Software for Whole-Genome Sequencing

The National Cancer Institute (NCI)’s Division of Cancer Epidemiology and Genetics (DCEG) Integrative Tumor Epidemiology Branch (ITEB) plans to procure on a sole source basis software for whole-genome sequencing.

This acquisition will be processed in accordance with simplified acquisition procedures as stated in FAR Part 13.106-1(b)(1) via request for written quotation.

Only one (1) award will be made as a result of this solicitation. This will be awarded as a firm fixed price type contract. The Period of Performance is estimated to be a base period of twelve (12) months from the effective date stated in the award.

BACKGROUND

Recent advances in next generation sequencing technologies have dramatically increased the rate of data output while significantly reducing costs. The Integrative Tumor Epidemiology Branch (ITEB), Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI) is currently analyzing a large number of tumor and normal tissue samples of lung cancer and kidney cancer and plan to analyze additional cancer types in the future using whole-genome sequencing (WGS). However, highly accurate analysis of sequencing data is computationally intensive and creates a bottleneck in the overall sequencing workflow.

To address these challenges, ITEB is looking to procure a software that will significantly decrease the analysis time and the computational resource requirements for variant detection without compromising accuracy. The software will result is a 20-to-50-fold increase in processing speed on the same hardware with results that are identical to the currently used GATK pipeline. Due to the large sample size of tumors we are analyzing, a software that can provide variant calling at high speed is essential for our ongoing and planned projects.

TYPE OF ORDER

It is anticipated that this requirement will be a firm fixed price purchase order

SPECIAL ORDER REQUIREMENTS

PRODUCT FEATURES/SALIENT CHARACTERISTICS

The following product features/characteristics are required for this requirement:

Sentieon Software is proprietary software only available through Sentieon. It has the following features: a) 20-to-50-fold increase in processing speed for key tools such as BWA-mem, STAR, minimap2, Picard, and GATK while maintaining mathematical conistency, b) exceptional accuracy and reproducibility for next-generation sequencing data variant calling with no run-to-run variation, c) process a 30x WGS sample data in under 30 minutes for less than $2 compute cost, d) support joint calling of large-number of WGS directly from gVCFs without intermediate merging to facilitate large-cohort studies, and e) support multiple complex use cases including short and long reads, germline and somatic variant calling, structural variants, copy number variants.

SOLE SOURCE JUSTIFICATION

ITEB is conducting large-scale whole-genome sequencing studies of lung, kidney, and other cancers to better understand the etiology and genomic drivers of cancer development and progression. These studies are essential to advancing knowledge that underpins future early detection, diagnosis, and clinical treatment strategies. A key barrier has been the computationally intensive nature of variant detection using standard pipelines such as GATK, which slows progress, limits the scale of research, and creates a bottleneck in the overall sequencing workflow.

The tasks outlined in the Special Order Requirements require that the software has features that will decrease the analysis time and the computational resource requirements for variant detection without compromising accuracy. The software required is proprietary and solely available through Sentieon Inc. Due to the large sample size of tumors being analyzed, Sentieon is the only known provider of a software that is capable of a 20-to-50-fold increase in processing speed with identical accuracy to the currently used GATK, enabling timely analysis of very large tumor cohorts. A software that can provide variant calling at high speed is essential for ITEB’s ongoing and planned projects.

SUBMISSION INSTRUCTIONS

This notice is not a request for competitive quotation. However, if any interested party, especially small businesses, believes it can meet the above requirement, it may submit a capability statement, which shall be considered by the agency.  The statement of capabilities and any other information furnished must be in writing and must contain material in sufficient detail to allow the NCI to determine if the party can perform the requirement. Information furnished must not exceed 5 pages (12-point font minimum) and should include an outline of previous or similar projects performed. Responses must be received in the contracting office by 2:00 PM ET, September 2, 2025.  All responses and questions must be in writing and emailed to Michelle Nguyen, Contracting Officer, via electronic mail at michelle.nguyen2@nih.gov. Reference Notice Number 75N91025Q00059 on all correspondence.

The Government’s determination to solicit quotations from the vendors to compete this proposed requirement, is solely within the discretion of the Government. Information received will be considered solely for the purpose of determining whether to conduct a competitive procurement. In order to receive an award, Contractors must be registered and have valid, current Entity Record, including current Representations and Certifications, in the System for Award Management (SAM) through SAM.gov.

DISCLAIMERS AND IMPORTANT NOTES

This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use the information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure its response is complete and sufficiently detailed to allow the Government to determine the organization’s qualifications to perform the work. Respondents are advised the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. Responses to this notice will not be considered adequate responses to a solicitation.

Confidentiality:

No proprietary, classified, confidential, or sensitive information should be included in your response.