SOLICITATION NOTICE
Q -- Laboratory services of fresh-frozen tissue samples from the study of lung cancer in Xuanwei, China
- Notice Date
- 9/4/2017
- 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
- N02CP72700-76
- Archive Date
- 9/15/2017
- 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), Div. of Cancer Epidemiology and Genetics (DCEG), Occupational and Environmental Epidemiology Branch (OEEB), plans to procure on a sole source basis the laboratory services of fresh-frozen tissue samples from the study of lung cancer in Xuanwei, China from Novogene Corporation Inc; 17F/21F, Jinma Building B, Haidian District, Beijing, China. 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. Period of Performance: September 30, 2017 through March 30, 2018. It has been determined there are no opportunities to acquire green products or services for this procurement. The Division of Cancer Epidemiology and Genetics (DCEG) is a research program of the National Cancer Institute (NCI), one of the National Institutes of Health (NIH). The Division is the world's most comprehensive cancer epidemiology research group. Its renowned epidemiologists, geneticists, and biostatisticians conduct population and multidisciplinary research to discover the genetic and environmental determinants of cancer and new approaches to cancer prevention. The Division's research impacts public health policy in the United States and around the world. The Occupational and Environmental Epidemiology Branch (OEEB) conducts studies in the United States and abroad to identify and evaluate environmental and workplace exposures that may be associated with cancer risk. The mutational signatures associated with cigarette smoke provide compelling evidence that environmental exposures can affect genomic architecture in specific ways which in turn, may lead to particular pathways to lung cancer development. Given its unique chemical components, we posit that environmental exposure to smoky coal emissions may contribute to the unique characteristics of lung cancer tissue that are found in non-smoking women from Xuanwei, China by inducing specific mutational signatures. Based on the previous observations, it is highly likely that lung cancer tissue from non-smoking women from Xuanwei will have distinct mutational spectra from the interaction between the distinct components and ratios of components in smoky coal including fine quartz, alkyl PAHs, PAHs, and others. There is no study to our knowledge that has conducted deep whole-genome interrogation of mutational signatures of lung tumors from Xuanwei. Further identifying and characterizing mutational signatures across the entire genome of lung tumor tissue may shed light onto the elusive etiologic mechanism underlying the relationship between smoky coal emissions and elevated lung cancer rates in Xuanwei. At the same time, findings from this study could also inform the coal-related pathogenesis of lung cancer in other rural regions around the world that use bituminous coal in their residences for cooking and heating, in addition to the U.S. where nearly 1,300 coal power plants across the country generate 30-40% of the nation's total electricity output. The NCI is conducting a study of 25 cases of lung adenocarcinoma from non-smoking women highly exposed to the most carcinogenic smoky coal from Xuanwei, and 5 cases from non-smoking women residing in the same province of Yunnan who did not have any history of exposure to smoky or any other type of coal. Whole genome sequencing of frozen tumor samples (90X) and frozen normal adjacent lung tissue (30X) will be conducted on these samples, and due to restrictions on the export of these biological samples, these analyses must be conducted in China. The purpose of the procurement is to support the human whole genome sequencing of the 60 frozen tissue samples (30 tumor tissues and 30 adjacent lung tissues) from non-smoking women. The Contractor shall provide the following: The contractor shall perform the following tasks for frozen tissue sampling: 1. Conduct tumor purity evaluation by using H&E staining of 40 potential tumor samples to identify the 30 tumor samples that have the highest tumor content and that will then be selected for sequencing under this procurement. 2. Extract DNA from the selected 30 frozen tumor samples and paired 30 normal frozen tissues. 3. Conduct library preparation, human whole genome sequencing (30X, 90 Gb raw data per sample, with HiSeq X PE150) for 30 adjacent lung tissues. 4. Conduct library preparation, human whole genome sequencing (90X, 270 Gb raw data, with HiSeq X PE150), and basic analysis for 30 lung tumor tissues. 5. Provide raw sequencing data to NCI. 6. Conduct basic bioinformatics analysis for the above 60 samples as follows: a. Standard quality control evaluation of sequencing data b. Alignment with reference genome, statistics of sequencing depth and coverage c. SNP/InDel, SV and CNV calling, annotation and statistics d. Somatic SNP/InDel, SV and CNV calling, annotation and statistics (for tumor-normal paired samples) e. Screening for predisposing genes f. Mutational spectrum & mutational signatures g. Driver gene analysis h. Significantly mutated statistical analysis and pathway analysis i. Circos chart analysis 7. Conduct advanced bioinformatics analysis: a. Correlation analysis of significantly mutated genes b. Driver gene prediction c. Display of the distribution of mutation sites d. Identification of significant somatic CNVs e. Fusion gene detection and Circos chart generation f. Tumor purity & ploidy estimation g. Loss of heterozygosity analysis h. Intra-tumor heterogeneity analysis i. Identification of significant mutations in non-coding regions GOVERNMENT RESPONSIBILITIES: Fresh-frozen tissue samples from the study of lung cancer in Xuanwei in China will be shipped to the contractor. Samples will not have any personal identifiers attached. REPORTING REQUIREMENT AND DELIVERABLES: The contractor shall call the NCI Technical Point of Contact biweekly to report the number of samples processed. The contractor shall deliver to the NCI Technical Point of Contact no later than March 10, 2018, the results by uploading the data files to a site to be set up by NCI, and URL provided to the Contractor. INSPECTION AND ACCEPTANCE CRITERIA: The NCI will have 15 days in which to review and accept these data. If no comments or request for revisions are provided within 15 days, the deliverables shall be considered acceptable. CLEARANCES: None PAYMENT: Payment shall be made in arrears after delivery, inspection and acceptance, of technical requirements and deliverables and reporting requirements stated above. Payment authorization requires submission and approval of invoices to the NCI Technical Point of Contact and the NIH Office of Financial Management (OFM), in accordance with the payment provisions in the order. 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. 20% of the payment will be made after receipt of the H&E tumor purity analysis and DNA extraction report on December 31, 2017. 50% of the payment will be made after receipt of the raw sequencing data on February 28, 2018. 30% of the payment will be made after receipt of This laboratory services are provided by Novogene Corp., Inc. Novogene is a genomic sequencing service provider based in China and has rapidly become a world-leader in next generation sequencing services. They have a unique capability to conduct the required analyses. First, they have the largest advanced sequencing capacity in China with an array of Illumina (25 NovaSeq, 30 HiSeq X HiSeq 4000, and 10 HiSeq 2500) and PacBio Sequence systems (10 PacBio Sequel) that will allow the analyses to be conducted rapidly. Second, they have a large bioinformatics team and unique bioinformatics resources and tools that are required for the contract. It has developed the proprietary bioinformatics software SOAP (Short Oligonucleotide Analysis Package) for ultra-fast sequence mapping, variation detection, and de novo genome assembly. Novogene is the only contract provider in China, where these samples must be analyzed because of Chinese governmental export restrictions for such samples, that is capable of conducting rapid whole genome sequencing and the advanced genomic statistical analyses that are required for this contract. 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, and a change would be disruptive. 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 3:00PM EDT, on Sept.14, 2017. 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. Ref
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