Statement_of_Work_(DRAFT)_(3-14-25)_1.docx

75N91025R00003

STATEMENT OF WORK

I. Objectives

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, under the terms of this contract.

This requirement seeks to facilitate project-specific scientific collaborations between the Division of Cancer Epidemiology and Genetics (DCEG), which has expertise in cancer, disease-specific variant interpretation, statistics and modeling and organizations (Contractor) with population-scale electronic health record (EHR)-linked exome and SNP array genotyping array and/or genomic sequencing data. The Contractor shall provide support for the retrieval, processing, and sharing of genetic variant and exome data with DCEG from a large (>150,000 individuals) cohort which 1) has undergone germline DNA exome sequencing with SNP array genotyping and/or genome sequencing and 2) has a linked longitudinal electronic health record (EHR) with a cancer registry as part of the EHR data. The Contractor shall provide genetic variant data that has undergone quality control processes and filtering. The variant data shall be provided in an electronic data format acceptable to DCEG (e.g., Excel spreadsheet). Data shall be available on all sequenced subjects who have passed quality control processes. For sequenced subjects with SNP array data, SNP array data shall be provided, as requested by DCEG, for individual projects.

Extraction of meaningful phenotype data from the linked EHR is a complex process. The Contractor shall be available for consultation with DCEG on the best approaches and methods to access project-specific data on individuals of interest in their sequenced cohort. These data may include but are not limited to query of structured fields such as specific diagnosis codes (e.g., ICD9/10), laboratory tests, imaging studies, medication data, procedure codes and pathology materials. In addition, the Contractor shall provide access to unstructured data (e.g., clinical notes). The phenotype data shall be provided in an electronic data format (e.g., Excel spreadsheet) acceptable to DCEG. A method to conduct individual chart abstraction shall be available, using a format and template acceptable to DCEG.

Phenotype data shall be available on individuals with genetic variation of interest plus appropriate controls, up to the size of the sequenced cohort. The Contractor shall be willing to engage in an iterative process to provide the requested variant and phenotype data. It is the Contractor’s responsibility to ensure the protection of protected health information (PHI) of the sequenced subjects, as per federal, state, local law and appropriate IRB regulations. The data delivered to DCEG shall be exclusively de-identified data.

The Contractor shall perform the specific tasks delineated below to provide exome/genome data linked to EHR. The contractor shall create and annotate the genotype/phenotype data sets required by DCEG.

II. Tasks

1. The Contractor shall obtain, and de-identify, variant and phenotype data from a cohort of at least 150,000 individuals who have undergone germline exome sequencing and/or SNP array data and/or genome sequencing and who are linked to an EHR with a cancer registry included as part of the EHR.

a. Variant and phenotype data sets shall be of adequate quality and size to answer the DCEG’s scientific question or hypothesis. Thus, fulfilling this requirement may include provision of variant or phenotype data on all the subjects in the current data build. Genotype, SNP array and phenotype data sets shall be determined by the Contracting Officer’s Representative (COR). These data shall be delivered within 1 month of a DCEG request via Secure File Transfer Protocol (SFTP) or other equally secure means.

b. The datasets shall be provided in a mutually agreeable format. The Contractor shall be able to query and extract structured data from the EHR record including (but not limited to): specific diagnosis codes (e.g., ICD9/10), laboratory tests, imaging studies, medication data, procedure codes and pathology material identifiers.

2. The Contractor shall query and extract unstructured data from the EHR record including (but not limited to) physician and nursing notes, radiology, pathology and surgical reports, and other “free text” fields. The Contractor shall provide advice to DCEG on how to best extract these data.

3. The Contractor shall conduct manual EHR review and document findings in a mutually agreed-upon format.

4. The Contractor shall perform orthogonal verification of germline variation (e.g., using Sanger sequencing) as requested by DCEG.

5. The Contractor shall provide administrative oversight for the project including but not limited to scheduling meetings with DCEG Principal Investigators and Contractor staff; organizing tele- or video- conference calls on a monthly basis and as needed; ensuring completion compliance and documentation with the relevant human subjects protection regulations in the Contractor’s organization prior to working with NCI on this project.

6. The Contractor shall consult genetic counselor(s) or Medical Genetics services for review of research results and the possibility of results disclosure as well as to serve as a resource for questions about DCEG protocols.

7. The Contractor shall obtain pathologic materials from cancer registries and prepare scrolls (or provide paraffin blocks) for nucleic acid extraction from appropriate subjects from the exome cohort, as determined by DCEG for research-specific projects. The Contractor shall be able to provide clinical pathology expertise to assist in the preparation of such scrolls.

III. Deliverables

The Contractor shall provide the following deliverables to NCI:

1. Variant data (from exome sequencing and SNP arrays and/or genome sequencing) from existing longitudinal data collection from the Contractor’s institution that is de-identified. This data shall be delivered within 1 month of a DCEG request via a secure FTP or other equally secure means. Results should be provided in a format that can be reviewed using Integrated Genomics Viewer (IGV) or equivalent.

2. Phenotype data sets from existing longitudinal data collection from the Contractor’s institution. These data shall be delivered within 1 month of a DCEG request via secure FTP or other equally secure means.

3. De-identified pathology scrolls on up to 500 individuals for DNA extraction per year.

4. Results of variant verification on up to 500 de-identified samples per year using Sanger sequencing or equivalent.

Statement of Work – March 14, 2025