Next-generation Sequencing of Nucleic-acid Libraries

Questions & Answers / Clarifications

This document provides responses to vendor questions regarding solicitation 1232SA26Q0232.

• Sequencing Data Delivery: Vendors inquired if sequencing data could be delivered in a 151+10+10+151 format. The government confirmed that this format, or trimmed data as specified in the SOW, is acceptable.

This clarification confirms flexibility in data delivery format, which may impact how vendors prepare their submissions related to sequencing data.

Solicitation / RFP / RFQ

This is a combined synopsis/solicitation for commercial items, issued as a Request for Quotation (RFQ) for next-generation sequencing of nucleic-acid libraries. The acquisition is set-aside for small business concerns.

• The contractor must provide next-generation sequencing of nucleic acid libraries using stated cycling and sequencing arrangement.

• Refer to Attachment 2 - Statement of Work (SOW) for detailed requirements.

• Anticipated award type: Firm-fixed-price requirements contract.

• The government intends to make one award.

• Submission Deadline: Questions are due by February 27, 2026, 4:00 PM Central Time. Offers must be submitted by the solicitation closing date (not explicitly stated in this section, but implied by the question deadline).

• Offer Acceptance Period: Offers must be held firm for 90 calendar days from the specified receipt date.

• Evaluation Criteria: Quotes will be evaluated based on the lowest price technically acceptable (LPTA) criteria. This includes:

  • Price: Evaluated for fairness and reasonableness.
  • Technical Acceptability: Rated as "acceptable" or "unacceptable" based on the offeror's ability to provide a sound and compliant approach. Offerors must provide minimum information and documentation to demonstrate capability. Exceptions to the SOW may result in technical unacceptability.
  • Past Performance: Evaluated as "Acceptable," "Neutral," or "Unacceptable" based on prior contract performance.

• Award will be made to the offeror representing the best value to the Government.

• This acquisition is a Total Small Business Set-Aside.

• All responsible sources may submit a quotation.

• North American Industry Classification Standard (NAICS) Code: 541380.

• Small business size standard: $19.0M.

• Solicitation number: 1232SA26Q0232.

• This announcement constitutes the only solicitation; a separate written solicitation will not be issued.

• Refer to "Attachment 1 - Solicitation Terms and Conditions" for applicable clauses, instructions, and evaluation criteria.

• Numerous Federal Acquisition Regulation (FAR) clauses and provisions are incorporated by reference. Key clauses include those related to commercial items, contractor responsibilities, small business concerns, and payment terms.

• The Service Contract Labor Standards may apply; place of performance is currently unknown.

• Offerors are not required to meet any specific qualification requirements to be eligible for award.

• Information on filing agency protests with the USDA Ombudsman Program is provided.

Statement of Work (SOW) / Performance Work Statement (PWS)

To provide next-generation sequencing of nucleic acid libraries using stated cycling and sequencing arrangements to support the analysis of immune status, gene expression, and DNA epigenetic status.

• Utilize Illumina Novaseq X Plus for next-generation sequencing of prepared Illumina libraries.

• Perform specific sequencing runs with defined read pair totals, cycling parameters, and sample pooling for whole-transcriptome assays and ATACseq.

• Each sequencing run must be performed sequentially, with data from each run provided before the next sequential run begins.

• Library quantitation may be performed by the sequencing facility.

• A quality report for each sequencing run and FASTQ files are deliverable for each Run.

• Data must be provided within 14 days of contractor's receipt of samples.

• Not explicitly stated, but data is made available for download via cloud or hard drive.

• Contractor must use Illumina Novaseq X Plus.

• Specific cycling parameters for different runs (Run 1, Run 2, Run 3) are detailed, including read counts, cycles, index cycles, and PhiX spike-in percentages.

• Run 3 requires the entire 25B flow cell (8 lanes) with specific parameters for whole transcriptome and ATACseq on separate pools.

• Government Furnished: N/A

• Both price and ability to deliver in a timely manner will be used for evaluation.

• Dr. Crystal Loving at 515-337-7364 or crystal.loving@usda.gov