SOLICITATION NOTICE
B -- Identify Viruses Present in Tumor Tissues by Utilizing Next Generation Sequencing
- Notice Date
- 4/24/2018
- Notice Type
- Presolicitation
- 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
- N02CO82560-95
- Archive Date
- 5/16/2018
- 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) plans to procure, on a sole source basis, next generation sequencing services to analyze viruses present in tumor samples from Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215. The response close date of the notice for this requirement is in accordance with FAR 5.203(a)(1). This acquisition will be processed under FAR Part 12 - Acquisition for Commercial Items and will be made pursuant to the authority in FAR Part 13.106-1(b)(1); and is exempt from the requirements of FAR Part 6. The North American Industry Classification System code is 622310 and the business size standard is $38.5M. The period of performance shall be 12 months from the date of award. The anticipated award shall be firm fixed price. It has been determined there are no opportunities to acquire green products or services for this procurement. Contractor Requirements The purpose of this acquisition is to acquire services to identify viruses present in tumor tissues by utilizing next generation sequencing. The Contractor shall receive the tumor specimens shipped to them by the Iowa and Hawaii state cancer registries. There will be up to 30 ALCL (Anaplastic Large Cell Lymphoma), 5 DLBCL (Diffuse Large B Cell Lymphoma), and 5 breast cancer cases. The Contractor shall be blinded 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) using 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 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 has been used successfully to identify novel micro-organisms that are associated with several human diseases. The method using PathSeq is the best way to identify microorganisms in ALCL tissue samples for our proposed study. The Contractor shall report the findings to the NCI on an ongoing basis as the sequencing and analyses of each case is completed. The frequency of reports will depend upon how many tumor tissue samples we are able to send to the Lab at a time. report the findings of the analyses every month in an electronic format, such as Microsoft word or excel document attached to an email. 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 The Contractor shall report the findings to the NCI on an ongoing basis as the sequencing and analyses of each case is completed. The frequency of reports will depend upon how many tumor tissue samples are sent to the Lab at a time. The Contractor shall report the findings of the analyses every month in an electronic format, such as Microsoft word or excel document attached to an email. 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. 12 months after award Task 6-The Contractor shall report the findings to the NCI on an ongoing basis as the sequencing and analyses of each case is completed. 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. This notice is not a request for competitive quotation. However, if any interested party, especially small business believes it can meet the above requirement, it may submit a proposal or quote for the Government to consider. The response and any other information furnished must be in writing and must contain material in sufficient detail to allow NCI to determine if the party can perform the requirement. Responses must be received in the contracting office by 11:00 AM EST, on May 1, 2018. All responses and questions must be via email to Ricky Watson, Contract Specialist at ricky.watson@nih.gov. A determination by the Government not to compete this proposed 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 be registered and have valid certification through SAM.GOV and have Representations and Certifications filled out. Reference: N02CO82560-95 on all correspondence.
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