Whole Exome Sequencing

The U.S. Food and Drug Administration (FDA), Office of Acquisition and Grants Services (OAGS), is soliciting quotes for the National Center for Toxicological Research (NCTR), Division of Bioinformatics and Biostatistics (DBB) for service to sequence genomic deoxyribonucleic acid (DNA) samples derived from acute liver failure patients (approximately 80% female) using an Illumina NovaSeq platform system to conduct Whole Exome Sequencing (WES). Background: The Division of Bioinformatics and Biostatistics (DBB) requires service to sequence 95 genomic deoxyribonucleic acid (DNA) samples derived from drug-induced liver injury patients for Protocol E0779001, - Identify genetic and nongenetic factors with increasing susceptibility to herbal dietary supplement (HDS)-induced liver injury in women. The resulting whole exome sequencing (WES) data shall be utilized to identify the potential genetic variants associated with increasing susceptibility for herbal dietary supplement induced liver injury. Mandatory Requirement: Due to recent National Security concerns for this type of service, vendors and the likelihood of a contract award will have to be review by the FDA Division of Counterintelligence and Insider Threat. In addition, the attached Contractor's Commitment to Protect Non-Public Information (NPI) Agreement (FDA FORM 3398) shall be signed and returned with quote submission. Tasks: At the request of DBB, the genomic DNA samples derived from drug-induced liver injury patients will be provided by University of Malaga, Spain for the base year. The estimated time for delivery of samples is 2 months based on the estimate information provided by University of Malaga. Provider of samples for option years will be determined prior to option exercise. Minimum Technical Requirements: 1. The contractor shall provide library preparation services using the genomic DNA for Whole Exome Sequencing. Exome kit used shall be either Twist or Agilent kits to ensure comparability/compatibility/viability and no loss of data between previous studies. Other kits have not been used nor compared so only these two kits will be acceptable. 2. Contractor shall conduct sequencing with the sample volume of 2 micro liter (uL) or less. 3. One library shall be prepared for each sample and the libraries shall be sequenced utilizing a - Brand Name or Equal Illumina NovaSeq platform with pair-end 2'100 base pair reads at the average coverage of 80-120x, and a higher coverage is preferred. 4. The sequencing data from the - Brand Name or Equal Illumina NovaSeq shall be de-multiplexed into FASTQ data files. The read counts shall conform with 80-120x coverage of the targeted regions. 5. The Contractor shall transfer all sequence data to FDA investigators through an FDA-approved external hard drive. The provided data shall be in FASTQ data files. The drive shall be shipped 2nd Day Air (UPS or FedEx) to the FDA Technical Point of Contact (TPOC). Deliverables and Milestones: The contractor will deliver the data on an FDA approved external hard drive. Base year /Description/Delivery Sequence 95 genomic DNA samples derived from drug-induced liver injury patients using a - Brand Name or Equal Illumina NovaSeq (PE100, 80-120x coverage) platform and provide library preparation services. The DNA samples shall be provided to the contractor within two (2) months of the contract award. The contractor shall send the results within four (4) months of receiving the samples. Option 1 Sequence 95 genomic DNA samples derived from drug-induced liver injury patients using a - Brand Name or Equal Illumina NovaSeq (PE100, 80-120x coverage) platform and provide library preparation services. The DNA samples shall be provided to the contractor within two (2) months of the contract award. The contractor shall send the results within four (4) months of receiving the samples. Option 2 Sequence 95 genomic DNA samples derived from drug-induced liver injury patients using a - Brand Name or Equal Illumina NovaSeq (PE100, 80-120x coverage) platform and provide library preparation services. The DNA samples shall be provided to the contractor within two (2) months of the contract award. The contractor shall send the results within four (4) months of receiving the samples. Place of Performance: Work to be performed at Contractor's facility. Period of Performance (PoP): Base year 12 months from award date. Option 1 12 months from award date. Option 2 12 months from award date. Inspection and Acceptance The FDA Contracting Officer Representative (COR) and/or TPOC shall inspect and make acceptance decisions for all materials, documents, and services provided under this contract. The COR/TPOC shall monitor the Contractor's performance, evaluate the quality of services, and perform the final inspection and acceptance of all deliverables. The Contractor is prohibited from any use of the data. The data is solely owned by the FDA. The TPOC shall verify sample data received and acceptable within 15 days and notify contractor of acceptability. Contractor shall not invoice until notified data is acceptable. If data is not acceptable, the experiment should be repeated to generate acceptable data and provided to the FDA investigator within 30 days. FOB Destination: U.S. Food and Drug Administration National Center for Toxicological Research 3900 NCTR Rd Jefferson, AR 72079 Contract Type- Commercial Item - Firm Fixed Price Contract Clauses- FAR 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/these address(es): http://www.acquisition.gov/far/ & http://farsite.hill.af.mil/vfhhsara.htm The clause at FAR 52.212-4 Contract Terms and Conditions - Commercial Items, applies to this acquisition (Nov 2021) The following FAR 52.212-4 addenda apply: The FDA does not accept documents which contain the use of macros. Document submissions required throughout the award period(s) shall not have enabled macro functionality. Any document(s) delivered having macro functionality will be deemed delinquent, if not corrected prior to the due date. Addendum Paragraph (a). Supplies and/or services delivered hereunder shall be inspected and accepted at destination by the Contracting Officers Representative (COR) or Technical Point of Contact (TPOC) specified below. If the supplies or services are acceptable, the COR/TPOC shall promptly forward a report of inspection and acceptance to the paying office. If the supplies or services are not acceptable, the COR/TPOC shall document the nonconforming items/services and immediately notify the contracting officer. FAR Clause 52.204-4 Printed or Copied Double-Sided on Postconsumer Fiber Content Paper (May 2011) FAR Clause 52.204-13 System for Award Management Maintenance (Oct 2018) FAR Clause 52.204-18 Commercial and Government Entity Code Maintenance. (Jul 2016) HHSAR Clause 352.203-70 Anti-lobbying December 2015 HHSAR Clause 352.222-70 Contractor Cooperation in Equal Employment Opportunity Investigations December 2015 HHSAR Clause 352.239-74 Electronic and Information Technology Accessibility (Dec 2015) Paragraph (c). The Section 508 standards applicable to this contract are: Must meet WCAG 2.0 A and AA E101.2 Equivalent Facilitation (Appendix A, Application and Scoping Requirements) E203 Access to Functionality (Appendix A, Application and Scoping Requirements) E204 Functional Performance Criteria (Appendix A, Application and Scoping Requirements) E205 Electronic Content (Appendix A, Application and Scoping Requirements) 302 Functional Performance Criteria (Appendix C, Functional Performance Criteria and Technical Requirements) Electronic content must be accessible to HHS acceptance criteria. Checklist for various formats are available at http://508.hhs.gov/, or from the Section 508 Coordinator listed at https://www.hhs.gov/web/section-508/additional-resources/section-508-contacts/index.html. Materials that are final items for delivery should be accompanied by the appropriate checklist, except upon approval of the Contracting Officer or Representative. E207 Software (Appendix A, Application and Scoping Requirements) E208 Support Documentation and Services (Appendix A, Application and Scoping Requirements) Chapter 5 Software (Appendix C, Functional Performance Criteria and Technical Requirements) Chapter 6 Support Documentation and Services (Appendix C, Functional Performance Criteria and Technical Requirements) Payment Terms Net 30 Days After Government Acceptance of Supplies/Services No Advance Payment(s) Shall be Made. CONTRACTOR SHALL SUBMIT ALL INVOICES AS FOLLOWS: FDA Electronic Invoicing and Payment Requirements - Invoice Processing Platform (IPP) (Jan 2022) a. All Invoice submissions for goods and or services must be made electronically through the U.S. Department of Treasury's Invoice Processing Platform System (IPP). http://www.ipp.gov/vendors/index.htm b. Invoice Submission for Payment means any request for contract financing payment or invoice payment by the Contractor. To constitute a proper invoice, the payment request must comply with the requirements identified in FAR 32.905(b), "Content of Invoices" and the applicable Payment clause included in this contract, or the clause 52.212-4 Contract Terms and Conditions - Commercial Items included in commercial items contracts. The IPP website address is: https://www.ipp.gov c. The Agency will enroll the Contractors new to IPP. The Contractor must follow the IPP registration email instructions for enrollment to register the Collector Account for submitting invoice requests for payment. The Contractor Government Business Point of Contact (as listed in SAM) will receive Registration email from the Federal Reserve Bank of St. Louis (FRBSTL) within 3 - 5 business days of the contract award for new contracts or date of modification for existing contracts. Registration emails are sent via email from contact@example.gov. Contractor assistance with enrollment can be obtained by contacting the IPP Production Helpdesk via email to contact@example.gov or phone +1 (555) 000-0000. The Contractor POC will receive two emails from IPP Customer Support, the first email contains the initial administrative IPP User ID. The second email, sent within 24 hours of receipt of the first email, contains a temporary password. You must log in with the temporary password within 30 days. If your company is already registered to use IPP, you will not be required to re-register. If the Contractor is unable to comply with the requirement to use IPP for submitting invoices for payment as authorized by HHSAR 332.7002, a written request must be submitted to the Contracting Officer to explain the circumstances that require the authorization of alternate payment procedures. d. Invoices that include time and materials or labor hours Line Items must include supporting documentation to (1) substantiate the number of labor hours invoiced for each labor category, and (2) substantiate material costs incurred (when applicable). e. Invoices that include cost-reimbursement Line Items must be submitted in a format showing expenditures for that month, as well as contract cumulative amounts. At a minimum the following cost information shall be included, in addition to supporting documentation to substantiate costs incurred. Direct Labor - include all persons, listing the person's name, title, number of hours worked, hourly rate, the total cost per person and a total amount for this category; Indirect Costs (i.e., Fringe Benefits, Overhead, General and Administrative, Other Indirects)- show rate, base and total amount; Consultants (if applicable) - include the name, number of days or hours worked, daily or hourly rate, and a total amount per consultant; Travel - include for each airplane or train trip taken the name of the traveler, date of travel, destination, the transportation costs including ground transportation shown separately and the per diem costs. Other travel costs shall also be listed; Subcontractors (if applicable) - include, for each subcontractor, the same data as required for the prime Contractor; Other Direct Costs - include a listing of all other direct charges to the contract, i.e., office supplies, telephone, duplication, postage; and Fee - amount as allowable in accordance with the Schedule and FAR 52.216-8 if applicable. f. Contractor is required to attach an invoice log addendum to each invoice which shall include, at a minimum, the following information for contract administration and reconciliation purposes: (a) list of all invoices submitted to date under the subject award, including the following: (1) invoice number, amount, & date submitted (2) corresponding payment amount & date received (b) total amount of all payments received to date under the subject contract or order (c) and, for definitized contracts or orders only, total estimated amounts yet to be invoiced for the current, active period of performance. g. Payment of invoices will be made based upon acceptance by the Government of the entire task or the tangible product deliverable(s) invoiced. Payments shall be based on the Government certifying that satisfactory services were provided, and the Contractor has certified that labor charges are accurate. h. If the services are rejected for failure to conform to the technical requirements of the task order, or any other contractually legitimate reason, the Contractor shall not be paid, or shall be paid an amount negotiated by the CO. i. Payment to the Contractor will not be made for temporary work stoppage due to circumstances beyond the control of U.S. Food and Drug Administration such as acts of God, inclement weather, power outages, and results thereof, or temporary closings of facilities at which Contractor personnel are performing. This may, however, be justification for excusable delays. j. The Contractor agrees that the submission of an invoice to the Government for payment is a certification that the services for which the Government is being billed, have been delivered in accordance with the hours shown on the invoices, and the services are of the quality required for timely and successful completion of the effort. k. Questions regarding invoice payments that cannot be resolved by the IPP Helpdesk should be directed to the FDA Employee Resource and Information Center (ERIC) Helpdesk at 301-827-ERIC (3742) or toll-free 866-807-ERIC (3742); or, by email at contact@example.gov. Refer to the Call-in menu options and follow the phone prompts to dial the option that corresponds to the service that's needed. All ERIC Service Now Tickets will either be responded to or resolved within 48 hours (2 business days) of being received. When emailing, please be sure to include the contract number, invoice number and date of invoice, as well as your name, phone number, and a detailed description of the issue. The clause at FAR 52.212-5 Contract Terms and Conditions Required To Implement Statutes or Executive Orders'Commercial Products and Commercial Services. (OCT 2022) (Deviation 2017-02, Jun 2017) (Deviation APR 2020) (Deviation 2020-05 Oct 2020) (Deviation 2021-03) The following additional FAR clauses cited in this clause are applicable: 52.219-4, Notice of Price Evaluation Preference for HUBZone Small Business Concerns (Oct 2022). 52.219-28, Post Award Small Business Program Rerepresentation (Oct 2022). 52.222-3, Convict Labor (Jun 2003) (E.O.11755). 52.222-21, Prohibition of Segregated Facilities (Apr 2015). 52.222-26, Equal Opportunity (Sep 2016) (E.O.11246). 52.222-36, Equal Opportunity for Workers with Disabilities (Jun 2020). 52.222-50, Combating Trafficking in Persons (Nov 2021). 52.223-18, Encouraging Contractor Policies to Ban Text Messaging While Driving (Jun 2020) (E.O. 13513). 52.225-13, Restrictions on Certain Foreign Purchases (Feb 2021) (E.O.s, proclamations, and statutes administered by the Office of Foreign Assets Control of the Department of the Treasury). 52.232-33, Payment by Electronic Funds Transfer-System for Award Management (Oct2018). 52.239-1, Privacy or Security Safeguards (Aug 1996). Solicitation Provisions: The provision at FAR 52.212-1 Instructions to Offerors - Commercial Items applies to this solicitation (Nov 2021). The following addenda apply: Offerors shall not submit electronic documents using Microsoft Office suite products that contain the use of - macros. If the offeror submits documents that contain macros the Government will not be able to view or open such documents and the submission will be considered non-responsive to the solicitation. No additional time will be given to an offeror to correct the document submission and the Government will not inform the offeror that their submission is non-responsive prior to award. It is the offeror's responsibility to ensure all electronic documents are submitted without the use of macros. Paragraph (c) Period for acceptance of offers. (Addendum) The offeror agrees to hold the prices in its offer firm until September 30, 2023. Paragraph (c) Period for acceptance of offers. The offeror shall state on its quote that quoted prices are firm until September 30, 2023. Paragraph (j) Unique Entity Identifier - To be considered for an award the offeror shall be registered and active in System for Award Management (SAM) (www.sam.gov) by the date and time set forth for receipt of quotes/proposals. The Offeror shall enter, in the block with its name and address on the cover page of its offer, the annotation "Unique Entity Identifier" followed by the unique entity identifier that identifies the Offeror's name and address. The Offeror also shall enter its Electronic Funds Transfer (EFT) indicator, if applicable. The EFT indicator is a four-character suffix to the unique entity identifier. The suffix is assigned at the discretion of the Offeror to establish additional SAM records for identifying alternative EFT accounts (see FAR subpart 32.11) for the same entity. If the Offeror does not have a unique entity identifier, it should contact the entity designated at www.sam.gov for unique entity identifier establishment directly to obtain one. The Offeror should indicate that it is an offeror for a Government contract when contacting the entity designated at www.sam.gov for establishing the unique entity identifier. The provision at FAR 52.212-2 Evaluation-Commercial Items (Nov 2021) applies to this solicitation. The following subparagraph (a) factors apply: The Government will award a contract resulting from this Request for Quote to the lowest priced technically acceptable and responsible offeror. Offers will be evaluated on their ability to meet the requirements provided herein. The lowest priced offer will be evaluated first. If the lowest priced offeror is not technically acceptable, the next lowest priced offer will be evaluated and so on until a technically acceptable offer is determined. Technical Acceptability will be determined by review of information submitted by the offeror who shall provide sufficient descriptive material to demonstrate the proposed meet all requirements and by addressing each technical requirement as stated above for the Government to conclusively determine the proposed will satisfy its requirement. Quotes shall include technical specifications, descriptive material, literature, brochures and other information corresponding to each minimum required item, which demonstrates the capabilities of the offeror. The government is not responsible for locating or securing any information, which is not identified in the proposal. Please respond no later than 1:00 PM Central Time - Local Prevailing Time in Jefferson, Arkansas January 24, 2024.