CSS: Whole genome sequencing for HANDLS participants

(i) This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6 as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; proposals are being requested and a written solicitation will not be issued. (ii) The solicitation number is 75N95024Q000495 and the solicitation is issued as a request for quotation (RFP). The anticipated award date is September 20, 2024. This acquisition is for a commercial item or service and is conducted under the authority of the Federal Acquisition Regulation (FAR) Part 13'Simplified Acquisition Procedures; and FAR Part 12'Acquisition of Commercial Items and the value is not to exceed the simplified acquisition threshold. (iii) The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular (FAC) Number 2023-04, with effective date 06/02/2023. (iv) The associated NAICS code is 541380 Testing Laboratories and Services. This requirement is set-aside to small business. (v) Health disparities in age-related chronic conditions such as obesity and chronic kidney disease (CKD) are well documented. Importantly, diseases such as obesity and CKD have been linked to accelerated aging, the risk for age-associated conditions at younger ages than usual. Although genetics may contribute to observed health disparities, there are only limited studies in the racial and ethnic minority populations. The objective of this work is expanding our current research to examine health disparities associated with age-related diseases through whole genome sequencing to investigate the contributions of genomics to the disproportionate burden of disease incidence, prevalence, morbidity, and mortality in minority groups within the United States. The long term goal is to create a consistent dataset of whole genome sequencing to complement the longitudinal HANDLS behavior and health data. (vi) The Statement of Work with a description of all services to be acquired is included as an attachment to this Solicitation. Investigators in the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) study require whole genome sequencing (WGS) data to expand our current research examining whether rare genetic variants present in racial minority populations contribute to observed health disparities in age-related diseases. Samples from HANDLS participants have been obtained over the longitudinal study, starting in 2004, and thus some samples are over 15 years old and many are over 10 years old. A contract is required because the Government does not have available facilities or resources to perform this work consistent with other WGS performed on HANDLS samples. The contractor will deliver plates to the Government sufficient to run 95 samples, some of which have been stored for ten or more years. The contractor will perform whole genome sequencing, and specifically shall: Sequence libraries on the NovaSeq 6000 platform using 150 bp paired end runs and NovaSeq 6000 S4 v1.0 Reagent Kit with NovaSeq Xp v1.0 4-Lane kit or standard workflow confirm genomic DNA quantity and quality by performing DNA concentration measurements and volume checks Re-attempt sequencing in the case that DNA quality and quantity is sufficient, but sample fails sequencing-based QC Examine agarose gels on all samples as an industry-standard method for screening DNA marker quality prepare PCR-free sequence libraries for all samples Sequence the libraries at a minimum of 30x coverage with 2'150 base pair runs Perform primary and secondary analysis of the sequencing data including but not limited to read alignment, variant calling, and quality control analyses Quality control checks will include: confirming sex, identifying unexpected duplicates and relatedness, confirming relatedness, providing sample performance information and sample identity confirmation against the sequencing data, in addition to confirming coverage, contamination, mapped reads, and other general quality metrics. Alignment and variant calling will be performed with the DRAGEN Germline v4.0.3 pipeline. After quality is confirmed, joint variant calling should be performed producing a multi-sample VCF file. Provide written summaries and documentation of the methods used to perform the whole genome sequencing pipeline Supply the whole genome sequencing data in a mutually acceptable electronic format that preserves study participants confidentiality. Data delivered will include: per sample CRAMs per sample gVCFs per sample VCFs joint-called multi-sample VCF per sample structural variant and CNV calls QC report and data dictionary Sample manifest with flagged problems Following data delivery and upon request by the Government, the contractor shall provide attendance at Government laboratory staff meetings and the contractor shall provide technical consultations as needed. Delivery or Deliverables: The contractor will provide the following deliverables: Analytic plates delivered to the Government at the Biomedical Research Center in Baltimore, MD Written summaries and documentation of the methods used to perform the whole genome sequencing pipeline Whole genome sequencing data in a mutually acceptable electronic format that preserves study participants confidentiality. Data delivered will include: per sample CRAMs per sample gVCFs per sample VCFs joint-called multi-sample VCF per sample structural variant and CNV calls QC report and data dictionary Sample manifest with flagged problems Return any leftover DNA on dry ice by overnight shipping to the Government at the Biomedical Research Center. Upon the Government's request, attend staff meetings and provide technical consultations as needed. Government Responsibilities: The Government will provide genomic DNA samples with a minimum concentration of 500 nanograms (ng; per sample) to the contractor for quality control metrics, library preparation, and sequencing. The Government will load the genomic DNA samples on contractor-provided plates. Other important considerations: The National Institute on Aging shall have unlimited rights to and ownership of all deliverables provided under this contract, including reports, data updates and statistical results. This includes the deliverables provided under the basic contract and any optional task deliverables exercised by the contracting officer. In addition, it includes any additional deliverables required by contract change. The definition of - unlimited rights is contained in Federal Acquisition Regulation (FAR) 27.401, - Definitions. FAR clause 52.227-14, - Rights in Data-General, is hereby incorporated by reference and made a part of this contract/order. In case domestic sources are available and capable of fulfilling the Government's need, and a future solicitation is published, the Government will use evaluation preferences in accordance with FAR 25. (vii) Period of performance will be a One Year ARO (viii) The provision at FAR 52.252-1, Solicitation Provisions Incorporated by Reference (Feb 1998), applies to this acquisition. This solicitation incorporates one or more solicitation provisions 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. The offeror is cautioned that the listed provisions may include blocks that must be completed by the offeror and submitted with its quotation or offer. In lieu of submitting the full text of those provisions, the offeror may identify the provision by paragraph identifier and provide the appropriate information with its quotation or offer. Also, the full text of a solicitation provision may be accessed electronically at these addresses: https://www.acquisition.gov/browse/index/far https://www.hhs.gov/grants/contracts/contract-policies-regulations/hhsar/index.html (End of provision) The following provisions apply to this acquisition and are incorporated by reference: FAR 52.204-7, System for Award Management (Oct 2018) FAR 52.204-16, Commercial and Government Entity Code Reporting (Aug 2020) FAR 52.211-6, Brand Name or Equal (Aug 1999) FAR 52.212-1, Instructions to Offerors'Commercial Products and Commercial Services (Mar 2023) FAR 52.212-3, Offeror Representations and Certifications'Commercial Products and Commercial Services (Dec 2023) FAR 52.214-34 Submission of Offers in the English Language (Apr 1991) FAR 52.214-35 Submission of Offers in U.S. Currency (Apr 1991) FAR 52.225-25 Prohibition on Contracting with Entities Engaging in Certain Activities or Transactions Relating to Iran'Representation and Certifications (Jun 2020) HHSAR 352.239-73, Electronic and Information Technology Accessibility Notice (December 18, 2015) The clause at FAR 52.252-2, Clauses Incorporated by Reference (Feb 1998), applies to this acquisition. 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 these addresses: https://www.acquisition.gov/browse/index/far https://www.hhs.gov/grants/contracts/contract-policies-regulations/hhsar/index.html (End of clause) The following clauses apply to this acquisition and are incorporated by reference: FAR 52.204-13, System for Award Management Maintenance (Oct 2018) FAR 52.204-18, Commercial and Government Entity Code Maintenance (Aug 2020) FAR 52.212-4, Contract Terms and Conditions'Commercial Products and Commercial Services (Dec 2022). Addendum to this FAR clause applies to this acquisition and is attached. FAR 52.225-13, Restrictions on Certain Foreign Purchases (Feb 2021) HHSAR 352.239-74, Electronic and Information Technology Accessibility (December 18, 2015) The following provisions and clauses apply to this acquisition and are attached in full text. Offerors MUST complete the provisions at 52.204-24 and 52.204-26 and submit completed copies as separate documents with their proposal. FAR 52.204-24 Representation Regarding Certain Telecommunications and Video Surveillance Services or Equipment (Nov 2021) FAR 52.204-26 Covered Telecommunications Equipment or Services-Representation (Oct 2020) FAR 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders-Commercial Products and Commercial Services (Jun 2023) Invoice and Payment Provisions with and without IPP (Mar 2023) (ix) The Government will perform a comparative evaluation of responses in accordance with FAR 13.106-2(b) to award a purchase order from this solicitation to the responsible offeror whose response meets the solicitation's requirements and, as a whole, provides the best value, considering price and other factors in this solicitation. The evaluation will compare: (a) Technical capability of the service offered to meet the Government requirement; (b) Price; and (c) Past Performance as defined under FAR 13.106-2(b)(3). If only one quotation is received it will be evaluated on the preceding basis. Responses may exceed capability or performance characteristics of the solicitation's requirements. The Government reserves the right, but is not required, to award to a response that exceeds capability or performance characteristics of the solicitation's requirements if it provides a benefit to the Government; and the Government is not requesting or accepting alternate proposal(s). (x) The Offerors are to include a completed copy of the provision at FAR 52.212-3, Offeror Representations and Certifications-Commercial Products and Commercial Services (Dec 2022), with offers. If the offeror has completed FAR provision 52.212-3 at www.sam.gov, then the offeror does not need to provide a completed copy with its offer. (xi) The clause at FAR 52.212-4, Contract Terms and Conditions'Commercial Products and Commercial Services (Dec 2022), applies to this acquisition. Addendum to this FAR clause applies to this acquisition and is attached. (xii) The following additional contract requirement(s) or terms and conditions as determined by the contracting officer are necessary for this acquisition and consistent with customary commercial practices. There are no additional contract requirement(s) or terms and conditions applicable to this acquisition. (xiii) The Defense Priorities and Allocations System (DPAS) are not applicable to this requirement. (xiv) Responses to this solicitation must include sufficient information to establish the interested parties bona-fide capabilities of providing the product or service. The price quote shall include: unit price, list price, shipping and handling costs, delivery days after contract award, delivery terms, prompt payment discount terms, F.O.B. Point (Destination or Origin), product or catalog number(s), product description, and any other information or factors that may be considered in the award decision. Such factors may include: past performance, special features required for effective program performance, trade-in considerations, probable life of the item selected as compared with that of a comparable item, warranty considerations, maintenance availability, and environmental and energy efficiency considerations. Respondents proposing on an equal product of the brand-name product specified in this announcement must provide, as part of their response: (a) product, catalog, model, and/or part number(s); (b) product description; (c) all relevant information and documentation that the item(s) offered meets the salient physical, functional, or performance characteristics as specified in the purchase description; quantity; estimated price or cost; shipping, handling, and/or installation charges; and delivery date after receipt of order. All quotations must be received by 4 p.m., Eastern Time, on August 28, 2024, and reference Solicitation Number 75N95024Q00495. Responses must be submitted electronically to Kaitlyn Landi at contact@example.gov. Fax responses will not be accepted. Attachments: Statement of Work (SOW) FAR 52.204-24, Representation Regarding Certain Telecommunications and Video Surveillance Services or Equipment (Nov 2021) FAR 52.204-26, Covered Telecommunications Equipment or Services-Representation (Oct 2020) Addendum to FAR 52.212-4 Contract Terms and Conditions'Commercial Products and Commercial Services. FAR 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders'Commercial Products and Commercial Services (Jun 2023) Invoice and Payment Provisions