Att1SOWBaseIDIQ(4pools)12.6.22.pdf

GCC SOW dated 12/6/2022

Statement of Work (SOW) for the Genome Characterization Centers Base IDIQ

Independently and not as an agent of the Government, the Contractor shall furnish all the necessary services, qualified personnel, materials, equipment, and facilities, not otherwise provided by the Government, as needed to perform the Statement of Work.

This IDIQ contract requirement is designed to support the generation of cancer genomic data for the Center for Cancer Genomics (CCG). In performance of this SOW, the Contractor(s) shall serve as Genome Characterization Centers (GCCs) capable of providing high-throughput and quality-controlled pipelines for comprehensive genomic characterizations of different tumor types.

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 a number of 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 with a mission 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 has a need to establish Genome Characterization Centers (GCC) to provide a centralized approach to conducting molecular profiling on the same cancer tissue. This will achieve the goals of optimal data integration and data comparability.

B. Scope The overarching goal for the Genome Characterization Centers (GCCs) is to perform systematic and comprehensive characterizations of genomic alterations in multiple types of cancers. These genome-wide characterizations shall be conducted with validated methods using high-throughput and quality-controlled pipelines. The Contractors selected to operate GCCs shall receive cancer biomaterials (such as DNA, RNA, or other types of samples) and associated data from the Biospecimen Processing Center (BPC) funded separately by NCI. The primary objective is for the Contractor(s) operating a GCC to conduct molecular profiling on the same cancer tissue.

C. Description of Work The GCCs shall provide multiple genome characterization pipelines to produce cancer molecular data resources for the research community. The GCC contractor(s) shall be responsible for the following tasks for all projects conducted in performance of this contract:

1) Receive biomaterial from Biospecimen Processing Center (BPC) The contractors shall execute and maintain Material Transfer Agreements (MTAs) prior to receiving molecular analytes from BPC. The contractor shall meet its local institutes' IRB requirements if needed. Acceptable local IRB documents may be in the form of an approved protocol, a waiver, an exemption, or other documentation. The contractors shall develop

Standard Operating Procedures (SOPs) for receiving and managing the biomaterial for each study.

2) Operate genome characterization pipelines Contractors shall possess and maintain the appropriate laboratory equipment and infrastructure to support the proposed technologies for genome characterizations. Contractors shall be able to characterize molecular analytes from both fresh frozen tissues and formalin-fixed paraffin-embedded (FFPE) tissues.

The CCGs are intended as high-throughput facilities to support a large number of cases from NCI projects. The contractor shall build up characterization pipelines to meet a minimum operational capacity at 100 cases per year. The minimum operational capacity shall be described for each platform in the individual task order SOWs. NCI anticipates task order award(s) to have a minimum operational capacity of one hundred cases per month.

The contractor shall use platforms with prior data validated in large-scale genomic research programs such as The Cancer Genome Atlas (TCGA). Unless requested by the NCI Program Office, the contractor shall use widely adopted commercial off-the-shelf products. These products and platforms shall have produced validated datasets for the public. There shall be sufficient studies to demonstrate the capabilities of the proposed platforms. These datasets shall corroborate statistically by other validated technologies in published studies. For specific task orders, modifications of protocols shall be reviewed and pre-approved by the NCI’s Program Office.

The contractors shall submit proposals for at least one pool as listed below in this section.

Offerors are permitted but not required to respond to multiple pools.

Pool 1. High-throughput DNA Sequencing Next-generation sequencing (NGS) offers ultra-high throughput, accurate, and cost-effective ways to analyze DNA samples. DNA sequencing technology produces large data sets of nucleotide sequences for entire genomes or targeted genomic regions. The sequencing results can be used in identifying novel cancer mutations, detecting familial cancer mutation carriers, and providing clues for effective and targeted treatments.

The Contractor shall analyze DNA aliquots extracted from the tumor or normal tissues using approved technologies for high-throughput DNA Sequencing or DNA microarrays.

Contractors shall generate molecular data for cancer genomes. The scale of the DNA sequencing or microarray can range from targeted genes to the whole exome or whole genome.

Pool 2. High-throughput RNA Sequencing High-throughput RNA sequencing (RNA-seq) is a sequencing method for studying transcriptome and non-coding RNAs such as MicroRNAs (miRNAs). RNA-seq data can be used in studies such as whole transcriptome analysis of differential gene expression and differential splicing of mRNAs.

The Contractor shall analyze RNA aliquots extracted from the tumor or normal tissues using approved technologies for high-throughput sequencing. Contractors shall generate RNA sequencing data for cancer transcriptome and non-coding RNA expression profiles.

Pool 3. Epigenomic Characterization with Sequencing-based Assays or Array-based Assays Epigenomics involves the profiling and analysis of epigenetic marks across the genome.

The types of epigenomic characterization assays have expanded in recent years. The whole epigenome analysis can be carried out with array-based assays or sequencing-based assays.

The Contractor shall analyze biospecimens extracted from the tumor or normal tissues using approved technologies for high-throughput methylation sequencing or methylation arrays. Contractors shall generate molecular data for methylation profiles.

The Contractor shall analyze biospecimens extracted from the tumor or normal tissues using approved technologies to study chromatin accessibility across the genome.

Contractors shall generate molecular data for ATAC-seq (Assay for Transposase- Accessible Chromatin with high-throughput sequencing).

Pool 4. Single-Cell/Single-Nuclei Sequencing Single-cell/Single-Nuclei sequencing-based assays have advanced significantly.

Different types of sequencing technologies such as DNA-seq, RNA-seq, Methylation- Seq, and ATAC-seq have been developed in single cell/single nuclei studies. These applications help to tackle problems such as tumor heterogeneity and cell population characterization with a high resolution not available with bulk sequencing methods.

The Contractor shall analyze biospecimens of tumor tissues or cells using approved technologies for high-throughput single-cell or single-nuclei sequencing. Contractors shall generate molecular data for profiling the genomes, the epigenomes, or transcriptomes on the level of individual cells.

3) Improve performance of characterizations Contractors shall describe a process to continue evaluating the proposed technology and upgrade to more advanced technologies when properly validated. In general, improvements/optimization efforts shall include, but are not limited to:

• Enhancing detection of molecular abnormalities by improving sensitivity and/or resolution

• Increasing characterization pipeline throughput

• Optimizing genome coverage

• Obtaining high-quality data sets from small tumor samples

• Reducing unit costs per platform

4) Implement quality control procedures Contractors shall propose specific quality assurance criteria and quality control procedures to ensure and monitor the data quality from characterization pipelines. Contractors shall monitor, identify and take steps to mitigate sources of systematic error and bias to improve experimental reproducibility.

5) Support Informatics and Data Delivery Public sharing of data is critical to facilitate discoveries of clinical significance. Data produced by GCCs shall be transmitted into NCI Genomic Data Commons (GDC) as soon as they are validated, in general within four weeks of generation. GCCs shall submit primary data and metadata to GDC by adapting their submission process to meet the submission requirements of

GDC.

Contractors shall submit a Data Sharing Plan documenting how data will be released and shared. The Data Sharing Plan must be consistent with the goals of CCG and NCI research programs, with adherence to NCI and NIH data-sharing policies (https://datascience.cancer.gov/data-sharing, https://sharing.nih.gov).

6) Conduct transition activities The Contractor shall:

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

2. Prepare a close-out transition plan for the end of the contract. The plan shall include mechanisms to transmit data and materials to parties designated by the Contracting Officers as contractually obligated.

7) Ramp On As stated above, contractors may propose on one or more of the IDIQ pools below, if they can accomplish each of the unique platforms under that specific pool. NCI has elected to include a process to add new contractors to the multiple award IDIQ pools. This process is called “Ramp On” and can be utilized at the discretion of the Government. The "Ramp On" period can be announced at any time during the effective period of performance of the IDIQ base awards, but no earlier than annually from the date of the award.

D. Meeting and Communications The Offeror shall participate in required communications such as biweekly regular teleconferencing calls and monthly operation reports.

E. 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 https://datascience.cancer.gov/data-sharing https://sharing.nih.gov/ 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

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