Pre-Sol Notice 75N92023R0194.pdf

Pre-Solicitation Notice

75N92023R0194

NHLBI Trans-Omics for Precision Medicine (TOPMed) Informatics Research Center (IRC)

The National Heart, Lung, and Blood Institute (NHLBI) is seeking a five year renewal of the program entitled “NHLBI Trans-Omics for Precision Medicine (TOPMed) Informatics Research Center (IRC)”.

The purpose of this announcement is to provide a Pre-Solicitation Notice for the release of Solicitation 75N92023R0194. The intended procurement is classified under NAICS code 541380. THIS

IS A SYNOPSIS. THIS IS NOT A SOLICITATION.

Background and Program Objectives

The National Heart, Lung, and Blood Institute (NHLBI) is seeking a five year renewal of the program entitled “NHLBI Trans-Omics for Precision Medicine (TOPMed) Informatics Research Center (IRC)”.

NHLBI's Trans-Omics for Precision Medicine (TOPMed) program started in 2014 as the flagship program supporting the development of precision medicine for heart, lung, blood diseases and sleep disorders.

The main goal is to generate a large volume of genomics data that have sufficient statistical power for scientific discovery. The data are generated and processed first in TOPMed before being uploaded to external databases, database of Genotypes and Phenotypes (dbGaP) and BioData Catalyst (BDC) for researchers to access.

The NHLBI has nine (9) Centralized Omics REsource (CORE) centers that have generated approximately 200,000 whole genome sequencing data. As TOPMed enters its next phase, TOPMed2.0 is focusing on functional genomics and disease mechanisms. To that end, TOPMed is generating multi-omics data that is added on top of the WGS data, including bulk RNA-seq, metabolomics, methylation (mostly array-based), proteomics (Olink), and single-cell omics (RNA-seq and ATAC-seq).

All genomics data generated by the CORE centers are stored in the NHLBI Cloud and processed by TOPMed’s Informatics Research Center (IRC). The workflow below is managed by the Administrative Coordinating Center (ACC), starting with samples shipping from the various studies to the CORE for data generation, followed by data processing in IRC and data release to the scientific community by dbGaP and BDC.

TOPMed’s Informatics Research Center (IRC) is the central location for processing all TOPMed data and submitting it to dbGaP/BDC. It has three intertwined task areas.

1. Administration task

2. Tools for data dissemination

3. Performing/hosting data processing procedures

Project Requirements

The IRC will continuously use the NHLBI Cloud to securely store and process all types of genomics and other Omics data. The IRC will work closely with multiple stakeholders, including study investigators, CORE centers, ACC, NHLBI, dbGaP, and BDC to disseminate high quality data to the scientific community, and significantly improve the quality and throughput for its existing data processes (WGS, RNA-seq, and metabolomics) and implement capacity to process new types of data (methylation, proteomics, single-cell omics).

TASK AREA ONE (TA1): Management of Data Integration

TOPMed is to generate large volume of genomics data for the research community. The IRC is the data center that must work together with the ACC to manage dataflow and processing of every project.

Specifically, IRC works 1) with study investigators to track their samples and metadata inside TOPMed,

2) with NHLBI to manage data storage and processing using NHLBI’s cloud system, 3) with CORE centers to obtain all genomics data for processing, and 4) with dbGaP/BDC to submit all genomics data for public release. An efficient data flow system in TOPMed requires IRC to constantly monitor and communicate with key personnel of every project.

TASK AREA 2 (TA2): Data Dissemination

While dbGaP and BDC provide users with control-access data at individual levels, the IRC has been quickly disseminating the summary of the genomics and other Omics data from its processes and providing a window of opportunity for users to have better understanding of the data before applying to access the data at individual Levels. The IRC has developed a few widely used the tools supporting the dissemination of processed data, including TOPMed Imputation Server, BRAVO Variant-Server, and report on data generation from all CORE centers. While those are expected to be maintained/improved throughout the new contract, the development of additional new tools for the research community is encouraged. In addition, the IRC is responsible for submitting all genomics data to dbGaP, dbSNP, and BDC. On an as-needed basis, the IRC supports research and scientific discovery when it is best positioned to perform data analysis for TOPMed investigators.

TASK AREA THREE (TA3): Data Processing

The biggest challenge for IRC is to be able to process all TOPMed data. So far, TOPMed has implemented data processing pipeline for WGS, RNA-seq, and metabolomics. The IRC needs to improve those pipelines and build new pipelines for methylation, proteomics, and single-cell omics as well. All data will be stored and processed in a designated NHLBI Cloud, and the cost of computing shouldn’t be included in the budget. The basic functions of TA3 include 1) monitoring and enforcing data quality from CORE centers, 2) combining data from all studies and centers for large scale data processing and analysis, supporting data dissemination through the imputation server and the variant server as well as discovery research, 3) mapping functions units on the genome, molecular Quantitative Trait Locus (QTL), and 4) preparing data for dbGaP, dbSNP, and BDC.

Considering the scope and complexity of the data types in TOPMed, it may not be possible for one award to have the best methods covering all data types. NHLBI reserve the right not to fund all proposed methods in this task area. Offerors may consider using one or more subcontracts to strength the process of certain types of data. NHLBI reserves the right to directly interact with subcontracts on any subject matters and cancel the process of any data type. In general, offerors are required to address the following areas:

1. Describe state-of-the-art procedure/method in data processing in comparison with other existing tools used elsewhere.

2. Describe the cost-effectiveness of the procedure.

3. Describe the plan to enhance the tool or implement a new/better tool in data processing.

4. Describe the deliverables, life circle of the procedure, and production timeline.

Currently, the data processing includes one data type at a time. Innovation to efficiently integrate data from all the processed pipelines is strongly encouraged, especially the introduction of ML/AI to make the data-processing and analysis progressively more accurate and faster.

This is not a Request for Proposal (RFP) and the Government is not committed to award a contract pursuant to this announcement. This advertisement does not commit the Government to award a contract.

When available, the RFP will be able to access via FedConnect at https://www.fedconnect.net/FedConnect/default.htm. Additionally, the RFP will be available on SAM.gov. Prospective offerors are responsible for downloading the RFP and all attachments. The offeror is responsible for monitoring FedConnect and Beta.SAM.gov for the release of the solicitation and any amendments. The RFP will be available from FedConnect and Beta.SAM.gov on or about December 18, 2023.

Electronic Submission of Proposals must be submitted through FedConnect.

Offerors must submit all technical questions/responses concerning this synopsis/solicitation electronically through FedConnect. Notices of any modifications to this FedConnect procurement announcement will be posted using the FedConnect web portal. FedConnect can be accessed at www.fedconnect.net.

Vendors can register with FedConnect at https://www.fedconnect.net/FedConnect/default.htm. Please https://www.fedconnect.net/FedConnect/default.htm http://www.fedconnect.net/ https://www.fedconnect.net/FedConnect/default.htm note that FedConnect is used by multiple federal agencies and therefore FedConnect assistance will be provided by Compusearch Software Systems, not the NHLBI OA. More information about registration requirements can be found by downloading the FedConnect Ready, Set, Go! Guide at https://www.fedconnect.net/fedconnect/Marketing/Documents/FedConnect_Ready_Set_Go.pdf. For assistance in registering or for other FedConnect technical questions please call the FedConnect Help Desk at (800) 899-6665 or email at support@fedconnect.net.

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