A Public Health Genomics Approach to Cancer Etiology and Risk Estimation

Presolicitation

THIS IS A NOTICE OF INTENT, NOT A REQUEST FOR PROPOSAL. A SOLICITATION WILL BE ISSUED ON A LATER DATE.

Title:   A Public Health Genomics Approach to Cancer Etiology and Risk Estimation
 

Background

The Division of Cancer Epidemiology and Genetics (DCEG), NCI conducts broad-based, high quality, high impact research to uncover the causes of cancer and the means of its prevention. DCEG maintains a national and international perspective, giving priority to emergent issues identified through epidemiologic, clinical, and laboratory observations, as well as to public health concerns identified by the NCI, Congress, regulatory agencies, and other appropriate bodies. The Division develops research resources and strategic partnerships in cancer epidemiology and genetics across NCI, NIH, and the global research community.

 The Clinical Genetics Branch (CGB), National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics Branch (DCEG), needs to access anonymized genomic data linked to longitudinal clinical data from clinical programs that have created platforms for genomic discovery, drug development and clinical genomic implementation.

Purpose and Objectives

The goal of this acquisition is to acquire highly specific and detailed EHR data with matching exome sequence and SNP array data that will allow the investigation of the genome-first approach in a comprehensive way using numerous cancer-associated genes studied by DCEG investigators in established, funded protocols. Specifically, the scientific needs of this acquisition include obtaining pre-existing EHRs with matched exome sequence and SNP array data.
 

Tasks

1. The Contractor shall obtain, and de-identify, variant and phenotype data from a cohort of at least 25,000 individuals who have undergone germline exome sequencing and/or SNP array data and who are linked to an EHR.

• 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 2 months of a DCEG request via Secure File Transfer Protocol (SFTP) or other equally secure means.
• 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, 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., sing 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 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.

 Mandatory Criteria

An offeror must have at least 25,000 phenotype and variant linked data records at the time of initial proposal submission to be considered technically acceptable. Offerors must provide documentation of having the appropriate number of records with its Technical Proposal at time of soliciation. 
 

Additional Information
 
This potential acquisition will be competed through Full and Open Competition procedures. Multiple awards may be made from a single solicitation.  It is anticipated that any resultant contract award(s) will be cost reimbursement with a level of effort component (hours) with a twelve- month (12) base period and four (4), twelve-month (12) option periods.

The RFP will be available electronically on or around May 20, 2020 and may be accessed through the Contract Opportunities at https://beta.sam.gov/. IT IS THE OFFERORS’ RESPONSIBILITY TO MONITOR THE AFOREMENTIONED SITE FOR THE RELEASE OF THE SOLICITATION AND ANY AMENDMENTS. WE ENCOURAGE ALL RESPONSIBLE SOURCES, PARTICULARLY SMALL BUSINESSES, TO SUBMIT A PROPOSAL WHICH WILL BE CONSIDERED BY THE AGENCY. 
 
This notice does not commit the Government to award a contract. No collect calls will be accepted. No facsimile or email transmissions will be accepted.
 

Contracting Office

Primary Point of Contact:

Rukshani Levy
Contracting Officer
Rukshani.Levy@nih.gov

Secondary Point of Contact:

Tom Conroy

Contracts Specialist

thomas.conroy@nih.gov