PRESOL | 66 | CleanSeq Kit, 5,000 rxns, a Biomek Disposable 96 ALP Tip Wash Station and a CleanSEQ 96 Batch method

FBO DAILY ISSUE OF SEPTEMBER 06, 2008 FBO #2476
SOLICITATION NOTICE

66 -- CleanSeq Kit, 5,000 rxns, a Biomek Disposable 96 ALP Tip Wash Station and a CleanSEQ 96 Batch method

Notice Date: 9/4/2008
Notice Type: Modification/Amendment
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-80225-KM
Response Due: 9/19/2008 11:00:00 AM
Archive Date: 10/4/2008
Point of Contact: Karri L. Mares,, Phone: 3014357774, Caren N Rasmussen,, Phone: (301) 402-4509
E-Mail Address: maresk@mail.nih.gov, cr214i@nih.gov
Small Business Set-Aside: N/A
Description:   Soliciation has been changed to the following:   The National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics (DCEG), Laboratory of Translational Genomics (LTG), plans to procure the brand name a CleanSeq Kit, 5,000 rxns, a Biomek Disposable 96 ALP Tip Wash Station and a CleanSEQ 96 Batch method from Agencourt Bioscience; 500 Cunnings Center, Suite 2450; Beverly, MA 01915. This acquisition will be processed under FAR Part 12 – Acquisition for Commercial Items and will be made pursuant to the authority and FAR 13.5 to use simplified procedures for commercial acquisitions. The North American Industry Classification System Code is 334516 and the business size standard is 500 employees. One of the goals of the Laboratory of Translational Genomics is to dissect the genetic basis of single nucleotide polymorphisms (SNPs) validated in large scale; genome-wide association studies (GWAS). This approach will identify new regions to be studied in great detail and eventually applied to large molecular epidemiology studies to estimate the magnitude of the effect. To accomplish this goal, thousands of patient DNA samples are sequenced each year to identify common gene variants, known as single nucleotide polymorphisms (SNPs). This genotyping is done using a well-established, high- throughput sequencing platform that utilizes ABI Prism BigDye Terminator (BDT) cycle sequencing chemistry. These PCR and sequencing techniques are comprised of four main steps:  1)  PCR reaction set up  2)  PCR product clean up  3)  Sequencing reaction set up  4)  Sequencing reaction clean up (dye terminator removal) PART II: Facts and Reasons to Justify Other than Full and Open Competition  1.  Statute: 13.106-1 (b)(2) (b) Solicitation from a single source.  (2)  For Sole source acquisition of commercial items in excess of the simplified acquisition threshold conducted pursuant to subpart 13.5, the requirements at 13.501 (a) apply.  2.  Sole Source Justification. CleanSeq Kit, 5,000 rxns In order for our laboratory to carry out functional studies of candidate genetic variants, we need a dye terminator removal method that can be carried out in an automated, high throughput system using our newly acquired Biomek® FX Automated Workstation. High-throughput processing on this instrument cannot need vacuum filtration, centrifugation, heating or cooling, and must be faster and less expensive than our current Sephadex clean up method. The "CleanSEQ" kit from Agencourt Bioscience satisfies all of the above requirements. This unique SPRI® chemistry comprising the CleanSEQ kit has been validated and has written optimized software for use on our Biomek® FX Automated Workstation from Beckman Coulter. The kit does not need vacuum filtration or centrifugation, does not require heating or cooling, and takes about 20 minutes per 96-well plate. The "CleanSEQ" kit significantly lowers the, cost of the entire <img src="file:///C:/DOCUME~1/maresk/LOCALS~1/Temp/msohtml1/12/clip_image001.gif" alt="" width="2" height="95" align="left" /> BDT sequencing process. SPRI enables researchers to use 1/8 th of the amount of BDT used for the Sephadex method. Biomek Disposable 96 ALP Tip Wash Station The Biomek Disposable Tip Wash Station is configured specifically for our Biomek® FX robot and includes a wash station, wash pump, supply tank, and drain/waste tank, and ALP platform. The Tip Wash ALP is controlled by the Biomek System Software via the Biomek Device Controller. The inside of the pipet tip is washed by aspirating and dispensing the flow of liquid. The clean pipet tips can then be reused, thereby reducing waste and expenditures. Since our Biomek® FX is manufactured by Beckman Coulter, owner of Agencourt Bioscience Corporation, Agencourt is therefore the only company that sells a tip washer system and the corresponding Biomek Device Controller that is compatible with our Biomek® FX robot. The Biomek Disposable Tip Wash Station, or any similar system, is unavailable from any other source. The addition of a tip wash station to our robot will enable us to automate and speed up step 2 in the DNA sequencing process (PCR product clean up). This is done by using AMPure® PCR purification system. This system is based on a novel chemistry called SPRI®, an acronym for S olid P hase R eversible I mmobilization and is licensed exclusively to Agencourt under U.S. Patents 5,705,628,5,898,071 and 6,534,262. This system includes the AMPure® 25,000 reaction kit, 96 well ring magnets, direct inject plates, and V.3 AMPure 96 script software (automation software specific for the Biomek® FX robot). AMPure® is highly efficient – much more than standard PCR purification methods – which translates into improved downstream performance and significantly reduced costs for step 3 in the DNA sequencing process (BDT sequencing reaction set up). Since AMPure® utilizes magnetic beads; it also eliminates the need for centrifugation and filtration thereby reducing manual handling and error risk. AMPure®, is the only PCR purification system that has a validated method, and written, optimized software for our Biomek® FX Laboratory Automated Workstation from Beckman-Coulter. The Agencourt AMPure® PCR purification system, or any similar system, is unavailable from any other source. CleanSEQ 96 Batch method In order for our laboratory to sequence thousands of candidate genetic variants, we need a dye terminator removal method that can be carried out in an automated, high throughput system using our newly acquired Biomek® FX Laboratory Automated Workstation. The Biomek® FX (also called ‘robot’) automates all liquid handling processes including pipetting, dilution, dispension and integration that are currently performed manually for DNA sequencing. It increases accuracy, speed and production efficiency by decreasing the risk of mistakes due to manual handling. To successfully perform high-throughput dye terminator removal on our robot, we need chemistry and protocols that do not require vacuum filtration, centrifugation, heating or cooling, and must be faster and less expensive than our current Sephadex clean up method. The “CleanSEQ” kit and V.3 CleanSEQ 96 script software (batch method) from Agencourt Bioscience satisfy all of the above requirements. This script software is an automation method designed specifically for dye terminator removal using Agencourt SPRI® paramagnetic bead-based reagents on our Biomek® FX Laboratory Automated Workstation. The methods include pre-defined labware and pipetting templates, and the software contains optimized processing times for maximum high-throughput capabilities. Biomek Software version 3.2 is required to upgrade the current system. This latest version will provide the robot with improved performance, accuracy, throughput, and reliability and the ability to support new automation methods. The Biomek Software upgrade includes trade-in of the existing PC Workstation for an XP Workstation with V3.2 Biomek FX Software already installed ( Automation PC Controller Windows XP ). It also includes a new 17” Flat Panel Monitor, and installation/validation by a qualified Beckman Coulter service technician. Because our Biomek® FX robot is manufactured by Beckman Coulter, owner of Agencourt Biosciences, Agencourt is the only company that sells Beckman Software V3.2 and V.3 CleanSEQ 96 script (batch method) that is compatible with our Biomek® FX Laboratory Automated Workstation. Agencourt is therefore the only company that can properly install and validate the software in-house. These products and services are unavailable from any other source. The following salient characteristics apply: A. For Dye Terminator Removal Method ( CleanSeq Kit, 5,000 rxns) : 1. The method must not need vacuum filtration. 2. The method must not need centrifugation. 3. The method must not need shaking, 4. The method must be optimized for the Biomeke FX Automated Workstation. 5. The method must be able to use 96-well or 384-well formats. 6. The method must not require heating or cooling. 7. The method must not need the use of chaotropic salts. 8. The method must not involve covalent binding. 9. Method must not involve pH dependent ion exhange. 10. If the method is bead-based, the average core bead particle Size must be 1 micron + 10%. B. For Disposable Tip Wash Station ( Biomek Disposable 96 ALP Tip Wash Station):  1.  The entire tip wash station must be compatible with a Biomek® FX Laboratory Workstation.  2.  The tip wash station must include a Biomek Device Controller.  3.  The tip wash station must include a supply tank.  4.  The tip wash station must include a drain/waste tank.  5.  The tip wash station must have separate positions for tip loading (loader) and tip washing (washer).  6.  The tip wash station must provide automated loading and unloading of disposable tips on the Biomek FX Multichannel Pipetting Heads.  7.  The tip wash station loader must be available in 96- or 384-well channel formats.  8.  The tip wash station loader must provide controlled liquid flow to 96-channels allowing reduced tip usage.  9.  The tip wash station loader must be software controlled.  10.  The tip wash station loader must have internal air pressure boosters to reduce air pressure requirements during tip loading and unloading.  11.  The tip wash station must be able to handle up to eight loaders on the Biomek® FX Laboratory Workstation.  12.  The tip wash station washer must be available in 96- or 384-well channel formats.  13.  The tip wash station washer must be software controlled.  14.  The tip wash station washer must have a peristaltic pump that provides liquid flow.  15.  The tip wash station washer must have a manifold design that is optimized for reliable tip washing.  16.  The tip wash station washer must be able to provide multiple washers for different wash solutions.  17.  The tip wash station washer must be solvent resistant.  18.  The tip wash station must come with two 96-well magnet plates.  19.  The tip wash station must come with several adapter plates that allow a 96-well PCR reaction plate to be placed directly into Applied Biosystem 3130 and 3730xl DNA Analyzers. C. For CleanSEQ script software (CleanSEQ 96 Batch method):  1.  The CleanSEQ script software must be an automation method that is specifically designed for Agencourt SPRI® paramagnetic beads.  2.  The CleanSEQ script software must be compatible with a Biomek® FX Laboratory Workstation.  3.  The CleanSEQ script software must be validated for a Biomek® FX Laboratory Workstation.  4.  The CleanSEQ script software must be compatible with Microsoft XP operating systems.  5.  The CleanSEQ script software must come with supporting documentation.  6.  The CleanSEQ script software must feature user interfaces that easily allow editing the method without the need for programming expertise.  7.  The CleanSEQ script software methods must include pre-defined labware.  8.  The CleanSEQ script software methods must include pre-defined pipetting templates.  9.  The CleanSEQ script software must have optimized processing times for maximum plate throughput.  10.  The CleanSEQ script software must be LIMS compatible.  11.  The CleanSEQ script software must include the following features:  i.  Ability to change parameters  ii.  Conditions recalled from previous run  iii.  Incubation timer with countdown display  iv.  Use of tip wash station to reduce consumable costs  v.  Hardware components specifically designed for automation  vi.  Optional plate stacking integration This is not a solicitation for competitive quotations. However, if any interested party believes it can perform the requirement as detailed they may submit a statement of capabilities. All information furnished shall be in writing and must contain sufficient detail to allow the NCI to determine if it can meet the above unique specifications described herein. An original and one copy of the capability statement must be received in the contracting office by 11:00 am EDT, on September 19, 2008. All questions must be in writing and must be emailed to Karri Mares at maresk@mail.nih.gov faxed to (301) 402-4513. A determination by the Government not to compete this proposed contract 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. In order to receive an award from the NCI contractors must be registered in the Online Representations and Certifications Applications (ORCA). Please refer to http://orca.bpn.gov In addition; contractors must be registered in the Central Contractor Registration (CCR) www.ccr.gov. No collect calls will be accepted. Please reference NCI-80225-KM on all correspondence.
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66 -- CleanSeq Kit, 5,000 rxns, a Biomek Disposable 96 ALP Tip Wash Station and a CleanSEQ 96 Batch method