SOLICITATION NOTICE
B -- Identify Viruses Present in Tumor Tissues by Utilizing Next Generation Sequencing
- Notice Date
- 8/15/2018
- Notice Type
- Combined Synopsis/Solicitation
- NAICS
- 622310
— Specialty (except Psychiatric and Substance Abuse) Hospitals
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 9609 Medical Center Drive, Room 1E128, Rockville, Maryland, 20852, United States
- ZIP Code
- 20852
- Solicitation Number
- N02CO82638-95
- Archive Date
- 9/14/2018
- Point of Contact
- Ricky J. Watson, Phone: 2402766594
- E-Mail Address
-
ricky.watson@nih.gov
(ricky.watson@nih.gov)
- Small Business Set-Aside
- N/A
- Description
- The Department of Health and Human Services (DHHS), National Institutes of Health (NIH), National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics (DCEG), Infections and Immunoepidemiology Branch (IIB) is requesting the sequencing of tumor tissues in order to identify viruses by utilizing Next Generation Sequencing. This is a combined synopsis/solicitation for a commercial item, prepared in accordance with the format in FAR 12.6 as supplemented with additional information included in this notice. This announcement constitutes the only solicitation and a separate written solicitation will not be issued. This solicitation, # N02CO82582-95 is issued as a request for quote (RFQ) and includes all applicable provisions and clauses in effect through FAR Federal Acquisition Circular (FAC) 2005-95 / 01-19-2017, simplified procedures for commercial items. The North American Industry Classification System code is 334516 and the business size standard is 1000 employees. Only one award will be made as a result of this solicitation. This will be awarded as a firm fixed price type purchase order. DESCRIPTION OF CONTRACTOR REQUIREMENTS The contractor shall receive the tumor specimens shipped to them by the Iowa and Hawaii state cancer registries participating in this study. There will be up to 30 ALCL, 5 DLBCL, and 5 breast cancer cases. The contractor shall not be privy to the type of tumor tissue for sequencing and analyses The Contractor shall purify and quantify the total RNA from the tumor tissue using RNeasy FFPE Kit (Qiagen) and following the manufacturer's instructions. The Contractor shall then determine the integrity of the RNA using the 2100 Bioanalyzer System (Agilent). The Contractor shall prepare the total RNA sequencing libraries using the NEBNext® Ultra TM Directional RNA Library Prep Kit for Illumina® (New England Biolabs) per manufacturer's instructions. The Contractor shall pool the samples following library quantification using the KAPA Library Quantification Kits for Next-Generation Sequencing (KAPA Biosystems) and library insert size visualization using the 2100 Bioanalyzer system (Agilent). The Contractor shall sequence the total RNAseq libraries on the Illumina HiSeq2500 platform in "Rapid Run" mode using 100 bp paired end sequencing, with 6 samples per lane. These methods have been previously used in next generation sequencing to isolate and sequence RNA from tumor tissue and successfully identify novel organisms in human diseases. The Contractor shall use the algorithm from the PathSeq software to perform computational subtraction of human reads, followed by alignments of residual reads to human reference transcriptomes and microbial reference genomes (which include bacterial, viral, archaeal, and fungal sequences). The contractor shall use these alignments and perform taxonomical classification of the residual reads as bacterial, viral, archaeal, and fungal sequences from total RNA sequencing (RNASeq) data. The contractor shall deposit the reads from novel micro-organisms into "unmapped reads" for further analysis. The PathSeq software, developed by the Meyerson laboratory at Dana Farber Cancer Institute, has been used successfully to identify novel micro-organisms that are associated with human disease. The contractor shall provide final results in an Excel workbook listing bacteria, viruses, and fungi detected in the tumor tissue samples, including details of the family, genus, and species. The contractor shall provide the raw BAM or fastq files to the NCI, interpret the raw data and provide information on bacterial abundance or viral/fungal read counts, and perform a BLAST search of the unmapped reads and assemble them using Fermi-lite to gain insights into the identify of these sequences. The Contractor shall interpret the results obtained after RNA sequencing and report the findings to the NCI on an ongoing basis as the sequencing and analyses of each case is completed. Reports will include a summary of the quality of the RNA sequencing reads, detailed RNA sequencing results, and annotation of mapped sequences regarding the matched species, genes, and variants, in terms of degree of similarity with archived sequences and level of evidence for matching. The contractor shall assist NCI with interpreting the level of evidence for proposed matches. The contractor will be scientific collaborators on this research project and will participate in writing the manuscript (particularly the methods and the results sections) and prepare tables and figures for publication in peer-reviewed journals according to the specific requirements of the journals. TYPE OF ORDER This is a firm fixed price purchase order. PERIOD OF PERFORMANCE One year from the date of award. PLACE OF PERFORMANCE The service shall be conducted at the Contractor's facility. REPORT(S)/DELIVERABLES AND DELIVERY SCHEDULE All deliverables shall be provided in accordance with the following deliverables schedule: DELIVERABLE DELIVERABLE DESCRIPTION / FORMAT REQUIREMENTS DUE DATE Task 1 The contractor shall report the receipt of each tumor specimen in an email to the NCI investigators. The contractor shall be blinded to the type of tumor tissue for sequencing and analyses. 8 months after award Task 2 The contractor shall purify and quantify the total RNA from the tumor tissue of each case and determine the integrity of the RNA. 8 months after award Task 3 The contractor shall prepare the total RNA sequencing libraries and pool the samples following library quantification. 8 months after award Task 4 The contractor shall sequence the total RNAseq libraries on the Illumina HiSeq2500 platform in "Rapid Run" mode using 100 bp paired end sequencing, with 6 samples per lane. 12 months after award Task 5 The contractor shall use the algorithm from the PathSeq software to perform computational subtraction of human reads, followed by alignments of residual reads to human reference transcriptomes and microbial reference genomes. The contractor shall perform taxonomical classification of the residual reads as bacterial, viral, archaeal, and fungal sequences from total RNA sequencing (RNASeq) data. The contractor shall deposit the reads from novel micro-organisms into "unmapped reads" for further analysis. The contractor shall provide final results in an Excel workbook listing bacteria, viruses, and fungi detected in the tumor tissue samples, including details of the family, genus, and species. The contractor shall provide the raw BAM or fastq files to the NCI, interpret the raw data and provide information on bacterial abundance or viral/fungal read counts, and perform a BLAST search of the unmapped reads and assemble them using Fermi-lite to gain insights into the identify of these sequences. 12 months after award Task 6 The contractor shall interpret the results obtained after RNA sequencing and report the findings to the NCI on an ongoing basis as the sequencing and analyses of each case is completed. The contractor will participate in writing the manuscript (particularly the methods and the results sections) and prepare tables and figures for publication in peer-reviewed journals according to the specific requirements of the journals. 12 months after award PAYMENT The payment shall be made upon receipt of all deliverables for the tasks based on the deliverable schedule in the above table. Payment authorization requires submission and approval of invoices to the COR and NIH OFM, in accordance with the payment provisions listed below: The following clause is applicable to all Purchase Orders, Task or Delivery Orders, and Blanket Purchase Agreement (BPA) Calls: PROMPT PAYMENT (JUL 2013) FAR 52.232-25. Highlights of this clause and NIH implementation requirements follow: I INVOICE REQUIREMENTS A. An invoice is the Contractor's bill or written request for payment under the contract for supplies delivered or services performed. A proper invoice is an "Original" which must include the items listed in subdivisions 1 through 12, below, in addition to the requirements of FAR 32.9. If the invoice does not comply with these requirements, the Contractor will be notified of the defect within 7 days after the date the designated billing office received the invoice (3 days for meat, meat food products, or fish, and 5 days for perishable agricultural commodities, dairy products, edible fats or oils) with a statement of the reasons why it is not a proper invoice. (See exceptions under II., below.) Untimely notification will be taken into account in the computation of any interest penalty owed the Contractor. 1. Vendor/Contractor: Name, Address, Point of Contact for the invoice (Name, title, telephone number, e-mail and mailing address of point of contact). 2. Remit-to address (Name and complete mailing address to send payment). 3. Remittance name must match exactly with name on original order/contract. If the Remittance name differs from the Legal Business Name, then both names must appear on the invoice. 4. Invoice date. 5. Unique invoice #s for all invoices per vendor regardless of site. 6. NBS document number formats must be included for awards created in the NBS: Contract Number; Purchase Order Number; Task or Delivery Order Number and Source Award Number (e.g., Indefinite Delivery Contract number; General Services Administration number); or, BPA Call Number and BPA Parent Award Number. 7. Data Universal Numbering System (DUNS) or DUNS + 4 as registered in the Central Contractor Registration (CCR). 8. Federal Taxpayer Identification Number (TIN). In those exceptional cases where a contractor does not have a DUNS number or TIN, a Vendor Identification Number (VIN) must be referenced on the invoice. The VIN is the number that appears after the contractor's name on the face page of the award document. 9. Identify that payment is to be made using a three-way match. 10. Description of supplies/services that match the description on the award, by line billed.* 11. Freight or delivery charge must be billed as shown on the award. If it is included in the item price do not bill it separately. If identified in the award as a separate line item, it must be billed separately. 12. Quantity, Unit of Measure, Unit Price, Extended Price of supplies delivered or services performed, as applicable, and that match the line items specified in the award.* * NOTE: If your invoice must differ from the line items on the award, please contact the Contracting Officer before submitting the invoice. A modification to the order or contract may be needed before the invoice can be submitted and paid. B. Shipping costs will be reimbursed only if authorized by the Contract/Purchase Order. If authorized, shipping costs must be itemized. Where shipping costs exceed $100, the invoice must be supported by a bill of lading or a paid carrier's receipt. C. Mail an original and 1 copy of the itemized invoice to: National Institutes of Health Office of Financial Management, Commercial Accounts 2115 East Jefferson Street, Room 4B-432, MSC 8500 Bethesda, MD 20892-8500 For inquiries regarding payment call: (301) 496-6088 In order to facilitate the prompt payment of invoices, it is recommended that the vendor submit a photocopy of the invoice to the "Consignee" designated for the acquisition in blocks 6A - 6E of the face page of the Order/Award document. II. INVOICE PAYMENT A. Except as indicated in paragraph B., below, the due date for making invoice payments by the designated payment office shall be the later of the following two events: 1. The 30th day after the designated billing office has received a proper invoice. 2. The 30th day after Government acceptance of supplies delivered or services performed. B. The due date for making invoice payments for meat and meat food products, perishable agricultural commodities, dairy products, and edible fats or oils, shall be in accordance with the Prompt Payment Act, as amended. III. INTEREST PENALTIES A. An interest penalty shall be paid automatically, if payment is not made by the due date and the conditions listed below are met, if applicable. 1. A proper invoice was received by the designated billing office. 2. A receiving report or other Government documentation authorizing payment was processed and there was no disagreement over quantity, quality, or contractor compliance with a term or condition. 3. In the case of a final invoice for any balance of funds due the contractor for supplies delivered or services performed, the amount was not subject to further settlement actions between the Government and the Contractor. B. Determination of interest and penalties due will be made in accordance with the provisions of the Prompt Payment Act, as amended, the Contract Disputes Act, and regulations issued by the Office of Management and Budget. IV. PROVIDING ACCELERATED PAYMENT TO SMALL BUSINESS SUBCONTRACTORS, FAR 52.232-40 (DEC 2013) a) Upon receipt of accelerated payments from the Government, the Contractor shall make accelerated payments to its small business subcontractors under this contract, to the maximum extent practicable and prior to when such payment is otherwise required under the applicable contract or subcontract, after receipt of a proper invoice and all other required documentation from the small business subcontractor. b) The acceleration of payments under this clause does not provide any new rights under the prompt Payment Act. Include the substance of this clause, include this paragraph c, in all subcontracts with small business concerns, including subcontracts with small business concerns for the acquisition of commercial items. DELIVERY POINT: All information furnished must be in writing and must contain sufficient detail to allow the NCI to determine if it can meet the unique specifications described herein. All questions must be in writing and should be emailed to Ricky Watson, Contract Specialist at ricky.watson@nih.gov. A determination by the Government not to compete this 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 have valid registration and certification in the System for Awards Management (SAM) at www.sam.gov. No collect calls will be accepted. Please reference number N02CO82638-95 on all correspondence. Disclaimer and Important Notes: This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization's qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, an RFQ may be published. However, responses to this notice will not be considered adequate responses to a solicitation(s). POINT OF CONTACT: Inquiries concerning this Notice may be direct to: Ricky Watson 9609 Medical Center Dr. Bethesda, MD 20892-9705 Ricky.watson@nih.gov CLAUSES AND PROVISIONS The following FAR provisions and clauses apply to this acquisition: FAR 52.252-1 SOLICITATION PROVISIONS INCORPORATED BY REFERENCE (FEB 1998) 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 this/these address(es):http://www.acquisition.gov/far/ and/or http://www.hhs.gov/policies/hhsar/. Full text copies of the representations and certifications for other cited provisions and clauses may be obtained on line at the NCI website at http://ncioa.cancer.gov/oa-internet/reference.jsp or from Ricky Watson, Contract Specialist at ricky.watson@nih.gov. FAR 52.212-1 INSTRUCTION TO OFFERORS COMMERCIAL ITEMS (JAN 2017) FAR 52.212-2 EVALUATION COMMERCIAL ITEMS (OCT 2014) FAR 52.212-3 OFFERORS REPRESENTATIONS AND CERTIFICATIONS -COMMERCIAL ITEMS (JAN 2017) FAR 52.212-4 CONTRACT TERMS AND CONDITIONS - COMMERCIAL ITEMS (JAN 2017) 52.222-22 PREVIOUS CONTRACTS AND COMPLIANCE REPORTS. Previous Contracts and Compliance Reports (Feb 1999) The offeror represents that -- (a) It has, has not participated in a previous contract or subcontract subject to the Equal Opportunity clause of this solicitation; (b) It has, has not filed all required compliance reports; and (c) Representations indicating submission of required compliance reports, signed by proposed subcontractors, will be obtained before subcontract awards. 52.222-25 -AFFIRMATIVE ACTION COMPLIANCE. Affirmative Action Compliance (Apr 1984) The offeror represents that -- (a) It has developed and has on file, has not developed and does not have on file, at each establishment, affirmative action programs required by the rules and regulations of the Secretary of Labor (41 CFR 60-1 and 60-2); or (b) It has not previously had contracts subject to the written affirmative action programs requirement of the rules and regulations of the Secretary of Labor. HHSAR 352.222-70 CONTRACTOR COOPERATION IN EQUAL EMPLOYMENT OPPORTUNITY INVESTIGATIONS (DEC 2015) HHSAR 352.224-71 CONFIDENTIAL INFORMATION (DEC 2015) FAR 52.212-5 CONTRACT TERMS AND CONDITIONS REQUIRED TO IMPLEMENT STATUTES OR EXECUTIVE ORDERS---COMMERCIAL ITEMS (MAR 2016). The following additional far clauses cited in this clause are applicable: (b) The Contractor shall comply with the FAR clauses in this paragraph (b) that the Contracting Officer has indicated as being incorporated in this contract by reference to implement provisions of law or Executive orders applicable to acquisitions of commercial items: 52.204-10 Reporting Executive Compensation and First Tier Subcontract Awards (OCT 2015) (Pub.L. 109-282) (31 U.S.C. 6101 note). 52.209-6, Protecting the Government' Interest When Subcontracting with Contractors Debarred, Suspended, or Proposed for Debarment (OCT 2015) (31 U.S.C. 6101 note). 52.219-1 Small Business Program Representations 52.219-6 Notice of Total Small Business Set-Aside 52.219-28 Post Award Small Business Program Representation (JUL 2013) (15 U.S.C. 632(a) (2)). 52.222-3 Convict Labor (JUN 2003) (E.O. 11755). 52.222-21 Prohibition of Segregated Facilities (APR 2015) 52.222-26 Equal Opportunity (APR 2015) (E.O. 11246). 52.222-50 Combating Trafficking in Persons 52.223-18 Encouraging Contractor Policies to Ban Text Messaging while Driving (AUG 2011)(E.O. 13513). 52.225-13 Restrictions on Certain Foreign Purchase (JUN 2008) (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 (JUL 2013) (31 U.S.C. 3332). SUBMISSION INFORMATION Questions must be submitted electronically (via email) to Contract Specialist, Ricky Watson, at ricky.watson@nih.gov in MS Word or Adobe Portable Document Format (PDF), no later than 11:00 AM EST on Wednesday, August 15, 2018. Quotations must be submitted electronically (via email) to Contract Specialist, Ricky Watson, at ricky.watson@nih.gov in MS Word or Adobe Portable Document Format (PDF), no later than 11:00 AM EST, on Thursday, August 23, 2018. All responses must be received by the specified due date and time in order to be considered. QUOTATIONS RECEIVED AFTER THIS DATE AND TIME WILL NOT BE CONSIDERED. No collect calls will be accepted. Please refer to solicitation no: N02CO82638-95 on all correspondence. Evaluation Award will be made to the responsible firm submitting the lowest priced technically acceptable (LPTA) offer; and meeting or exceeding the acceptability standards for the requirements/technical specifications stated above. A technically acceptable quotation is one in which the Quoter complies with the requirements/technical specifications stated above, and does not take exception, nor object to any of the terms contained in this request. Quotations that are not technically acceptable will not be considered further. The technical evaluation will be a determination based on information furnished by the Contractor. The Government is not responsible for locating or securing any information which is not identified in the proposal. The Government reserves the right to make an award without discussions. However, the Government reserves the right to conduct discussions if later determined by the Contracting Officer to be necessary. The Government may reject any or all quotations if such action is in the public interest; accept other than the lowest quotation; and waive informalities and minor irregularities in quotations received. NOTE: Quoters must submit information sufficient to evaluate their quotations based on the detailed factors listed below: Price Quotation The Quoter shall prepare a price quotation that contains all information necessary to allow for a comprehensive evaluation of the prices quoted. Specifically, your quote must include the following: Federal Tax Identification Number (TIN); Data Universal Numbering System (DUNS) Number; and Business Size (e.g., small or large). Corporate Experience The Quoter shall provide documented experience of performing RNA extraction and sequencing from formalin-fixed paraffin-embedded (FFPE) cancer tissue specimens. Information provided may include number of completed projects, success rate when the RNA concentration is low or RNA is fragmented, and techniques used to address poor specimen quality. Results should be supported by published reports in peer-reviewed journals. The Quoter shall provide documented experience on the use of PathSeq software and other bioinformatics approaches to analyze and interpret the data obtained from RNA sequencing and identification of novel infectious agents. Of interest would be use of RNA sequencing and PathSeq to identify novel infectious agents in human tissue specimens, or detection of associations of infectious agents with human diseases. Information provided should be supported by published reports in peer reviewed journals. Interpretation / Support The Quoter shall provide a description of support to be provided to NCI in interpretation of sequencing data and preparation of results for publication. Relevant information includes description of data reports in terms of level of detail, annotation of sequences, and narrative explanation; description of key personnel qualifications and experience; availability to provide explanations of sequencing results to NCI by email or telephone; level of assistance in drafting tables and figures for publication; and availability to write or edit methods and results text as part of manuscript authorship.
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