Att3SOWBaseIDIQ_4pools.pdf

Attachment 3 - Base IDIQ SOW (12/19/2023)

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) and other NCI Program Offices. In the performance of this SOW, the Contractor(s) shall serve as Genome Characterization Centers (GCCs) to provide high-throughput and quality-controlled pipelines for genomic sequencing and/or microarray platform support.

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.

B. Scope The overarching goal for the Genome Characterization Centers (GCCs) is to provide centralized sequencing and array platform services for NCI. The contract shall generate large quantities 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 using the appropriate format specified by the repository submission process. All datasets produced by the GCCs will be shared with the community at large. The contract does not support specific research projects or clinical trials with restricted internal data usage.

C. Description of Work The GCCs shall provide genomic sequencing or microarray characterization pipelines to produce molecular data resources for the research community at large. These pipelines shall be conducted with validated methods using high-throughput and quality-controlled protocols. The Contractors selected shall receive analytes (such as DNA, RNA, or other types of samples such as tissues or collection of isolated cells) from the Biospecimen Processing Center (BPC) funded separately by

NCI. The contractor(s) will run the pipelines with the received analytes and generate high-quality raw sequencing and microarray data.

The GCC contractors shall be responsible for the following tasks for all projects:

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. If required, the contractor shall meet its local institutes' IRB requirements. The contractors shall develop Standard Operating Procedures (SOPs) for receiving and managing the biomaterial for the period of performance of the contract.

2) Operate genome characterization pipelines Contractors shall possess and maintain the appropriate laboratory equipment and infrastructure to support the proposed pipelines for genome sequencing and array platforms. The proposed pipelines shall be able to work with molecular analytes extracted from both fresh frozen tissues and from formalin-fixed paraffin-embedded (FFPE) tissues.

The CCGs are intended as high-throughput facilities to support a large number of cases from NCI projects per year. In general, the contractor shall support pipelines with an operational capacity of at minimum 500 cases per year. The minimum operational capacity for specific platforms will be described in the individual task order SOWs.

The pipelines proposed by the contractor shall have prior validation in large-scale genomic 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 in the proposed pipelines. There shall be sufficient studies and datasets to demonstrate the capabilities and validity of the proposed platforms. These datasets shall be corroborated statistically by other validated technologies in published studies. Unless specified, pipeline specifications and modifications of protocols shall be reviewed and pre-approved by the NCI’s Program Office.

Offerors 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 datasets of nucleotide sequences for entire genomes or targeted genomic regions. The sequencing results can be used in identifying cancer mutations, detecting familial cancer mutation carriers, and providing clues for effective and targeted treatments.

The Contractor shall process DNA analytes extracted from the tumor or normal tissues using approved technologies for high-throughput DNA Sequencing. Contractors shall perform genomic sequencing for provided molecular analytes. The genomic target requirements of DNA sequencing can range from targeted genes, the whole exome, to the 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 sequencing data can be used in studies such as whole transcriptome analysis of differential gene expression, differential splicing of mRNAs, and non-coding RNA expression.

The Contractor shall process RNA analytes 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.

Pool 3. Epigenome Characterization with Sequencing-based 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 process DNA analytes extracted from the tumor or normal tissues using approved technologies for high-throughput methylation sequencing or methylation arrays.

Contractors shall generate raw methylation data for downstream analysis.

The Contractor shall process 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/Spatial Characterization

Single-cell/Spatial platforms have made significant advances. Different types of technologies such as DNA-seq, RNA-seq, Methylation-Seq, and ATAC-seq have been developed for single-cell or spatial studies in the context of tumor microenvironment. These applications help to tackle problems such as tumor heterogeneity and cell sub-population characterization with a high resolution not available with bulk sequencing methods.

The Contractor shall process biospecimens of tumor tissues or tumor cells using approved technologies for high-throughput single-cell or spatial studies. Contractors shall generate molecular data for genomes, epigenomes, transcriptomes, or other omics on the level of individual cells.

3) Improve the performance of pipelines 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 accuracy, sensitivity, and/or resolution

• Increasing pipeline throughput

• Optimizing genome coverage

• Obtaining high-quality data sets from low-quantity analytes

• Reducing unit costs per sample

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) or other NCI designated repositories 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 to one or more of the IDIQ pools. NCI has elected to include a process to add new contractors to the multiple award IDIQ pools. This process is called “Ramp On”. This process can be utilized at the discretion of the Government when a task need is not satisfied by awarded contractors. 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 regular communications with the program office 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 Accessibility of Information and Communications Technology (ICT) (07/2020) all 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 https://www.hhs.gov/web/governance/digital-strategy/it-policy-archive/hhs-policy-section-508-compliance-accessibility-information-communications-technology.html 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/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