SOLICITATION NOTICE
66 -- Two Pair End Modules - Illumina Genome Analyzer
- Notice Date
- 6/16/2008
- Notice Type
- Presolicitation
- NAICS
- 334516
— Analytical Laboratory Instrument Manufacturing
- 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-80099-MM
- Archive Date
- 7/16/2008
- Point of Contact
- Ashley L. Virts, , Melissa P Marino, Phone: 301-402-4509
- E-Mail Address
-
virtsa@mail.nih.gov, marinome@mail.nih.gov
- Small Business Set-Aside
- N/A
- Description
- The National Cancer Institute (NCI) plans to procure as a sole source Two Paired End Modules for Illumina Genome Analyzer with Illumina Inc; 9885 Towne Center Drive; San Diego, California 92121-1975. This acquisition will be conducted under the procedures for acquiring commercial items authorized in FAR Part 12 and under the authority to use simplified procedures for commercial requirements as provided in FAR 13.501. The North American Industry Classification System code is 334516 and the business size standard is 6.5M employees. This notice 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 NCI to determine if the party can perform the requirement. No faxed or emailed capability statements will be accepted. Contractor shall provide one (1) original and one (1) copy of the capability statement. Capability statements must be received in the contracting office by 11:00 AM EST, by June 23, 2008. All questions must be in writing and can be faxed or emailed to: Melissa Marino, via electronic mail at marinome@mail.nih.gov or fax 301-402-4513. It is the vendors’ responsibility to ensure all questions have been received in the contracting office. 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 Central Contractor Registration (CCR) and the Online Representations and Certifications Applications (ORCA). Reference: NCI-80099-MM on all correspondence. JUSTIFICATION FOR OTHER THAN FULL AND OPEN COMPETITION: Part I: Background information and description of requirements: The Illumina Genome Analyzer is a currently installed instrument which generates large quantities of DNA sequence in a single run (approximately 1Gb) in the form of millions of short reads (25-35 nucleotides in length). This has become an important technology within NCI for a number of DNA sequencing applications. However, the very short sequence reads are difficult to align with the normal reference genome. The sequencer as currently configured reads only one end of the template molecule. Illumina has released a hardware module (the PE Module) which can be installed in the existing sequencer as an upgrade which allows sequencing of both ends of the template generating “paired end reads”. The result of installation of this upgrade will be doubling the sequence productivity of the instrument with a substantial increase in the fraction of template molecules which can be successfully aligned to the human genome. In cancer research applications, this will also allow the recognition of cancer specific abnormalities that have developed between the two ends of the template molecule. The requested module is the only product available to modify the existing instrument to generate paired end reads. No competing module is available. The only alternative would be an entirely new sequencer outfitted for paired end reads procured from Illumina or another vendor at greater than 10 times the cost of the upgrade module. The proposed contractor, Illumina Inc., built the instrument and is the sole source of qualified parts for the instrument due to proprietary technology within the instrument. Part II: Facts and Reasons to Justify Other than Full and Open Competition: 1 Statute: This justification has been prepared under the authority of 41 U.S.C. 253 (c)(1) as set forth in 13.106-1 (b)(1). (b) Soliciting from a single source. (1)For purchases not exceeding the simplified acquisition threshold, contracting officers may solicit from one source if the contracting officer determines that the circumstances of the contract action deem only one source reasonably available (e.g., urgency, exclusive licensing agreements, or industrial mobilization). No other requirement and/or type for supply or service will satisfy agency need. Justification: The cited authority is being used to propose that Illumina Inc., supply the require instrument. The module must provide fully automated template preparation for the second round of sequencing in a paired-end sequencing run. It must work with the Illumina Genome Analyzer to generate ≥36 bp reads from both ends of the templates in the library for a total of ≥3 Gb of paired-end data per run. Paired-end sequencing data is required by CCR for long-range positional information and easy detection of structural variations such as chromosomal rearrangements, copy number variations, and insertions deletions (indels). The Center for Cancer Research (CCR), National Cancer Institute (NCI), recently installed two Illumina Genome Analyzers, that are being used to generate large quantities of DNA sequencing in a single run (approximately 1 Gb) in the form of millions of short, >36 bp reads. However, as configured, the sequencers produce sequences that difficult to align to reference genomes because the reads are from only one end of the template molecule. The CCR now requires the ability to sequence both ends of a template molecule using a module that can be easy attached to the existing Illumina Genome Analyzers and used after completion of the first read to regenerate the templates in situ. The module must be able to connect to the Genome Analyzer through a single fluidic connection, providing a walk-away automated workflow. Additional salient characteristics of the paired-end sequencing module include: •Simple workflow: must use the same simple protocol to create single-read or paired-end gDNA libraries in <8 hours; generate clonal clusters in <7 hours with <2 hours of hands-on time •Low sample amount: must be able to use ≤ 1 µg of DNA to generate human genomic paired-end DNA libraries •Highest daily throughput: generate ≥ 3 Gb of data in no more than 5 days; 2× ≥36 bp reads for ≥600 Mb per day •Optimal data density: must obtain highly granular sequence information with optimal insert sizes of 200-500 bp; paired-end protocol must also be compatible with larger DNA fragment libraries •Highest quality data: must achieve ≥99.99% consensus accuracy at ≥3× coverage
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- Record
- SN01594205-W 20080618/080616215903-fd44411fb34a370824c35fb0c2153003 (fbodaily.com)
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