SOLICITATION NOTICE
Q -- Laboratory testing to assess alternative polyadenylation on lung cancer samples from the NCI-MD case control study sequencing the 3’UTR of 110 normal tissues and 110 cancer tissues
- Notice Date
- 8/25/2015
- Notice Type
- Presolicitation
- NAICS
- 621511
— Medical Laboratories
- 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
- N02RC52671-76
- Archive Date
- 9/5/2015
- Point of Contact
- Catherine Muir, Phone: (240) 276-5434
- E-Mail Address
-
muirca@mail.nih.gov
(muirca@mail.nih.gov)
- Small Business Set-Aside
- N/A
- Description
- Contracting Office Address: Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 9609 Medical Center Drive, Room 1E144, Bethesda, MD 20892, UNITED STATES Description: National Cancer Institute (NCI), Center for Cancer Research (CCR), Laboratory of Human Carcinogenesis (LHC), plans to procure, on a sole source basis, the laboratory services to sequence the 3'UTR of 110 normal tissues and 110 cancer tissues from Lexogen, Inc.; 51 Autumn Pond Park, Greenland, NH 03840, USA. The response close date of this 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 in accordance with simplified acquisition procedures as stated 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 621511 and the business size standard is $32.5M. Only one award will be made as a result of this solicitation. This will be awarded as a firm fixed price, type contract. The period of performance will be twelve (12) months from date of award. It has been determined there are no opportunities to acquire green products or services for this procurement. The Laboratory of Human Carcinogenesis has a multifaceted research program integrating basic, translational, clinical, and population research, with a major focus on common and lethal human cancers that include tumors of the breast, colon, esophagus, liver, lung, pancreas and prostate. Our studies utilize a Precision Medicine Strategy. Our main objectives are to conduct investigations that assess: (1) Mechanisms of carcinogenesis including the cellular functions of cancer driving genes; (2) experimental approaches in biological systems for the extrapolation of carcinogenesis data and mechanisms from in vitro models and experimental animals to humans; (3) molecular integrative epidemiology of human cancer risk; and (4) cancer biomarkers of diagnosis, prognosis, and therapeutic outcome. Smoking is the main factor associated with lung cancer Studies have shown that exposure to cigarette smoke and nicotine can alter gene expression and lead to cellular transformation. Recent work suggests that cancer cells have shorter 3'UTRs than normal cells and our initial work suggested that smoking could play a role in this. The LHC therefore conducted an experiment exposing cancer cells to nicotine and used the novel 3T fill sequencing method to specifically sequence the 3'UTR of these cells. The LHC also performed the 3T fill experiment on human lung cancer samples. The LHC's study provided evidence that alternative polyadenylation is indeed affected by smoking and is perturbed in cancer. The LHC now needs to extend this study and look at the effect on human cancer cells in a larger study. The LHC proposes to assess alternative polyadenylation on lung cancer samples from the NCI-MD case control study, specifically the LHC will sequence the 3'UTR of 110 normal tissues and 110 cancer tissues. To accurately assess the 3'UTR, we will use the novel 3T' Fill method which uses primers specific to the 3'UTR of mRNAs. Following sequencing, the data will be analyzed by the LHC to identify specific alternative polyadenylation patterns and polyadenylaion site usage in the cancer and normal samples and in smokers and non smokers. This work is important to assess the role of alternative polyadenylation in lung cancer and the contribution of smoking to this process. The Contractor shall perform the following tasks: The Contractor will perform the 3'T-Fill reaction and RNA-seq on the 220 libraries generated from human samples using the HiSeq 2000 and 100 SE runs. Complete sequencing, mapping and specific analysis of this unique method will be performed on our sample set. Government Responsibilities: The LHC will be extracting RNA from normal and human cancer cells from a total of 220 samples obtained from smoker and never smoker individuals equally represented. The LHC will be generating cDNA libraries from these RNA samples, performing QC of the libraries prior to subjecting them to the 3'T-fill NGS method, a new technology. Based on the data provided by the Contractor, the LHC will analyze and define the differences of the whole genome landscape of alternative polyadenylation in normal and cancer cells and the effect determined by cigarette smoke using patient information. Reporting Requirement and Deliverables: Following the novel 3'T-fill reaction and HiSeq2000, the Contractor will also provide: 1. raw data analysis: FastQC reports, including read counts per barcode, over-represented sequences, read quality; 2. trimming, including statistics; 3. alignment and the QC (quality control) of the alignment, with the statistics of the coverage, strandedness, detected biotype-classes, inner-distance estimation - either for selected libraries, pooled set or each library individually provided.
 4. reads per gene and a table including annotated polyadenylation site statistics. 5. assessment of 3'UTR and polyadenylation sites. Once library samples are received and the 3'T-Fill reaction is performed, the results of the assays and analyses described above will be sent to the Technical Point of Contact within six (6) weeks. Inspection and acceptance criteria: The NCI will have fifteen (15) business days in which to review and accept these data. If no comments or request for revisions are provided within fifteen (15) business days the deliverables shall be considered acceptable. This laboratory service is provided by Lexogen, Inc.. This laboratory developed this method and is the only company that can perform the 3'T Fill reaction as the sequencing primers are specific to this assay required in the SOW. The bioinformatic analysis of the data are very complex and contain many quality control and performance metrics that can only be assessed by qualified personnel that developed the assay and methodology. Services of the proposed Vendor are needed to ensure the maximal and most accurate analysis of the data. There are no other known sources that are capable of providing the required sequencing with the same sensitivity, specificity, throughput, and demonstrated performance and quality as that of proposed Vendor. The LHC has used this laboratory with their specific methods for novel 3T fill sequencing to specifically sequence the 3'UTR of these cells on prior studies. The LHC's study is ongoing, and the performance characteristics and quality of the needed services, uniquely provided by the proposed Vendor, are required for maintaining the integrity of on-going studies. A change would be disruptive to the ability to analyze our cumulative results. This notice is not a request for competitive quotation. However, if any interested party, especially small businesses, believes it can meet the above requirement, it may submit a capability statement, proposal, or quotation, which shall be considered by the agency. The statement of capabilities and any other information furnished must be in writing and must contain material in sufficient detail to allow the NCI to determine if the party can perform the requirement. Responses must be received in the contracting office by 3:30PM EDT, on Sept. 4, 2015. All responses and questions must be in writing and faxed (240) 276-5401 or emailed to Catherine Muir, Contracting Officer via electronic mail at muirca@mail.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, current Entity Record, including current Representations and Certifications, in the System for Award Management (SAM) through SAM.gov. Reference: N02RC52671-76 on all correspondence.
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- SN03854601-W 20150827/150825235654-0995821f56d4981caba4e330d969a566 (fbodaily.com)
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