Attachment_3_General_SOW.pdf

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Attachment 3: Statement of Work

Biospecimen CORE Resource

Independently and not as an agent of the Government, the Contractor shall furnish all the necessary services, qualified personnel, material, equipment, and facilities, not otherwise provided by the Government as needed to perform the Statement of Work to support the National Cancer Institute (NCI) mission.

TASK AREA A: Biospecimen Processing Center (BPC) Services

A. Scope The BPC represents a centralized approach to biospecimen processing to ensure consistent quality of the biomaterials and associated data distributed to the characterization centers and provides the foundation for data comparability across characterization platforms and laboratories. The processing and distribution shall be fully tracked, quality controlled, and documented. The purpose of Task Area A of this contract is to provide biospecimen receipt, processing to molecular analyte, and distribution services for an expanding list of National Cancer Institute (NCI)-supported genomics projects. The Contractor shall have the capability or the ability to procure and provide services for other molecular testing and pathology services.

These specific or mandatory requirements will be identified in a separate Task Order Statement of Work. The Contractor shall perform the following tasks:

1) Biospecimen and Associated Data Procurement

2) Biospecimen Management and Biorepository Operations

3) Biospecimen Quality Control

4) Biospecimen Processing into Molecular Analytes

5) Informatics and Data Delivery

6) Other BPC-related Services

7) Conduct Transition Activities

B. Description of Work

1) Biospecimen and Associated Data Procurement The Contractor shall:

i. Develop case and sample inclusion criteria as maintained in Standard Operating

Procedures (SOPs).

ii. Implement a Laboratory Information Management System (LIMS) system which supports and logs all sample receipts, locations, accesses, movements, processes and modifications, process results, and distributions.

iii. Procure biospecimens to meet the biospecimen needs for each genomics study and ensure that samples are collected, handled, shipped and received with full maintenance of quality in accordance with contracts and SOPs.

iv. Execute and maintain Material Transfer Agreements (MTAs)/Data Use Agreements (DUAs) with each source entity for transfer of biospecimens.

v. Coordinate with other program entities including, but not limited to The Center for Cancer Genomics (CCG), Biospecimen Processing Center (BPC), Biorepository and

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Archive (BA), Clinical Data Center (CDC), Genome Characterization Center(s) (GCC), Tissue Source Sites (TSS), Genomic Data Commons (GDC), and NCI to meet project needs.

a. Required Coordination with CCG Clinical Data Center (CDC)

Note: The CCG Clinical Data Center (CDC) serves several significant roles: a) it is the primary contact with Tissue Source Sites (TSS), clinical sites, and any program from which subject data and samples will enter the CCG characterization network;

b) it is the source of authority to the network for the registration of each subject and generates the CCG Subject ID for distribution to the network; c) it is responsible for ensuring human subjects compliance for all relationships accessioning subjects and samples into the network; and d) it is responsible for collecting from Tissue Source Sites all demographic and clinical data on subjects.

The BPC Contractor shall coordinate with the Clinical Data Center to:

1. Receive the CCG Network Subject ID linked to the TSS ID (as provided) for all

Subjects for which the BPC is authorized to receive samples. IDs will be provided along with an assertion that the Subject being registered has entered the CCG Characterization network under verified human subjects’ compliance.

2. Receive De-Identified pathology reports, digital images, and other data for those Subjects where such data are necessary for the BPC to perform histological verification on received samples. Subject data received from the CDC shall meet the HIPAA definition of “De-Identified.”

3. Receive from the CDC any notifications of subject withdrawal or other human subjects’ status change that would impact sample processing or distribution.

4. Transmit to the CDC an assertion that samples from a particular subject were successfully, or not, processed into analytes. Transmit to the CDC a list of the BPC-generated biospecimen IDs.

b. Required Coordination with CCG Genomics Data Commons (GDC)

Note: The CCG Genomics Data Commons (GDC) serves as the integrated repository and access portal for CCG projects. It houses subjects’ demographic, clinical, biospecimen, molecular characterization, and analysis data as submitted by numerous NCI contractors, grantees, and projects.

The BPC shall coordinate with the GDC to:

1. Transmit biospecimen processing logistical and shipment data, in the technical format and mechanism specified by the Contracting Officers Representative (COR), within twenty four (24) hours of every shipment.

2. Transmit biospecimen processing pathology verification and QC data, in the technical format and mechanism to the GDC.

c. Required Coordination with CCG Biorepository and Archive (CBA)

Biospecimens shall be transferred to the CBA after projects have been completed and there is a reasonable expectation that no more sample or analyte shipments will be required.

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The BPC shall coordinate with the CCG Biorepository and Archive (CBA) to:

1. Execute Material Transfer Agreements (MTAs) with the CBA, with enough lead time based upon expected duration of a project, to ensure that administrative issues do not impede eventual transfer of materials.

2. Establish logistical relationships and education to enable safe transfer of materials.

3. Transfer project biospecimens and associated inventory data to the long term CBA upon receiving specific direction from the COR.

4. Provide associated data to accompany biospecimens shipped to the CCG Biorepository and Archive that shall include but are not necessarily limited to, the following:

a. A tab-delimited/spreadsheet format document with, minimally, the following data elements: sample UUID, sample latest semantic barcode, sample TSS, case ID, received sample type, received sample numeric sequence, and if applicable, processed biospecimen portion numeric sequence, processed biospecimen type, and sample quantity. This form shall be substantially similar in overall design to the Sample Information Form (SIF) distributed by the BPC with shipments to a GCC.

b. The relevant instance of the Biospecimen Extensible Markup Language files (XML) up-to-date and accurate at the time of transfer.

vi. Establish a Quality Management (QM) program and Quality Control (QC) results for all inventory processes, and electronically record the status of samples as they progress through receipt and storage.

Note: CCG has implemented a project-wide The Cancer Genome Atlas Quality Management System (TCGA QMS) with which all project entities shall be required to coordinate.

CCG QMS will set policies and guidelines for every process and procedure within the program to which BPC will adhere. The TCGA QMS shall adhere to the QMS structure outlined in the Clinical and Laboratory Standards Institute (CLSI) Laboratory Quality Manual Guidelines (HS1-A2, “A Quality Management System Model for Healthcare;

Approved Guideline – Second Edition” (http://shop.clsi.org/quality-management-systems-documents/QMS07.html).

The BPC shall develop a management practice of quality which documents the policies, processes and procedures within the BPC in a manner that is compliant with the CCG QMS. As a component of the CCG QMS, the BPC shall provide data to the CCG QMS information management system to enable the QMS to measure quality and throughput, including the ability to determine trending, of biospecimen and data receipt, processing and distribution.

The BPC shall participate in, and provide data to, CCG project-wide Quality Management System.

1. The BPC shall implement the guidelines and policies of the CCG QMS

2. The BPC shall document its QMS in compliance with the CCG QMS specifications.

3. The BPC shall adapt its informatics systems to provide data, in real time and when otherwise requested, as required by CCG QMS to support the overall CCG quality goals.

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4. Informatics requirements in support of TCGA QMS shall require BPC to expose in real time, read-only data to from BPC LIMS and other software systems holding the relevant data. BPC shall expose these data as required.

vii. Establish all the necessary policies, systems, and technologies to ensure patient protection as specified by regulation, and ensure that National Institutes of Health (NIH) policies are met.

viii. Transfer biospecimen associated data to a designated data center(s).

2) Biospecimen Management and Biorepository Operations

i. Store all biospecimens including, but not limited to cells, solid tissue, blood, and other tissues, according to standardized protocols and best practices.

ii. Implement SOPs, systems, software, and technology to ensure documentation of biospecimen access, control, and access logging.

iii. Provide working storage space in the appropriate environments to support the internal operations of the BPC for activities such as processing, QC, backup, and working storage prior to shipment of analytes.

iv. Store materials for the expected duration of the study or as required by the NCI Contracting Officers Representative (COR).

v. Develop plans and SOP’s to govern the eventual transfer of materials to a designated NCI long-term biorepository or as required by COR.

3) Biospecimen Quality Control The Contractor Shall:

i. Implement necessary systems and SOPs to implement histology laboratory services to verify and document the consistency of received research sample characteristics with the donor institution’s diagnostic result such as correct tissue and tumor content, and to evaluate each biospecimen’s suitability for use in its genomics study.

ii. Collect digital images at an appropriate resolution to allow histological review on the digital image.

iii. Make available all histological QC data online and export to the designated data center.

iv. Conduct proper storage, quality maintenance and shipping as required by COR.

4) Biospecimen Processing into Molecular Analytes

i. Perform the following biospecimen processing activities upon receipt of specimens:

a. DNA and RNA extraction from frozen or Formalin Fixed Paraffin Embedded (FFPE) tumor tissue using an approved protocol, and

b. Germline DNA extraction from blood and/or lymphocytes and/or frozen normal solid tissue and/or buccal cells using an approved protocol.

ii. Store stock plates of nucleic acids.

iii. Distribute nucleic acid as required to meet study needs.

a. Develop and implement SOPs to distribute analytes and tissues to GCC(s) in compliance with Department of Transportation (DOT) requirements.

b. Execute MTAs with institutions that shall be receiving materials. MTAs shall be approved by the COR.

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c. Develop and deploy a support system for GCCs, to rapidly analyze, understand and correct analyte quantity, quality and logistics issues.

d. Record all analyte/tissue shipments and related QC in the LIMS.

iv. Use laboratory automation whenever possible to improve economy of scale.

v. As required, develop and implement new isolation technologies for different cancer tissues, different types of analytes and/or initiate different methods of preparation if the genomics study will require it.

vi. Implement testing systems, including laboratory protocols and information systems to perform molecular QC processes as required to meet study needs.

vii. Document and report biospecimen molecular extract quality data for each type of analyte created, and these data shall be available on a web-based portal for NCI COR designated parties.

viii. Develop protocols to minimize or eliminate cross-contamination, and to measure rates of contamination.

ix. Electronically record in the LIMS the results of all QC processes and the status of samples as they progress through QC and make available online.

5) Informatics and Data Delivery

i. Export data to a designated data center via processes supported by the data center.

ii. Export data in a format supported by the data center at the time of data export.

iii. Export biospecimen and analyte GCC shipment data within one (1) business day of the material’s shipment.

6) Other BPC-related Services The Contractor shall perform services for other molecular testing and pathology services.

7) Transition Activities The Contractor Shall:

i. Prepare a Start-up transition plan outlining processes for commencement of operations, including specifically the scale up of staffing (including key personnel) and operational resources as well as the incorporation of data, SOPs, and materials and other transition information.

ii. Prepare a Close-out transition plan for the end of the contract. The plan shall include mechanisms for transmission of data (including computer-based data) and materials to parties designated by the Contracting Officers Representative (COR) or as contractually obligated.

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TASK AREA B: CCG Biorepository and Archive (CBA) Services

A. Scope The Center for Cancer Genomics (CCG) Biorepository and Archive (CBA) provides long-term biorepository and biospecimen archive services for an expanding list of CCG-supported genomics projects. The Contractor shall provide the following services:

1) Biospecimen and Associated Data Receipt and Storage: receive samples and associated data from the other CCG biospecimen source entities and other sources to provide long-term storage.

2) Biospecimen Management and Biorepository Operations: provide biospecimen management services encompassing the logistics of the biospecimens collected, including receipt, annotation, storage management, location management, internal movement and distribution.

3) Biospecimen and Analyte Distribution: distribute molecular analyte aliquots and other biospecimens using strictly controlled procedures and documentation.

B. Description of Work

1) Biospecimen and Associated Data Receipt and Storage

The Contractor shall:

i. Receive, store, and index bulk archival shipment/collections. The Contractor shall support the following storage environments to include but not be limited to:

a. vapor phase liquid nitrogen freezers (-190°C to -150°C).

b. -80°C and -20°C mechanical freezers.

c. 4°C refrigerators and controlled RT storage.

d. humidity and room temperature controlled areas.

ii. Receive, store, and index bulk archival shipment/collections as needed when studies conclude.

iii. Coordinate with the institutions providing the archival collection.

iv. Store and maintain, in the long-term, biospecimens and materials.

2) Biospecimen Management and Biorepository Operations

i. Store all biospecimens according to best practices.

ii. Execute and maintain Material Transfer Agreements (MTAs)/Data Use Agreements

(DUAs) with each source entity for transfer of biospecimens.

iii. Implement a Quality Assurance program, SOPs, systems, software, and technology to ensure documentation of biospecimen access, control, and access logging.

iv. Provide working storage space in the appropriate environments to support the internal operations of the CBA for activities such as intake, storage, and Quality Control (QC).

v. Provide long term storage of materials to meet the needs of the NCI.

3) Biospecimen and Analyte Distribution

i. Retrieve, process and ship individual and aggregate biospecimens as needed.

ii. Coordinate with the institutions to ship biospecimens as needed.

iii. Develop a transition in/out plan

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C. Applicable to both Task Area A Biospecimen Process Center (BPC) Services and Task

Area B, CCG Biorepository and Archive (CBA) Services

Use of Standard Operating Procedures (SOPs)

NOTE: Standard Operating Procedures developed for The Cancer Genome Atlas (TCGA) Bio pecimen Core Resource (BCR) are provided in Attachment entitled “Technical Information to Offerors” as examples and are referenced throughout the Statement of Work (SOW).

The BPC/CBA Contractor shall develop a set of SOPs for the CCG BPC/CBA. When necessary, the BPC/CBA Contractor shall develop additional CCG BPC/CBA SOPs for a specific genomics study.

Many operating details for the BPC/CBA will be subjected to frequent changes to meet the needs of the rapidly evolving CCG genomics studies and the molecular characterization platforms and bioinformatics analysis pipelines the program encompasses. Many such details for each of the requirements in this SOW shall be enumerated in a compendium of SOPs to be developed by the BPC/CBA Contractor and maintained by the CCG Program Office.

These SOPs shall include, but are not limited to, protocols that govern laboratory protocols, specimen logistics, standard templates for various documents and data collection forms, and data transmission formats. The Contractor shall submit any modified SOPs to the Contracting Officer Representative (COR) for review as contract deliverables. The SOP compendium will be made available to the Contractor (see Technical Information to Offerors attachment).

1) Standard Operating Procedures and Quality Assurance

The BPC/CBA Contractor shall implement a stringently followed set of SOPs for generation of DNA, RNA and potentially other molecular derivatives to minimize variability and provide

QC.

The BPC/CBA Contractor SOPs shall: 1) support collection and histological review of large numbers of biospecimens of varying biological characteristics; 2) Describe processing of these materials into a large inventory of molecular derivatives; 3) Describe quality control for starting materials, intermediates and final products; 4) Describe management of the biospecimens and derivatives at all stages from initial receipt, through processing, storage and distribution, to include complex logistics and an infrastructure to ship and transfer molecular analytes to outside scientific investigators; 5) and become the foundation of the BPC/CBA Contractor’s Quality Management System (QMS), against which the center’s operations shall be measured.

2) Specific Requirements for SOPs The BPC/CBA Contractor shall obtain, modify and develop (as necessary), implement and manage SOPs to govern all activities. SOPs shall address these activities, as they are carried out within BPC/CBA, including:

i. Methods for administrative management, including establishing contracts, financial considerations, and material transfer agreements (MTAs) with source sites for the purpose of receiving samples and data at the BPC/CBA. (BPC and CBA)

ii. Methods for complying with notification of a subject withdrawal from any study for which the BCR has received, or may inadvertently receive, biospecimens. (BPC and CBA)

iii. Methods of biospecimen acquisition and biorepository management, including collection, processing, preservation, and storage. (BPC and CBA)

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iv. Methods for processing tissue samples into molecular analytes. SOPs shall be designed, optimized and actively managed to maximize yields and quality of nucleic acids. (BPC)

v. Methods for distributing biospecimens, including logistics and MTAs. (BPC and CBA)

vi. The SOPs shall become part of BPC/CBA Contractor’s QMS program. SOPs shall include specification of quality parameters which shall govern the QC activities required under this SOW, including, but not limited to, pathology verification and molecular derivative testing. (BPC and CBA)

vii. Routine process improvement shall be part of the Contractor’s Quality Management System (QMS).

viii. Biospecimen specifications, including expertise in definition of the histology, and definition of quality control procedures. (BPC and CBA)

ix. Molecular isolation and profiling technologies current, and future, likely to be used as part of CCG, and how this shall impact tissue preparation and processing. (BPC)

SOPs for laboratory automation shall be distinct from SOPs for manual methods and be developed, validated and implemented by an automation staff that is distinct from production staff.

The BPC/CBA Contractor shall provide update of these SOPs to the COR and the CCG Program Office in accordance with the applicable Program Management Plan. (BPC and

CBA)

D. Meeting and Communications

The Offeror shall be available for meetings, and for receipt and delivery of reports and materials to and from the tissue source sites and the NCI work site, currently 9609 Medical Center Drive, Rockville, MD. Communications methods such as teleconferencing and telephone conference calls shall be necessary as no reimbursable travel will be included.

E. Section 508

The following Section 508 Standards are applicable to this procurement:

1. Software Applications and Operating Systems (1194.21)

2. Web-based Intranet and Internet Information and Applications (1194.22)

3. Functional Performance Criteria (1194.31)

4. Information, documentation, and support (1194.41) https://www.access-board.gov/guidelines-and-standards/communications-and-it/about-the-section-508-standards/guide-to-the-section-508-standards/software-applications-and-operating-systems-1194-21 https://www.access-board.gov/guidelines-and-standards/communications-and-it/about-the-section-508-standards/guide-to-the-section-508-standards/web-based-intranet-and-internet-information-and-applications-1194-22 https://www.access-board.gov/guidelines-and-standards/communications-and-it/about-the-section-508-standards/section-508-standards#subpart_c https://www.access-board.gov/guidelines-and-standards/communications-and-it/about-the-section-508-standards/section-508-standards#subpart_d