SOLICITATION NOTICE
B -- Services for NimbleGen hybridization exome capture and GS FLX Titanium 454 sequencing
- Notice Date
- 8/31/2009
- 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, 6120 Executive Blvd., EPS Suite 600, Rockville, Maryland, 20852
- ZIP Code
- 20852
- Solicitation Number
- NCI-90223-NG
- Archive Date
- 9/30/2009
- Point of Contact
- Malinda L Holdcraft, Phone: (301) 402-4509, Caren N Rasmussen, Phone: (301) 402-4509
- E-Mail Address
-
holdcram@exchange.nih.gov, cr214i@nih.gov
(holdcram@exchange.nih.gov, cr214i@nih.gov)
- Small Business Set-Aside
- N/A
- Description
- The National Cancer Institute (NCI), Urologic Oncology Branch (UOB) plans to procure on a sole source basis NimbleGen hybridization exome capture and GS FLX Titanium 454 sequencing of 4 proband DNA’s from Familial Renal Oncocytoma families, from Roche Diagnostics Corporation, 9115 Hague Road, Indianapolis, IN 46250-0414. The services herein are being procured in accordance with the simplified acquisition procedures authorized by FAR Part 13.106-1 (b) (1). The North American Industry Classification System Code is 621511 and the business size standard is $13.5. The period of Performance shall be from award through two (2) months. Only one award will be made as a result of this notice. One area of research in the Urologic Oncology Branch, National Cancer Institute, is focused on the discovery of new renal cancer susceptibility genes through the study of families with inherited kidney cancer. Inherited kidney cancer comprises about 4% of all cases of renal neoplasia and can be subclassified based on histology. Four major inherited kidney cancer syndromes have been described for which causative genes have been identified: von Hippel Lindau disease caused by germline mutations in the VHL gene (clear cell histology), Hereditary Papillary Renal Carcinoma resulting from germline mutations in the MET proto-oncogene (papillary type 1 histology), Hereditary Leiomyomatosis Renal Carcinoma caused by germline mutations in the fumarate hydratase gene (papillary type 2 histology) and Birt-Hogg-Dube’ syndrome resulting from germline mutations in the BHD gene (chromophobe and hybrid oncocytic histologies). Renal oncocytoma is a benign renal neoplasm with a unique histology that may be a precursor lesion to malignant chromophobe renal cancer. Five families with bilateral multifocal renal oncocytomas (Familial Renal Oncocytoma, FRO) have been described and additional families have been evaluated and surgically managed by the Urologic Oncology Branch medical staff at the NIH Clinical Center. The identification of the gene responsible for FRO will facilitate an understanding of the molecular mechanisms involved in the development of renal oncocytoma that may also be important for the progression to chromophobe renal cancer. Knowledge of the biochemical basis for renal oncocytoma/chromophobe renal cancer will facilitate therapeutic drug development to treat patients with FRO and sporadic renal oncocytoma/chromophobe renal cancer. Previously genetic linkage analysis was the method of choice employed to identify the cancer genes responsible for the four inherited renal cancer syndromes described above. However, FRO families are rare with small pedigrees and therefore, traditional gene-mapping approaches cannot been used successfully to identify FRO candidate genes. With the advent of next-generation sequencing technologies, entire protein-coding regions of the genome (‘exomes’) may be sequenced in the affected individuals from inherited renal cancer families. Mapping renal cancer–associated sequence variants to the human genome will localize the putative renal cancer gene to a particular coding region and facilitate the discovery of potential cancer-associated genetic changes that can be validated in other affected individuals from inherited renal cancer families. The UOB, NCI therefore proposes to select one affected individual from each of four FRO families and perform peripheral blood DNA sequencing of all protein-coding regions in these individuals using NimbleGen exome hybridization capture and Roche GS FLX Titanium 454 sequencing. Sequence variants will be compared with genomic sequence from unaffected individuals and available human genomic sequence databases to eliminate non-disease associated single nucleotide polymorphisms from consideration. Coding regions containing sequence variants that are shared among affected individuals particularly in multiple families are likely to harbor the FRO susceptibility gene(s) and will be validated in future studies. Roche Diagnostics offers the only ‘exome’ hybridization capture system of its kind on the market for capture of protein-coding regions of the genome for subsequent downstream sequence analysis. The unique features of the Roche NimbleGen exome hybridization capture system include utilization of a high density, long-oligonucleotide NimbleGen 2.1M array designed with an empirically tested and proven capture design algorithm to ensure a high level of human exome capture (180,000 exomes) from a single array. The NimbleGen capture system is specifically designed for use in tandem with the Roche/454 Life Sciences Genome Sequencer FLX Titanium instrument for downstream sequencing of these captured exomes through incorporation of specific adapters during the capture process that are unique for the GS FLX sequencing platform. No other sequencing platform may substitute because the NimbleGen capture system has been optimized specifically for the GS FLX Titanium platform. The unique features of this next-generation 454 Life Sciences GS FLX Titanium sequencing platform include the ability to obtain long 400 bp reads with one million sequence reads and 8x coverage per Picotiter Plate generating 400 Mb of raw sequence. Longer reads (exceeding other sequencing platforms) guarantee more accurate and efficient alignment by bioinformatics programs against the human genome sequence databases ensuring superior yield and data quality. Because Roche Diagnostics possesses the unique exome capture and GS FLX Titanium 454 instrumentation sequencing platform which specifically fits the study design necessary to complete the objectives of this research project, they are uniquely qualified to perform the work. This is not a request for competitive quotation. However, if any interested party believes it can meet the above requirement, it may submit a statement of capabilities. 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 meet this requirement. One (1) original and one (1) copy of the capability statement must be received in the contracting office by 11:00 a.m. ET on September 15, 2009. All questions must be in writing and can be faxed to 301-402-4513 or sent via email to Malinda Holdcraft: holdcram@exchange.nih.gov. It is the vendor’s responsibility to ensure questions have been received. 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, contractor must have valid registration and certification in the Central Contractor Registration (CCR) and the Online Representations and Certifications Application (ORCA). Please reference NCI-90223-NG on all correspondence.
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