Att5SOW Sample TO DNAseq.pdf

Attachment 5 –Sample Task Order SOW - DNAseq

Note to Offerors: Proposals for Sample Task Orders will not result in actual awards.

Sample Task Order Statement of Work for DNA sequencing Pool

A. Background Cancer is a complex and heterogeneous disease in which mutations and other genomic and epigenomic aberrations play a role in both its initiation and progression. Recent research data implicate numerous somatic mutations and several inherited mutations in carcinogenesis.

Understanding cancer-specific somatic mutations can provide important clues regarding the molecular processes underlying the development and progression of tumors.

The Center for Cancer Genomics (CCG) at the National Cancer Institute (NCI) was established in 2011 to lead the NCI efforts in generating critical datasets required to catalog the genomic alterations in human tumors. CCG promotes genomic data sharing and the development of analytical tools and approaches to improve understanding of large-scale, multi-dimensional genomic data. The Government needs to establish Genome Characterization Centers (GCC) to provide centralized pipelines to conduct a variety of sequencing and microarray platforms for cancers.

This Sample Task Order Statement of Work (sample SOW) aims to describe potential Genome Characterization Center (GCC) tasks. This is not an actual task order with schedules and deliverables. It is provided for the offerors to get a better understanding of the requirements.

B. Scope The overarching goal for the Genome Characterization Centers (GCCs) is to provide centralized genomic sequencing and array platform services for NCI. The contract shall generate a large quantity of raw sequencing and microarray datasets for multiple types of cancers. The contract will cover the raw data generation (including alignments) from the provided cancer cases. It does not include downstream analysis, interpretation, or discoveries based on the raw data. The raw sequencing or microarray data will be delivered to an approved NCI data repository. All datasets produced by the GCCs will be shared with the community at large as a resource. The contract does not support specific research projects or clinical trials with restricted internal data usage.

C. Objectives and Requirements The GCCs shall provide genomic sequencing or microarray pipelines to produce molecular data for different types of cancers. These pipelines shall be conducted with validated methods using high-throughput and quality-controlled protocols. The Contractors selected shall receive input material (such as DNA aliquot or other types of samples) from the Biospecimen Processing Center (BPC) funded separately by NCI. The contractor(s) will run the pipelines with the received samples and generate high-quality raw sequencing and microarray data.

The contractor shall demonstrate large-scale operation capability for proposed pipelines. Key objectives shall include ensuring that standards are developed, implemented, and continually improved to support the entire genomic characterization pipeline. Variables among studies shall be minimized with rigorous Quality Assurance/Quality Control (QA/QC) of all parts of the operation.

The GCC contractor(s) shall be responsible for the following requirements for all projects conducted in the performance of this contract:

Objective 1. Receive biomaterial from BPC The contractor shall describe plans to execute Material Transfer Agreements (MTAs) and Data Usage Agreements (DUAs). The contractor shall describe plans to implement protocols for receiving and handling biomaterial samples. The contractor shall develop a Standard Operating Procedure (SOP) to receive and manage the types of biomaterial samples received from BPC.

These samples from BPC shall be accompanied by a manifest file including de-identified information regarding the samples.

The contractor shall abide by NIH patient and data protection policies for all participating CCG genomics studies. (https://sharing.nih.gov) The contractor shall have a Standard Operating Procedure (SOP) governing the withdrawal of a participant from a CCG genomics study. Notification of such withdrawal will come from BPC.

The SOP shall include documentation of confirmation and actions following such notification.

Objective 3. Improve and optimize the performance of characterization pipelines

Because technologies have been evolving rapidly, the contractor shall continue to plan for technology improvements during the execution of the project. The contractor shall propose specific efforts to improve and optimize the prescribed technology platforms or switch to more advanced platforms when properly validated and approved by the Program Office. In general, improvements/optimization efforts sought include, but are not limited to:

1. Increasing throughput of the characterization pipeline

2. Enhancing detection sensitivity and/or resolution

3. Optimizing genome characterization coverage

4. Obtaining high-quality data sets from small tumor samples

5. Reducing unit costs per platform

• The contractor shall be able to increase operational capabilities beyond the initial minimum capacity requirement after the first year as CCG projects progress. CCG will provide the contractor estimates of needed capacity in advance throughout the project.

• The contractor shall develop plans to implement and validate new improvements to the characterization platforms when such advances become available. For example, these improvements could enhance sensitivity and resolution in the detection of cancer-associated genome, epigenome, or transcriptome alterations.

• Throughout the project, the GCC shall implement SOPs to minimize variability and improve detection sensitivity and resolution in laboratory processes. The contractor shall make changes with consultation and approval from the CCG program officials.

• The contractor shall plan to take advantage of technology development in selected characterization pipelines. The contractor shall evaluate relevant emerging technologies including a complete change in platform utilized, should it benefit the project (e.g., switching from array-based characterization methods to sequencing-based methods).

Technology platform changes must be validated for high throughput production and implemented with approval from the CCG Program Office.

Objective 4. Implement quality control procedures

• The contractor shall provide specific quality assurance and quality control procedures to monitor the performance of characterization pipelines.

• Quality checking shall be performed on characterization data before submission to the

CCG data repositories. The contractor shall work with the CCG Program Office to define specific quality criteria for each project. These specific criteria shall be established at the start of each project and monitored throughout the project.

• The contractor shall continuously monitor and identify sources of systematic error and bias. The contractor shall implement the necessary procedures to make corrections to achieve experimental reproducibility.

• The contractor shall implement the necessary system to provide reporting on the performance of characterization pipelines.

Objective 2. Operate molecular characterization pipelines The contractor shall provide current next-generation sequencing (NGS) and microarray technologies to characterize comprehensive genomic studies.

A molecular characterization platform should be a current version of the technology that has been validated in previous research programs, such as The Cancer Genome Atlas (TCGA).

Unless requested by the NCI Program Office for specific projects, the proposed platforms should use widely adopted commercial off-the-shelf products. This allows sufficient data to statistically validate the capabilities of the proposed platform. The available datasets of the chosen platforms should have been corroborated statistically by other validated technologies in published comparative analyses. The platforms adopted shall be reviewed and approved by NCI for the task order. Modifications of protocols or updates of platforms such as library protocols or chip designs should be reviewed and approved by the NCI Program Office.

• The contractor shall be able to conduct technologically state-of-the-art, comprehensive, reproducible, and quality-controlled characterization of the biomolecules from cancer samples and appropriately matched controls provided by a BPC.

• The contractor shall build up characterization pipelines to a specified minimum operational capacity within the first month of contract award. The minimum operational capacity is described under “Characterization Platforms”.

• The contractor shall operate characterization pipelines with the minimum capacity for each protocol. The volume of cases requested may vary up or down from the minimum operational capacity over the course of the task order performance period. In general, the contractor shall plan to increase their operational capacity above the minimum after the first year to accommodate potentially higher work volumes from task orders. The contractor shall provide pricing for the case volume specified in the Additional Business Proposal Instructions.

• All GCC genome characterization platforms shall utilize appropriate SOPs, developed and validated by the contractor to minimize variability in laboratory processes. The SOPs shall be approved by the Contracting Officer’s Representative (COR). The SOPs shall be maintained and made publicly available.

• The contractor shall develop and maintain a quality control process for production pipelines at the start of the contract. This process shall include evaluating quality metrics for data generated (e.g. sufficient coverage and depth) as well as capturing platform-specific metadata generated in production. The contractor shall continuously monitor systemic performance such as batch effects in the production pipeline.

• The contractor shall develop an automated process to deposit characterization data and metadata to an NCI repository, such as the NCI's Genomic Data Commons (GDC) within four weeks after data are generated and passed quality control.

Example Characterization platforms:

1) Whole Genome Sequencing low coverage depth (WGS 15X):

a. Perform WGS in DNA extracted from FFPE samples or fresh frozen samples with a validated, documented SOP methodology as approved by the Program Office.

b. Perform WGS with small DNA quantities from samples of limited sizes, such as core needle biopsies with a validated, documented SOP methodology as approved by the Program Office.

c. Perform WGS data with the following requirements:

i. Quality control metrics:

1. The average coverage of bases will be 15X or greater.

2. >85% of bases in the genome will have >8X coverage

3. At least 45 Gb sequence per sample

ii. Turnaround time: within 4 months

iii. Minimum operational capacity: 100 cases/month; 1200 cases/year

2) Whole Genome Sequencing high coverage (WGS 30X for normal and WGS 80X for tumor):

a. Perform WGS in DNA extracted from FFPE samples or fresh frozen samples with a validated, documented SOP methodology as approved by the Program Office.

b. Perform WGS with small DNA quantities from samples of limited sizes, such as core needle biopsies with a validated, documented SOP methodology as approved by the Program Office.

c. Produce WGS data with the following requirements:

i. Quality control metrics:

1. The average coverage of bases will be 30X or greater for non-tumor

2. The average coverage of bases will be 80X or greater for tumors.

3. >85% of bases in the genome will have >15X coverage for non-tumor sample; and >85% of bases in the genome will have >40x for a tumor sample.

4. At least 90 Gb sequence per normal sample and 240 Gb per tumor sample

ii. Turnaround time: within 4 months

iii. Minimum operational capacity: 100 cases/month; 1200 cases/year

3) Whole Exome Sequencing (WES 150X):

a. Perform WES in DNA extracted from FFPE samples or fresh frozen samples with a validated, documented SOP methodology as approved by the Program Office.

b. Perform WES with small DNA quantities from samples of limited sizes, such as core needle biopsies with a validated, documented SOP methodology as approved by the Program Office.

c. Develop methods and SOP for WES when specific commercial off-the-shelf capture products are required by the Program Office.

d. Support existing protocols for ongoing projects. Modifications or replacement of protocols shall be reviewed and approved by the Program Office.

e. Produce WES data with the following requirements:

i. Quality control metrics:

1. The average coverage of bases within the targeted exome shall be 150X or greater.

2. Percent of exome covered by capture targets shall be greater than 99% of Refseq protein-coding genes.

3. >75% of reads will be on target

4. >85% of bases in target exome will have >40X coverage

5. At least 8 Gb sequences per sample

ii. Turnaround time: within 4 months

iii. Minimum operational capacity: 100 cases/month

Objective 5. Support informatics and data delivery Public availability of data/information generated by NCI projects will be critical to facilitate disease-relevant discoveries. Therefore, sharing all rigorously verified data in a timely manner is essential for this contract. All data acquired by the contractor must be made available through the GDC in a timely manner. The contractor is required to submit a Data Sharing Plan documenting how and when data will be released and shared. The Data Sharing Plan must be consistent with the goals of CCG and NCI genomic programs, with adherence to NIH data-sharing policies for the protection of human subjects(https://datascience.cancer.gov/data-sharing).

• The contractor shall develop an informatics system to support sample receiving, sample tracking in pipelines, and data submission to designated NCI data repositories such as GDC.

The contractor shall develop informatics support to meet the data submission requirements by the designated NCI data repository.

• The informatics support shall interact with the CCG COR and GDC to ensure that data release is conformant to CCG project requirements.

• The contractor shall ensure that data submitted to the NCI GDC are compliant with GDC data submission requirements. The precise content of the data to be shared may vary on the data collected for the research projects. Nevertheless, the contractor will be expected to adhere to the general data-sharing principles established by the CCG.

• The contractor must acknowledge and agree that all data, datasets, algorithms, models, and protocols generated through this contract will rapidly become available through the GDC for public use in accordance with the data release requirements. The sharing/dissemination of intellectual property should also be described in the Data Sharing Plan.

• The contractor should develop plans for data evaluation and data submission process. The contractor should describe the expected schedule for data sharing, the format of the datasets, any documentation and analytic tools, and data storage capabilities needed. NCI requires that all data, datasets, and algorithms be released within 30 days to designated databases as they are generated and verified. Algorithms and software tools must be released as open-source. A plan to submit the data upon completion of the funding period is not acceptable. Data release plans should aim for immediate and automatic submissions once the data are produced and verified. In addition, the contractor shall demonstrate the capability to store and maintain the anticipated large amounts of genomic data in-house on a temporary basis and propose appropriate submission arrangements to the GDC.

Objective 6. Perform transition activities

• Transition-In Plan:

The contractor shall provide a transition plan for major steps to ramp up the production capability to meet at least the minimum case requirements within four weeks of the contract award. The contractor shall prepare necessary documentation such as Material Transfer Agreements (MTAs), Data Usage Agreements (DUAs), and Standard Operating Procedures (SOPs) required to perform the contract.

• Transition-Out Plan:

The contractor shall provide a closeout transition plan describing schedules and mechanisms for the transmission of all data and materials to parties designated by the NCI contracting officer or as contractually obligated. The contractor shall be prepared to execute the transition and closeout plans prior to the expiration of the contract.

D. Section 508, IT 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.

1. 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 Revised 508 Standards and 255 Guidelines (access-board.gov) (https://www.access-board.gov/ict/)

2. Per Section 508 and as mandated under HHS Policy for Section 508 Compliance and Accessibility of Information and Communications Technology (ICT) (07/2020) all documents or electronic files provided to the NIH NCI under contract must be conformant with Section 508 standards and accessible to persons with disabilities, as must all Information and Communication Technology (ICT) products and services.

a. Conformance shall be established by use of material provided at Accessibility Training Resources | HHS.gov and verified through the use of the HHS Checklist Documents (WCAG 2.0 Refresh), which shall be used as periodic reports to NCI. In addition, contractors and vendors are encouraged to make use of the instructional materials and checklists at HHS Accessibility Training Resources | HHS.gov as well as GSA Section 508.gov’s Create Accessible Digital Products. Products or services delivered as a result of this solicitation will be accepted based in part on satisfaction of identified Section 508 requirements for accessibility.

b. Any Information and Communication Technology (ICT) products and services, beyond those of documents, must be verified as being Section 508 conformant.

Submission of an Accessibility Conformance Report (ACR) based on the ITIC Voluntary Product Accessibility Template (VPAT), shall be deemed acceptable.

c. NCI retains the right to confirm the accessibility and Section 508-conformance of vendor submitted documents or other ICT and to return them for remediation, at no cost to the National Cancer Institute but at the contractor’s expense.

All Information and Communication Technology (ICT) shall be conformant with the above-listed 508 standards.

Applicable Functional Performance Criteria: All functional performance criteria apply when using an alternative design or technology that achieves substantially equivalent or greater accessibility and usability by individuals with disabilities, than would be provided by conformance to one or more of the requirements in Chapters 4-6 of the Revised 508 Standards, or when Chapters 4-6 do not address one or more functions of ICT.

Applicable requirements for software features and components: All WCAG Level AA Success Criteria, 502 Interoperability with Assistive Technology, 503 Application https://www.access-board.gov/ict/ https://www.access-board.gov/ict/ https://www.access-board.gov/ict/ https://www.hhs.gov/web/governance/digital-strategy/it-policy-archive/hhs-policy-section-508-compliance-accessibility-information-communications-technology.html https://www.hhs.gov/web/governance/digital-strategy/it-policy-archive/hhs-policy-section-508-compliance-accessibility-information-communications-technology.html https://www.hhs.gov/web/section-508/os-training-resources/index.html https://www.hhs.gov/web/section-508/os-training-resources/index.html https://www.hhs.gov/web/section-508/accessibility-checklists/index.html https://www.hhs.gov/web/section-508/os-training-resources/index.html https://www.hhs.gov/web/section-508/os-training-resources/index.html https://www.section508.gov/ https://section508.gov/create https://section508.gov/create https://www.itic.org/policy/accessibility/vpat

Applicable requirements for hardware features and components: All requirements apply Applicable support services and documentation: All requirements apply