Illumina NextSeq 2000 Sequencer

National Cancer Institute (NCI), Surgery Branch (SB) plans to procure an Illumina NextSeq 2000 sequencer from Illumina, Inc. of 5200 Illumina Way San Diego, CA 92122 on a sole source basis.

This acquisition will be processed under FAR Part 12 – Acquisition for Commercial Items and will be made pursuant to the authority in FAR 13.106-1 (b)(1)(i) using simplified acquisition procedures for commercial acquisitions.  The response close date of this notice for this requirement is in accordance with FAR 5.203(a)(1). The North American Industry Classification System code is 334516 and the business size standard is 1,000 employees.

The intent of this requirement is acquisition of a high-throughput desktop sequencer which shall facilitate the efforts of NCI SB to develop novel immunotherapies for the treatment of patients with a variety of malignancies that include melanoma, gastrointestinal, lung, and bladder cancer. This equipment shall be used to acquire whole genome, whole exome and whole transcriptome data that is essential for carrying out ongoing high priority projects to identify mutated antigens recognized by patient tumor-reactive T cells. Identification of these targets provides NCI with powerful tools that were recently used to guide cancer immunotherapy for a patient with a gastrointestinal tumor. The utilization of Next Generation Sequencing (NGS) genomic and proteomic studies will have significant applications for the treatment of a large population of patients with a variety of malignancies.

To ensure the continuity of ongoing experiments, NCI must continue to use an Illumina platform. NCI must ensure that future sequencing results can be analyzed in combination with the sequencing data already in hand. Other sequencing technologies use different molecular mechanisms for sequencing and different analytics that lead to platform-specific sequencing artifacts. To ensure comparability of new sequencing data with NCI’s extensive database of sequencing in malignancies, continued use of an Illumina platform is required. The libraries that are constructed for sequencing on a NextSeq platform can be used directly on any of the Illumina sequencers currently in use by NCI; iSeq, MiSeq, NextSeq, HiSeq or NovaSeq. All of the proprietary analytic pipelines that NCI has developed for RNA-seq, exome-seq, and whole genome-seq, scWTA, and TCR-seq are geared towards Illumina reagents and kits and would have to be completely recoded to use data from another type of sequencing machine. This requirement is critical to mission success and therefore, the NCI requires an Illumina NextSeq 2000 DNA sequencer. 

The following product features/characteristics are required:

1. Shall be able to run whole-genomes, whole-exomes, whole-transcriptomes and single-cell libraries
2. Shall perform a single run in 24-48hrs.
3. Shall have a read depth of 2 x 150bp and 2 x 250bp
4. Shall have a minimum of 300Gb worth of data which translates to roughly ~1.5-2 billion paired-end reads in ~24-48hrs.
5. Shall be capable of generating 150-200X coverage of 10 whole-exomes, 12-15 whole-transcriptomes, or some combination of the latter two in a single run.
6. Shall have 60-90X coverage of a whole-genome that can be achieved in a single 24-48 hour run.
7. Shall sequence one or two exomes or transcriptomes using a mid-output flow cell in 24+ hours.
8. Shall include all shipping costs in the quote.
9. Shall include a minimum 12-month warranty.

This notice is not a request for competitive quotation. However, if any interested party, especially small business believes it can meet the above requirement, it may submit a capability statement for the Government to consider. The response and any other information furnished must be in writing and must contain material in sufficient detail to allow NCI to determine if the party can perform the requirement.  Responses must be received in the contracting office by 12:00 PM ET, on July 20, 2021.  All responses and questions must be via email to Miguel Diaz, Contracting Officer at miguel.diaz@nih.gov.  A determination by the Government not to compete this proposed requirement based upon responses to this notice 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 certification through SAM.GOV and have Representations and Certifications filled out. Reference: 75N91021Q00146 on all correspondence.