponsor: Am. Assoc. Cancer Research

• Name: AACR Annual Meeting

• Location: San Diego, CA

• Dates: April 25-29, 2020

• Agenda: (Not yet available)

2. HCMI (Task 2)

• Sponsor: NCI CCG OCG, Wellcome Trust

• Name: HCMI Steering Committee

• Location: Hinxton, UK

• Dates: TBD

• Agenda: (Not yet available) Note: this is international travel.

3. International Cancer Genome ICGC ARGO project (Tasks 1, 3)

• Sponsor NCI

• Name: ICGC ARGO working groups meeting

• Location: (Edinburgh, Scotland – anticipated)

• Dates: TBD

• Agenda: (Working group schedule not yet available.)

Note: this is international travel.

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Accessibility Requirements

Section 508 of the Rehabilitation Act, as amended by the Workforce Investment Act of 1998 (P.L. 105-220) requires that when Federal agencies develop, procure, maintain, or use information and communication technology (ICT), it shall be accessible to people with disabilities. Federal employees and members of the public who have disabilities must have access to, and use of, information and data that is comparable to people without disabilities.

Products, platforms and services delivered as part of this work statement that are ICT, or contain ICT, must conform to the Revised 508 Standards, which are located at 36 C.F.R. § 1194.1 & Apps. A, C & D, and available at https://www.access-board.gov/guidelines-and-standards/communications-and-it/about-the-ict-refresh/final-rule/text-of-the-standards-and-guidelines.

The contractor shall submit applicable accessibility checklists found here:

https://www.hhs.gov/web/section-508/making-files-accessible/index.html. One checklist per deliverable format type (PDF, PowerPoint, Word, Excel, etc.) shall be submitted on an annual basis. The contractor shall follow the steps in the accessibility checklist for all corresponding deliverables to ensure the deliverable meets Section 508 requirements.

https://www.access-board.gov/guidelines-and-standards/communications-and-it/about-the-ict-refresh/final-rule/text-of-the-standards-and-guidelines https://www.access-board.gov/guidelines-and-standards/communications-and-it/about-the-ict-refresh/final-rule/text-of-the-standards-and-guidelines https://www.access-board.gov/guidelines-and-standards/communications-and-it/about-the-ict-refresh/final-rule/text-of-the-standards-and-guidelines https://www.hhs.gov/web/section-508/making-files-accessible/index.html

c. International Cancer Genome Consortium, ICGC ARGO