Attach3BaseIDIQ(allpools)SOW.pdf

Statement of Work for the Base IDIQ

Genome Characterization Centers

This request for proposal (RFP) is designed to support the Center for Cancer Genomics’ (CCG) large-scale generation of high-throughput genomic data. Under this RFP, the NCI is soliciting proposals for Genome Characterization Centers (GCCs) that must be capable of completing comprehensive genomic characterizations of different tumor types using high-throughput and quality-controlled pipelines.

A. Scope

The overarching goal for the GCCs is to perform high-resolution, systematic and comprehensive characterization of cancer-related genomic alterations in multiple types of cancers for an expanding list of National Cancer Institute (NCI)-supported genomics projects. These genome-wide characterizations should be conducted with validated methods using high-throughput and quality-controlled pipelines. The GCCs will receive cancer biomaterials (DNA, RNA or other types of samples required by a platform) and associated data from a centralized Biospecimen

Processing Centers (BPCs) funded as separate NCI contracts. The aim is to have all molecular characterizations conducted on biomolecules from the same biospecimens for optimal analytical integration and for data comparability.

The specific and mandatory requirements for characterization platforms will be identified in separate Task Order Statements of Work (SOW). Three representative Sample Task Orders are included as attachments in the RFP.

B. Description of Work

B.1 General Task Order Requirements

The following requirements shall apply to each Task Order:

1. Receive biomaterial from BPC

2. Operate molecular characterization pipelines

3. Improve and optimize performance of characterization pipelines

4. Implement quality control procedures

5. Support informatics and data delivery

6. Perform transition activities

1) Receive biomaterial from BPC

The contractor shall execute and maintain Material Transfer Agreements (MTAs) and Data

Usage Agreements (DUAs) before they start receiving molecular analytes from BPC. The contractor shall comply with their organization’s policies regarding commencement of this work. The contractor shall develop Standard Operating Procedures (SOPs) for handling molecular analytes or other type of samples according to requirements from individual genomic study.

2) Operate molecular characterization pipelines

The contractor shall describe one or more high-throughput, cost-effective technologies to characterize comprehensively (i.e., genome-wide) genomic, epigenomic or transcriptome alterations, or to characterize protein expression patterns. The contractor must have the appropriate laboratory infrastructure and quality control process to support the selected technologies for genome characterization. Molecular analytes from both fresh frozen tissues or formalin-fixed paraffin-embedded (FFPE) tissues will be characterized.

3) Improve and optimize performance of characterization pipelines

The contractor shall propose specific process to improve the prescribed technology platforms and/or switch to more advanced platforms when properly validated. In general, improvements/optimization efforts sought include, but are not limited to:

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

2. Increasing characterization pipeline throughput

3. Optimizing genome coverage

4. Obtaining high quality data sets from small tumor samples

5. Reducing unit costs per platform

4) Implement quality control procedures

The contractor shall provide specific quality assurance criteria and implement quality control procedures to ensure and monitor the data quality from characterization platforms. The contractor shall monitor and identify sources of systematic error and bias to improve experimental reproducibility.

5) Support Informatics and data delivery

Public availability of data/information generated by GCCs will be critical to facilitate disease-relevant discoveries of clinical significance. Data generated 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 will submit primary data and metadata to

GDC by adapting their submission process to meet the submission requirements of GDC.

The contractor is required to 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 genomic programs, with adherence to NIH data sharing policies for the protection of human subjects (https://www.cancer.gov/grants-training/policies-process/nci-policies/genomic-data/about-policy).

6) Perform transition activities

The contractor shall:

1. 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.

2. 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.

B.2 Description for Individual Task Areas

The contractor shall perform tasks with characterization platforms in one or multiple task areas listed below. The contractor can propose to use one or multiple characterization platforms in a task area.

Task Area 1: DNA characterization pipelines

• Whole Genome Sequencing (WGS) with low and high coverage

• Whole Genome Sequencing (WGS) with long-read sequencing technology

• Whole Exome Sequencing (WES)

• Target Validation with Deep Sequencing

• Whole Genome Methylation Sequencing (WGMetSeq)

• DNA microarray and Methylation Array (MetArray)

• Sequencing of cell-free circulating tumor DNA (ctDNA)

• Sequencing of DNA from circulating tumor cells

• Single cell DNA sequencing

Task Area 2: RNA characterization pipelines

• Total RNA sequencing (total RNAseq)

• Transcriptome Sequencing (mRNASeq)

• microRNA Sequencing (miRNASeq)

• Single cell RNA sequencing

Task Area 3: Protein characterization pipelines

• Reverse Phase Protein Arrays (RPPA)

• Immunohistochemistry (IHC) methodology

C. Meeting and Communications

The contractor shall participate in required communications such as regular biweekly teleconferencing calls and provide a monthly operation report.

D. Section 508

The following Section 508 Standards are applicable to this procurement and will be included in the resulting solicitation.

o 602 Support Documentation o 603 Support Services o All WCAG A & AA Success Criteria apply except:

2.4.1 Bypass Blocks

2.4.5 Multiple Ways

3.2.3 Consistent Navigation

3.2.4 Consistent Identification