Platform to study the expression of miRNAs from either biofluids, such as plasma, and/or Extracellular Vesicle (EV), using Next Generation Sequencing (NGS) in the Rhesus Macaques
The U.S. Department of Health and Human Services (DHHS), National Institutes of Health (NIH), National Cancer Institute (NCI), Center for Cancer Research (CCR), Vaccine Branch (VB) and Animal Models & Retroviral Vaccines Section (AMRVS), require a platform to study the expression of miRNA from either biofluids, such as plasma and/or Extracellular Vesicle (EV), using Next Generation Sequencing (NGS) adapted to the Rhesus Macaque species, provided as samples previously acquired from established protocols already in effect. The NCI intends to obtain the requested services, on a sole source basis, from Exiqon, Inc., 12 Gill St. Ste. 1650, Woburn, MA, 01801 - 6369.
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 FAR 13.501-(a)(1). The North American Industry Classification System code is 541990 and the business size standard is $15,000,000.
The period of performance shall be for 12 months. All work shall be performed at the Contractor's facility.
It has been determined there are no opportunities to acquire green products or services for this procurement.
Contractor Requirements
The Contractor shall:
• Assist with project design and set-up and post-study consultation, by the
Contractor's microRNA technicians, at no additional cost.
• Provide comprehensive workflow that shall include 100 sample extracts which
involves separation of one part from another and RNA isolation, NGS sequencing, qPCR based validation, analysis of the possible function (mimics/inhibitors), and Bioinformatics analysis and reporting.
• Provide a report detailing samples passing QC analysis one month after award.
• Provide a protocol optimized for RNA isolation and NGS library prep from biofluids to ensure high sensitivity and specificity which are required levels to be achieved whereby there is a true positive and a true negative rate correctly identified.
• Include hemolysis indicator as described in Blondal, et al., 2013 (http://www.ncbi.nlm.nih.gov/pubmed/23036329) to determine cellular contamination levels.
• Provide RNA isolation workflow including RNA spike-ins to monitor RNA isolation efficiency and presence of enzymatic inhibitors during library-prep: Scientifically rigorous Quality Control at every step of the workflow, including, but not limited to, qPCR-based RNA QC, Library preparation QC by Bioanalyzer, and raw data QC checks during data analysis pipeline.
• Provide RNA QC step that includes LNA enhanced qPCR for RNA levels too low to be detected using traditional methods (NanoDrop or Bioanalyzer).
• Provide report indicating microRNA content, extraction efficiency and levels of
possible inhibition for each sample before proceeding to library preparation for NGS analysis.
• Provide detailed procedures for addressing and replacing low-quality samples which are samples considered of low value or low quantity due to sample preparation or disease of the animal.
• Provide comprehensive bioinformatics data analysis pipeline, including specific serum/plasma sample spike-in analysis for data QC.
• Provide teleconference support following study completion to summarize data and provide biological interpretation of results.
• Provide downstream validation using LNA enhanced qPCR platform.
• Generate libraries from small quantities of total RNA for sequencing by NGS.
• Provide sequencing of libraries prepared from up to 100 samples on a high-throughput sequencing platform, which provides enhanced views of pathogen biology by rapidly and very inexpensively allowing for the whole-genome sequencing to be observed.
• Provide counting of sequencing reads and mapping to Rhesus Macaque reference genome annotated with the latest release of miRbase, which is the searchable database of published RNA sequences and annotation. Reads not mapped to annotated features shall be further analyzed to identify potential novel miRNAs. An analysis report, in addition to the final report, should include hierarchical clustering plots based on transcripts/million (TPM) normalized data. In addition to basic bioinformatics, test run library quality, alignment of reads, differential expression analysis and interpretation of experimental results must be included.
• Provide analysis to include specific comparisons of samples with the dataset listing differentially expressed miRNAs, as well as identification of statistically significant signals.
• Provide prediction of novel microRNAs by using a program, such as the miRPara prediction program.
• Provide extensive data analysis, including biological interpretation of results by using Gene Ontology (GO), a major bioinformatics initiative, to unify the representation of gene and gene product attributes across all species, in combination with a miRNA target prediction software tool.
Government Responsibilities
• Provide the Contractor with 100 samples and the adequate volumes to conduct the study.
• Set up monthly teleconference calls following each step of the study and thusly following the completion and to discuss summarizing of data and provide interpretation of results.
Deliverables
• Report detailing samples passing QC analysis, due 1 month after award
• Copy of protocol optimized for this specific type of RNA isolation and NGS library prep
from biofluids to ensure sensitivity and specificity, due 1 month after award
• Report indicating microRNA content extraction efficiency and levels of possible
inhibition for each sample, due 5 months after award
• Generation of analysis report showing the hierarchical clustering plots based on
normalized data, due 6 months after award
• By using MiRPara prediction program, provide estimate of new microRNAs obtained from the samples, due 8 months after award
• Generation of final report which includes extensive data analysis, biological interpretation of results using the Gene Ontology and all tools used to analyze miRNA,
due 12 months after award
The NCI requires a Contractor with experience conducting and understanding of miRNAs and how biofluids or other cellular products can be expressed using Next Generation Sequencing (NGS). The Contractor must be familiar with the Rhesus Macaque species so that a summary of the data using its genome can be analyzed and a novel discovery of the miRNAs can be obtained. The required services were conducted by Exiqon Inc. previously, under award # HHSN261201700114P. This allowed for generation of results which met the NCI/CCR/VB/AMRVS's experimental needs. Using an alternative Vendor would produce results that would not be scientifically comparable with the previous results. Therefore, it is critical that Exiqon Inc. provide the requested services.
This notice is not a request for competitive quotations. However, if any interested party, especially a small business, believes it can meet the above requirement, it may submit a capability statement, proposal or quotation which shall be considered by the agency. 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 no later than 11:00 AM EST, on May 8, 2017. All responses and questions must be via email to Contracting Officer, Megan Kisamore, at megan.kisamore@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. No collect calls will be accepted. In order to receive an award, Contractors must be registered and have valid certification in the System for Award Management (SAM.GOV) and have Representations and Certifications filled out. Reference: N02CO72567-8 on all correspondence.
Megan N. Kisamore, Contracting Officer, Phone (240)276-5261, Email megan.kisamore@nih.gov
