Sole_Source_Justification_to_Sole_Source_to_Life_Technologies_Corp._for_Applied_Biosystems_3500_Genetic_Analyzer.pdf

Sole Source Justification for Applied Biosystems 3500 Genetic Analyzer

A. GSA contract: The Applied Biosystems 3500 Genetic Analyzer is on GSA Contract. It is available from Thermo Fisher. This Genetic Analyzer has unique capabilities required by OMGS/aOGVFB/NEI to carry out its mission, and in addition, has reagents, assays, and output file formats that are consistent with those of the ABI 3130 Genetic Analyzer currently in use in our laboratory and required by our existing assay and analysis protocols. These are explained in more detail below:

B. Unique System Features and consistency with current protocols, programs, and reagents:

a. The system is fully automated from polymer loading and replacement, DNA separation, detection and data analysis to generate base-called or size-called results. This minimizes effort and training for postdoctoral fellows in OGVFB to use the machine. In addition, The 3500 Genetic Analyzer instrument is designed with pre-packaged, single use consumables for ease of use by postdoctoral fellows as shown below:

1. Performance Optimized Polymers ((POP-4®, POP-6®, POP-7™) available in ready-to-use, load and run, pouch format. Pouches available in three sizes: 96 samples, 384 samples and 960 samples.

2. Conditioning Reagent Consumables available in ready-to-use load and run, pouch format. It will contain enough reagents for a single use only.

3. Cathode Buffer Container available as a pre-filled container with 1X buffer with two separate compartments; the left side with cathode buffer for electrophoresis and the right side with spent polymer waste from capillary wash between injections.

4. Anode Buffer Container available as a pre-filled container with 1X buffer, with a primary chamber containing buffer and a secondary overflow chamber.

5. Each of the 3500 primary consumables are designed with a RFID (Radio Frequency Identification) tag integrated into the label. These labels allow tracking and reporting of the consumable usage, lot and part numbers, expiration dates and on-instrument lifetime through the instrument operation software.

b. The Applied Biosystems 3500 Genetic Analyzer systems are supplied in a versatile combination as follows:

1. A Capillary electrophoresis instrument capable of general use.

2. DNA Sequencing and/or Fragment Analysis, reagents and consumables for system qualification allow ease of versatile implementation of the various analytical capabilities.

3. Integrated software for instrument control, data collection, quality control and auto-analysis of data for ease of analysis of data.

4. Dell Computer Workstation with a flat-screen monitor relieving lab personnel from transferring large amounts of data through potentially unsecure devices.

c. Minimal and versatile space requirements: The 3500 instrument uses less lab bench space with a width of 61cm (closed door) & 122cm (open door), depth (61cm), Height (72cm). This is critical in light of the limited space available in our laboratory. In addition, the instrument can be used with 100V-240V without modification or special plug requirements, providing mobility in the laboratory.

d. Ease and low cost of maintenance: The 3500 Genetic Analyzer is built with a single-line 505nm, sold-state long life laser that utilizes a standard power supply and requires no heat removal ducting. This will decrease the cost of running and maintaining the machine over its lifetime.

e. Quality and consistency of electrophoretic and analytical conditions: The 3500 Genetic Analyzer system improved signal uniformity from instrument-to-instrument, run-to-run and capillary-to-capillary through the use of instrument normalization schemes. In addition, the 3500 Genetic Analyzer thermal systems are specifically designed to improve temperature control and can maintain temperatures from 18 to 70 degrees C.

f. Onboard computer: The instrument is designed to work with a Dell® Workstation running a Windows® 7 operating system SP1 operating system for instrument operation and data analysis—specifically a computing platform for receiving data from the instrument at a high rate.

1. The 3500 Genetic Analyzer system software is designed with a single software interface for instrument control to regulate the functions of the instrument, automatically perform primary analysis (i.e, base calling and/or fragment sizing) and provide functionality to for real-time data assessment as well as the ability to generate quality control reports.

2. The system software is designed with the ability to perform chemistry check to verify if the system meets the sequencing read length specifications, conforms to fragment analysis sizing precision, sizing range and peak height specifications.

3. The system software is designed with wizards for easy instrument maintenance operations, automatic notifications and tracking of performed tasks, as well as calendar functionality for scheduling tasks.

4. The system software includes optional features to support: Security, Audit trail and Electronic signature features that assist with certain 21 CFR Part 11 requirements.

5. These simplified control capabilities are critical in our laboratory, where the preparations, runs, and analysis will be done by students and fellows rather than experts solely dedicated to this job.

g. Superior Design: The 3500 Genetic Analyzer capillary arrays are designed with a useful life that exceeds 160 injections. These are identical to the capillary arrays currently in use in our assays, providing compatibility between previous and ongoing work and the results provided by this system.

h. High throughput and long reads: This is critical for us to be able to replace our current 16 capillary systems with an 8 capillary system. No other existing equivalent system can equal the throughput provided by the 3500 Genetic Analyzer. Using the DNA control standard provided with the 3500 Genetic Analyzer installation kit, the system is designed to meet the following sequencing specifications for each run module as shown below.

1. With the Rapid sequencing run module on a 36 cm array, the 3500 Genetic Analyzer can generate a sequence with a QV 20 CRL of greater than 600 bp, with a sample throughput of greater than or equal to 368 samples in 23 hours.

2. With the Standard sequencing run module on a 50 cm array, the 3500 genetic analyzer can generate a sequence with a QV 20 CRL of greater than 850 bp, with a sample throughput of greater than or equal to 88 samples in 23 hours.

3. DNA Sizing for fragments in the resolution range 60 to 500 bp using POP-7™ polymer on a 36 cm array. With the Fragment Analysis POP-7™ run module, for a given allele size across all capillaries in the same run, the system is designed to perform with a standard deviation of less than 0.15 bp. The sample throughput is greater than or equal to 368 samples in 23 hours.

i. Powerful and Versatile Software Support: The 3500 Genetic Analyzer system files are generated in industry standard ABIF format, which must be viewed on a Windows® computing system. Sample files will be compatible with secondary analysis applications for post processing such as Sequencing Analysis Software, Variant Reporter® Software, GeneMapper® Software and SeqScape® software programs. This is critical for our laboratory since we analyze both sequence reads and fragment lengths using a number of general and internal programs using both the final output files as well as a number of intermediate file types generated by the sequencer. For the latter, the input was designed to be compatible with output from the previously ABI supported 3130 Genetic Analyzer, which is distinct from other commercial sequencing platforms and identical to the 3500 Genetic Analyzer. If we switch platforms a large number of these programs will have to be rewritten, requiring much time and effort, and setting back our research considerably.

j. Superior Vendor Service and Support: The 3500 Genetic Analyzer is provided with a limited warranty for a period of one year from the date of installation (or fifteen months from the date of shipment – whichever is earlier). A factory trained service engineer is available to perform all repairs. Optional post-warranty service contracts including next-business-day on-site repairs are available. It is provided with a one-day basic user training session by a certified technical scientist (Field Application Specialist). Since this equipment is critical for our core mission, prompt service and replacement of parts is tremendously important in considering a new sequencer. In addition, Applied Biosystems is able to supply all the necessary consumables to perform DNA sequencing and size analysis, including PCR reagents designed for use with the 3500 Genetic Analyzer.

Perhaps most importantly for our laboratory, which relies heavily on postdoctoral fellows who often have minimal experience, Applied Biosystems/Life Technologies provides comprehensive assay design and development guidelines for sequencing and genotyping assays.

k. Consistency of chemistry and analysis with the 3130 Genetic Analyzer in current use in our laboratory. The 3500 Genetic Analyzer is designed to detect and analyze six fluorescent dyes simultaneously for DNA fragment analysis. We have developed internal multiplexing and pooling approaches based on the 3130 fluorescent dye system. These are not compatible with any other existing platform, but since the 3500 dye system is identical to that of the 3130, our assays will transfer seamlessly to the new system.

l. Lease to Own Agreement: The lease to own agreement is necessary to purchase this category of DNA sequencer given our budgetary constraints. The terms are very favorable to OMGS/OGVFB/NEI, with a total cost of only $101,858 for a 36 month agreement on equipment that costs $90,000 if purchased outright. This is in contrast to all other available lease to own agreements, which have a much steeper increase in the total price, including the ORS/DSEIS program, which in addition to higher monthly rent on average, charges the book value of the equipment plus 4% of the acquisition cost to purchase at the end of the lease.