Laboratory Testing Services for the Helicobacter pylori Genome Project

1.0 DESCRIPTION The Department of Health and Human Services, National Institutes of Health, National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics (DCEG) plans to procure, on a sole source basis, services for laboratory testing services for the Helicobacter pylori Genome Project from Vanderbilt University Medical Center at 1161 21st Ave S Ste D3300 MCN, Nashville, TN 37232-0011. The response close date of the notice for this requirement is in accordance with FAR 5.203(b). 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 541380 and the small business size standard is $16.5 million. The period of performance shall be 12 months from the date of award. The anticipated award shall be a firm fixed price purchase order for severable services. It has been determined there are no opportunities to acquire green products or services for this procurement. 2.0 BACKGROUND Helicobacter pylori, a Gram-negative bacterium associated with a spectrum of benign and malignant gastric conditions, is one of the most genetically variable pathogens. Variations in a few genes have been associated with risk of inflammation and carcinogenesis, but to date no systematic study has evaluated the entire bacterial genome. The U.S. Department of Health and Human Services, National Institutes of Health, National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics (DCEG) requires laboratory testing services to enlarge an informative collection of H. pylori clinical isolates from residents of defined geographic areas. Molecular characterization will be conducted at the NCI's Cancer Genomics Research Laboratory. DCEG is investigating the hypothesis that genetic and epigenetic variations in H. pylori strains among chronically infected individuals may affect risk of progression to gastric cancer. Additional testing is required from international populations to characterize the differential virulence among H. pylori isolates and suggest predictive biomarkers for early diagnosis of cancer. The bacterial isolates and databases from this requirement will also provide a foundation for further elucidation of H. pylori pathogenesis. 2.1 OBJECTIVE The specific aims of this requirement are: - To characterize the spectrum of genomic and epigenomic variations of benign strains of H. pylori based on isolates from chronically infected individuals. - To identify molecular features that may contribute to pathologic effects by comparing the profile of benign infection to corresponding spectra of isolates from individuals with gastric cancer and premalignant lesions - To establish a resource repository of multidimensional data and well-characterized strains for utilization by the scientific community 3.0 SCOPE The Contractor shall expand, extract and store DNA from H. pylori isolates; culture, isolate and extract DNA from H. pylori pools; perform H pylori analysis on successful patient biopsies or resections; and perform H pylori analysis on un-successful patient biopsies or resections as specified below. The Contractor shall use reduced oxygen conditions and other best practices for isolation of H. pylori, with appropriate laboratory biosafety provisions from the CDC. Samples shall be cultured in trypticase soy agar with 5% sheep blood, containing vancomycin (20 mg/L), bacitracin (200 mg/L), nalidixic acid (10 mg/L) and amphotericin B (2 mg/L) (Sigma-Aldrich). Agar plates shall be incubated under microaerobic conditions (6% O2, 6% CO2 and 88% N2; Campy Pak Plus envelope, BBL) at 37'C for 4 to 8 days until small grey translucent colonies appear. Gram stains and assays for oxidase and urease shall be performed to confirm bacteria as H. pylori. DNA (1.5-2ug) shall be extracted from single colonies using the DNAeasy Mini Kit. The cost of shipping samples to/from the Contractor's facility shall not be included in this order. NCI shall ship the samples for this requirement to the Contractor via the NIH shipping service. The samples shall be delivered to the Contractor's facility in six (6) separate shipments. The first sample shipment shall be delivered to the Contractor's facility within one (1) month of award; and the final (6th) shipment shall be delivered to the Contractor's facility within six (6) months of award. 3.1 TASKS The Contractor shall perform the following tasks: 3.1.1 Task #1: For existing H. pylori isolates: the Contractor shall expand (7 Petri plates); extract DNA (2 plates separately); and store (5 plates in separate vials). Total samples for task #1:450 samples 3.1.2 Task #2: For existing H. pylori pools: the Contractor shall culture, isolate 1 colony; expand (7 Petri plates); extract DNA (2 plates separately); and store (5 plates in separate vials). Total samples for task #2: 60 samples 3.1.3 Task #3: For successful patient biopsies or resections: the Contractor shall culture, store 3 pooled vials; isolate 1 colony; expand (7 Petri plates); extract DNA (2 plates separately); and store (5 plates in separate vials). Total samples for task #3: 135 samples 3.1.4 Task #4: For unsuccessful patient biopsies or resections: the Contractor shall perform analysis, attempted culture. Total samples for task #4: 36 samples 3.1.5 Task #5: The Contractor shall provide an electronic report to the NCI, containing the results of unsuccessful patient biopsies or resections in 3.1.4, task #4. See also: 3.1.7, task #7. 3.1.6 Task #6: The Contractor shall coordinate with and ship the resulting materials in multiple shipments to the NCI's Cancer Genomics Research Laboratory at 8717 Grovemont Circle, ATC, Room 149, Gaithersburg, MD 20877. 3.1.7 Task #7: The Contractor shall maintain a repository of bacterial isolates and provide information about availability. The Contractor shall provide this information to NCI electronically together with the final report for 3.1.5, task #5. 4.0 TYPE OF ORDER This is a firm fixed price purchase order. 5.0 PERIOD OF PERFORMANCE The period of performance shall be 12 months from the date of award. 6.0 SEVERABLE SERVICES The services acquired under this task order are severable services. Funds are only available for use for the line item to which they are obligated. Unused funds from one period (line item) may not rollover for use in other periods. 7.0 PLACE OF PERFORMANCE All services shall be performed at the Contractor's facility. 8.0 REPORT(S)/DELIVERABLES AND DELIVERY SCHEDULE DELIVERABLE DELIVERABLE DESCRIPTION / FORMAT REQUIREMENTS & DUE DATE 1. (3.1.1, Task #1) 450 DNA samples as specified in task 3.1.1, delivered to NCI's Cancer Genomics Research Laboratory. Due within 4 months of specimen receipt 2. (3.1.2, Task #2) 60 DNA samples as specified in task 3.1.2, delivered to NCI's Cancer Genomics Research Laboratory. Due within 4 months of specimen receipt 3. (3.1.3, Task #3) 135 DNA samples as specified in task 3.1.3, delivered to NCI's Cancer Genomics Research Laboratory. Due within 4 months of specimen receipt 4. (3.1.5, Task #4) Email report in WORD format for 36 unsuccessful cultures To be provided when applicable at the time of discovery of unsuccessful culture. Final version due within 12 months of award. 5. (3.1.7, Tasks #1 - #3) Repository of bacterial isolates information about availability, in EXCEL format via email. Due within 4 months of final specimen receipt 9.0 PAYMENT Payment shall be made upon receipt, review and acceptance of each deliverable in Section 8.0. Payment authorization requires submission and approval of invoices to the Government's Technical Point of Contact (TPOC) and NIH OFM. Electronic Email Submission: The current national emergency and the need to protect Federal and Contractor staff has resulted in a change to NIH's invoice submission process. Effective Wednesday, April 1, 2020, all NIH contractors/vendors invoices should be sent electronically via email to the NIH Office of Financial Management (OFM) and the NIH Contracting Officer (CO) using the electronic submission instructions contained in Attachment #1. Electronic invoice submission shall remain in effect until the Government formally notifies the Contractor of a return to mail-in invoice procedures detailed in this purchase order. This notice is not a request for competitive quotation. However, if any interested party, especially a small business, believes it can meet the above requirements, 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. All responses and questions must be sent via email to Contracting Officer, Megan Kisamore, at contact@example.gov by no later than 3:00 PM EST, on Friday, May 15, 2020 (5/15/20). 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. Please reference 75N91020Q00072 on all correspondence.