A--cRNA SEQUENCING

Correction to initial Description paragraph. TITLE: A- NOTICE OF INTENT TO AWARD SOLE SOURCE SOL: 36C24219Q0982 DUE: 26 July 2019 at 10:00am EST SET ASIDE: N/A NAICS: 541380 POP START: 8/12/2019 AGENCY: Department of Veterans Affairs - Bronx VAMC POC: Carlton Lunsford, email: contact@example.gov DESCRIPTION: NOTICE OF INTENT TO AWARD A SOLE SOURCE CONTRACT TO Novogene. Market research was conducted and determined that Novogene is the only vendor capable of providing the Novogene service necessary that meet the requirements. All items are proprietary to Novogene and not able to be sourced out to another. This Notice of Intent is not a request for Proposals or Quotations. No solicitation document exists and no telephone or email inquiries will be accepted. No contract award will be made on the basis of proposals, or quotations received in response to this notice. The government MAY consider all Expressions of Interest (EOI) received prior to 26 July 2019. A determination by the government not to compete this proposed contract 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. Responses to this notice must be emailed to contact@example.gov and received by 10:00AM EST on 26 July 2019. Submitters are responsible for ensuring their EOI reaches the designated contracting officer on-time. Department of Veterans Affairs Identification of secreted endothelial cell proteins Performance Work Statement (PWS) 1. Title: RNAseq analyses of the brain transcriptome of blast-exposed rodents 2. Purpose: Preparation of cDNA libraries, sequencing and transcription analyses of RNA prepared from the brains of rodent models of blast-induced traumatic brain injury. 3. Background: In previous published research we have found that the brain neurovascular unit is disrupted by blast exposure. The required services are needed to identify at the molecular level the blast-induced alterations in RNA transcription that are associated with the development of a PTSD-like condition in rodent models of blast-induced traumatic brain injury. 4. Scope: To identify alteration in RNA transcription associated with blast-exposure in the brain 5. Period of Performance: August 17, 2019-August 16, 2021 6. Place of Performance: We propose to use the services of Novogene, who is the largest sequencing center in the world and has the necessary capacity and efficient turnaround of data. 7. Tasks 7.1 Task 1: Project Management and Progress Reporting 7.1.1 VA scientists will be responsible for the preparation of RNA isolated from diverse regions of the rodent brain (rat or mouse). 7.2 Task 2: Data Collection and Reporting The contractor will perform reverse transcription of RNA samples, library preparation, DNA sequencing, quality control of material, mapping reads to reference genome, differential expression analyses, transcription (GO, KEGG Pathway, Reactome, DO) enrichment analyses of differentially expressed genes, protein-protein interaction analyses, transcription factor analyses. 7.3 Task 3: Simple and Complex Data Analyses Data analyses will be performed by scientists at the JJPVAMC and at Novogene. 7.3.5 The contractor shall send the sequence data and analyses to scientists at the VA via FTP. 7.4 Task 4: Educational and Informational Materials NA 8. Deliverable Table Note that the Deliverable Table is directly related to the tasks and deliverables in Section 7 above. Tasks Deliverable Planned Completion Date Task 1 7.1.1 reverse transcription of RNA samples, library preparation, DNA sequencing, quality control of material, mapping reads to reference genome, differential expression analyses, transcription (GO, KEGG Pathway, Reactome, DO) enrichment analyses of differentially expressed genes, protein-protein interaction analyses, transcription factor analyses 3-4 months after award of task order (TO) 9. Scope of Inspection This section will be a part of the Quality Assurance Surveillance Plan (QASP). Note that the table below is directly related to the tasks and deliverables in Sections 7 (Tasks) & 8 (Deliverable Table) above. The Contractor shall notify the CO/COR as soon as it becomes apparent to the contractor that a scheduled delivery shall be late. The contractor shall include in the notification the rationale for late delivery, the expected date for the delivery and the project impact of the late delivery. The CO/COR shall review the proposed schedule and provide guidance to the contractor via a TO modification. Such notification in no way limits the Government's right to any and all rights and remedies up to and including termination. All deliverables shall be inspected for content, completeness, accuracy and conformance to task order requirements by the CO/COR. Inspection may include validation of information as specified in the task order. All deliverables shall be checked for comprehensive to ensure the completeness, quality, and adequacy of all deliverables. The Government requires a period not to exceed thirty (30) days after receipt of deliverable items for inspection and acceptance or rejection. Inspection and acceptance of all work performance, reports and other deliverables under this task order shall be performed by the COR. Any further revisions required for government acceptance will be discussed between the COR and contractor. The COR s written approval of the draft and final documents shall constitute acceptance by the VA. The contractor shall notify the Government in writing, if problems arise that could adversely impact the performance of the Task Order. TASKS Task Ref Indicator/Deliverable Standard AQL Method(s) of Surveillance Program and Project Management Services 7.1.1 Provide and maintain a detailed Project Management Plan that includes a Quality Control Plan 15 business days after award of TO 95% 100% Inspection 7.1.2 Provide and maintain a detailed Project Plan 15 business days after award of TO 95% 100% Inspection 7.1.3 Provide a Confidentiality Plan and Data Security Procedures 15 business days after award of TO 95% 100% Inspection 7.1.4 Provide toll free number and email technical support 15 business days after award of TO 95% 100% Inspection 7.1.5 Prepare Agendas and minutes for weekly meetings Weekly after the start of the TO 95% 100% Inspection 7.1.6 Provide weekly reports during data collection Weekly after the start of data collection 95% 100% Inspection 7.1.7 Provide monthly reports during the award period Monthly 95% 100% Inspection Data Collection Surveys/Studies and Reporting 7.2.1 Assist with obtaining necessary IRB and OMB Approvals As agreed upon in the TO 85% Contractor-reported data 7.2.2 Develop Contact Information/ Locate Addresses: i.e. location algorithm (n=30,000) As agreed upon in the TO 90% Contractor-reported data 7.3.1 Provide focused methods and technique information papers As agreed upon in the TO PMP 85% Periodic Surveillance 7.3.2 Develop programming language for coding procedures As agreed upon in the TO PMP 90% Contractor-reported data 7.3.3 Develop an analysis plan for calculation of sampling weights and correction factors As agreed upon in the TO PMP 90% Contractor-reported data 7.3.4 Perform non-response analysis As agreed upon in the TO PMP 90% Periodic Surveillance 7.3.5 Write publications for peer-reviewed journals As agreed upon in the TO PMP 90% Contractor-reported data Educational and Informational Materials 7.4.1 Create an 1-page information sheet As agreed upon in the TO PMP 90% 100% Inspection; User Survey 7.4.2 Create and format brochures for marketing purposes As agreed upon in the TO PMP 90% User survey; Contractor-reported data 7.4.3 Create and format Fact Sheets As agreed upon in the TO PMP 90% User survey; Contractor-reported data 7.4.4 Create promotional materials As agreed upon in the TO PMP 90% Contractor-reported data; Progress Report