Acquisition of Clinical Whole Genome Sequencing

DESCRIPTION: This notice is a combined synopsis/solicitation for commercial items using Simplified Acquisition Procedures. This acquisition will be made in accordance with the format in Federal Acquisition Regulation (FAR) Subpart 12.6 - Streamlined Procedures for Evaluation and solicitation for commercial Items, as applicable, and as supplemented with additional information included in this notice. This announcement constitutes the only solicitation (a written solicitation will not be issued) and quotes are being requested. The Solicitation number is RFQ-NIAID-2086152 and the solicitation is issued as a Request for Quotes (RFQ). This acquisition will be processed under FAR Part 13 Simplified Acquisition Procedures (SAP). The solicitation documents and incorporated provisions and clauses are those in effect through Federal Acquisition Circular (FAC) 2021-05 March 10, 2021. The North American Industry Classification System (NAICS) code for this procurement is 541380, Testing Laboratories, with a small business size standard of $15 million. The requirement is being competed full and open competition, un-restricted and without a small business set-aside. The National Institute of Allergy and Infectious Diseases (NIAID) has a requirement for: Whole genome sequencing for 800 samples. 10 rapid turnaround time genomes. REQUIREMENTS: Period of Performance: One (1) 12-month period, to begin upon award. Specifications: Whole genome sequencing for 800 samples. 10 rapid turnaround time genomes. Clinical Whole Genome Sequencing (N = 800): Delivery of FASTQ files Data delivery via Globus endpoint Meets CLIA/CAP requirements for clinical sequencing Ability to accept DNA and blood samples SNP trace using Fluidigm for sample identity analysis, assessment of contamination, sex, and relationships with other samples Minimum sequencing read depth of at least 95% at 20X coverage Provision of QC information regarding data quality. Specifically, measures of read quality, median coverage, contamination screen, and % of genome >=20X Accept DNA isolated from multiple tissue types, including blood, saliva, fibroblasts, etc. We are willing to provide samples to validate the process. Provision of sample data upon request, e.g., NA12878, to aid in assessment of control data quality Ability to accept small batch sizes, < 60 samples in one batch Results returned within 6 weeks Rapid turnaround time Clinical Whole Genome Sequencing (N = 10): Delivery of FASTQ files Data delivery via Globus endpoint Meets CLIA/CAP requirements for clinical sequencing Ability to accept DNA and blood samples SNP trace using Fluidigm for sample identity analysis, assessment of contamination, sex, and relationships with other samples Minimum sequencing read depth of at least 95% at 20X coverage Provision of QC information regarding data quality. Specifically, measures of read quality, median coverage, contamination screen, and % of genome >=20X Accept DNA isolated from multiple tissue types, including blood, saliva, fibroblasts, etc. We are willing to provide samples to validate the process. Provision of sample data upon request, e.g., NA12878, to aid in assessment of control data quality Ability to accept small batch sizes, < 2 samples in one batch Results returned within 3 weeks CONTRACTOR SUPPLIED MATERIALS: The Contractor shall provide plates for shipping and all consumable reagents except those mentioned below. GOVERNMENT FURNISHED MATERIALS: If genomic DNA samples are used, NIAID will deliver them in 96-well plates with tubes containing 2D barcodes. Exclusionary criteria: NIAID will not be able to affix labels to individual tubes. REPORTING REQUIREMENTS AND DELIVERABLES FOR CLINICAL WHOLE GENOME SEQUENCING: The required turn-around time for sequencing and receipt of deliverables is 6 weeks, or less, from the time the contractor receives the patient sample. We also require the vendor to offer a - rapid option with 3-week turnaround time for receipt of deliverables from WGS from the time the contractor receives the patient sample. This option is expected to be used approximately once a month. DELIVERABLES DETAILS: FASTQ files for all samples within 6 weeks. Transfer shall occur via cloud-based platform that meets security requirements for transfer to NIH/NIAID servers. Reports on quality metrics , including measures of read quality, median coverage, contamination screen, and % of genome >=20X on each sample for use by the NIAID team. INSPECTION AND ACCEPTANCE All deliverables will be inspected by the project manager, a Government employee of the Division of Intramural Research. Acceptance will occur when results are successfully transferred to NIH per the specifications and format outline in the requirements above. Quotes must demonstrate in detail how these requirements will be met. END OF REQUIREMENTS. ____________________________________________________________________________ Place of Performance: NIH Clinical Center BLDG 10, Room 11C207 Bethesda, MD 20852, United States FOB: Destination The government intends to award a firm fixed price purchase order to the responsible contractor as a result of this RFQ that will include the terms and conditions set forth herein. The award will be based on the following: technical capability to meet the requirements and price. The following FAR provisions apply to this acquisition: FAR 52.212-1 Instructions to Offerors Commercial Items (June 2020) FAR 52.212-3 Offerors Representations and Certifications - Commercial Items (FEB 2021) FAR 52.204-7 System for Award Management (Oct 2018) (Offerors must complete annual representations and certifications on-line at http://www.sam.gov/ in accordance with FAR 52.212-3 Offerors Representations and Certifications- Commercial Items (Please ensure 52.209-2 -- Prohibition on Contracting with Inverted Domestic Corporations--Representation. (Nov 2015) is updated in your SAM record) FAR 52.203-18 Prohibition on Contracting with Entities that Require Certain Internal Confidentiality Agreements - Representation (Jan 2017) 52.204'26 Covered Telecommunications Equipment or Services-Representation (OCT 2020) *** Must complete representation if attached to this solicitation- see attachment 52.204-26 - MUST use the attached version. Quotes are not valid with out this completed form. The following FAR contract clauses apply to this acquisition: FAR 52-212-4 Contract Terms and Conditions Commercial Items (OCT 2018) FAR 52-212.5 Contract Terms and Conditions Required to Implement Statutes or Executive Orders Commercial Items (JAN 2021) *The applicable subparagraphs of FAR52.212-5 are included in the attachment to this posting. FAR 52.232-40 Providing Accelerated Payments to Small Business Subcontractors (Dec 2013) FAR 52.204-13 System for Award Management Maintenance (Oct 2018) FAR 52.204-25 Prohibition on Contracting for Certain Telecommunications and Video Surveillance Services or Equipment (Aug 2020) HHSAR 352.222-70, Contractor Cooperation in Equal Employment Opportunity Investigations (December 2015) 52.252-2 -- Clauses Incorporated by Reference. (Feb 1998) This contract incorporates one or more clauses by reference, with the same force and effect as if they were given in full text. Upon request, the Contracting Officer will make their full text available. Also, the full text of a clause may be accessed electronically at this address: http://farsite.hill.af.mil/vffara.htm By submission of an offer, the offeror acknowledges the requirement that a prospective awardee shall be registered in the System for Award Management (SAM) database prior to award, during performance, and through final payment of any contract, basic agreement, basic ordering agreement, or blanket purchasing agreement resulting from this solicitation (www.sam.gov). Copies of the above-referenced provisions and clauses are available from http://www.acquisition.gov/far/loadmainre.html & http: //www.hhs.gov/regulation/index.html or, upon request, by email. DEADLINE: Submission shall be received not later than 9/09/2021 at 5:00 PM EST. Offers may be e-mailed to Lu Chang at contact@example.gov Offers shall include RFQ number in the subject line (RFQ-NIAID-2086152). Late submissions shall be treated in accordance with the solicitation provision at FAR 52.212-1(f) All responsible sources may submit an offer that will be considered by this Agency. Any questions or concerns regarding this solicitation should be forwarded in writing via e-mail to Lu Chang at contact@example.gov ------------------------------------------------------------------------------------------------------------------------------ Edit: Response to Questions 9/8/2021 attached and listed below: Responses to Questions 9/8/2021 Question: The RFQ mentions the return of raw FASTQ data as well as QC metrics and contamination metrics on the specimens. However, it does not mention variant calls or clinical reporting. Are variant call outputs expected to be returned and are clinical reports expected to be issued as part of the SOW for this RFQ? Response: Variant call outputs are accepted but not required. Clinical reports are not expected to be issued as part of this SOW. Question: Is utilizing Fluidigm SNP Trace a requirement, or can other methods be used? Response: Utilizing Fluidigm SNP Trace is a requirement. Responses to Questions 9/9/2021 Question: Is the requirement for this hWGS service CLIA-environment or CLIA-validated workflows? In other words, will these results be returned to patients or be used to inform medical decision making? Response: We require a CLIA-validated workflow as opposed to a CLIA-environment for these genomes.