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Cost-Effectiveness in Sample Processing using the FTAÔ Treated Stain Card for High Throughput

The utilization of FTAÔ treated blood-stain cards represents a revolutionary improvement over traditional methods of DNA processing and storage. The use of FTAÔ offers a realistic means to significantly reduce the time, money and labor that would normally be required using existing protocols. The FTAÔ treated matrix has the unique ability to kill blood-born pathogens and protect genomic DNA from microbial and environmental degradation, allowing for long-term storage at room temperature and humidity. Furthermore, the intrinsic properties of FTAÔ treated matrix promotes the use of highly simplified DNA purification procedures, and offers the ability to perform completely automated, high through-put DNA processing for subsequent PCR-based testing. Cost analysis will demonstrate significant savings in sample processing and archiving over conventional methods.

FTAÔ is a reagent mixture composed of strong buffers, physical denaturants, and a free radical trap. This patented formula is applied to a cellulose-based matrix, which has been optimized for the stabilization of DNA and in-situ processing for PCR amplification. FTAÔ was designed for bio-safety and high throughput DNA preparation. FTAÔ was developed and patented by Dr. Leigh Burgoyne of Flinders University, South Australia and is licensed to Fitzco, Inc (1).

The FTAÔ blood-stain card simplifies and makes safe the collection, transport, processing and storage of whole blood, saliva, cultured cells and other biological fluids. It is the only matrix of its kind that offers the following proven benefits:

FTAÔ is Safe. Consideration for the safety of laboratory technicians handling potentially infectious materials was one of the primary goals in the development of the FTAÔ. In experiments conducted by Dr. Burgoyne at Flinders University, FTAÔ treated paper has been shown to aggressively inactivate blood-borne pathogens immediately upon contact with the paper. Despite these bacteriocidal and virucidal properties, FTAÔ treated matrix is considered non-toxic to humans and hypoallergenic. All of the components that make up FTAÔ are natural metabolites and/or have a long history of human use.

FTAÔ is Stable. The unique properties of FTAÔ treated matrix have been designed to protect and stabilize DNA from both microbial and environmental forms of degradation. In studies conducted by Dr. Burgoyne and Dr. Arthur Eisenberg, University of North Texas-Ft. Worth, specimens collected on FTAÔ were shown to be offered significant protection when exposed to the harmful effects of UV light, ozone and conditions of high humidity. FTAÔ also guards against degradation due to oxidation, the effects of acidic atmospheric gases, and completely prevents colonization by heterotrophic bacteria, fungus and mold.

FTAÔ is Transportable. The FTAÔ treated stain card and accompanying mailing system (also available from FITZCO, Inc.) offers the safest and most cost-efficient method available for the transport of DNA specimens. This unique system is the only one of its’ kind that has been formally approved by the U.S. Postal Service. The system consists of an FTAÔ card, a 7-layer Multi-Barrier Pouch, and an ordinary flat cardboard mailer. Transport of bio-hazardous materials in this simplified manner is only made possible through the unique characteristics attributed to FTAÔ; namely the eradication of pathogens, the prevention of bacterial and fungal growth, and the complete immobilization of the DNA within the stain card.

FTAÔ is a Technical Tool. As specimens are collected on FTAÔ paper, the DNA is securely bound and completely immobilized within the matrix. This aspect allows for the rapid in-situ purification of DNA to be performed directly on the paper, eliminating the need for lengthy extractions. Conventional steps such as long processing times, vortex mixing, boiling and centrifugation are totally uneccessary. A simple wash removes contaminants, with the strong advantage that the clean-up process can be easily and accurately monitered by noting the color intensity of the heme remaining. DNA remains immobilized within the paper during purification, eliminating the potential for cross-contamination between samples being prepared simultaneously. There is no handling of DNA in solution, thereby eliminating potential losses due to pipette malfunction or adsorption effects. DNA purification by the FTAÔ method can produce PCR or RFLP quality DNA in 30 minutes time or less. Although optimized for DNA technology, FTAÔ has also been shown to be amenable to non-DNA testing methods, such as protein or immunological-based assays.

FTAÔ is an Archiving Tool. FTAÔ was designed with long-term storage in mind. The protection from environmental insults and micro-organisms allow for room temperature archiving, eliminating the need for special handling requirements or refrigeration. Storage studies (Dr. Burgoyne) were performed on blood samples spotted on FTAÔ treated paper and archived at room temperature at intervals of 6 months, 4.5 years, 5.1 years, 7 years and 8.5 years. In all instances, results were obtained that gave clear, consistent and robust PCR amplification signals. No special strategies were required to recover the signals. (4) Successful RFLP studies carried out after one and two years of ambient storage also have substantiated the stability factor afforded by FTAÔ.

FTAÔ is Automatable. The ‘front-side’ of DNA processing, that is, the preparation of specimens for PCR or RFLP testing, has historically been the limiting step when attempting to process large numbers of samples. FTAÔ matrix-bound processing has made possible the development of a completely automated system for the isolation and purification of DNA from whole blood. Using a standard sized 96-well microtitre plate with FTAÔ treated paper incorporated, robotic workstations have demonstrated the capability of preparing literally thousands of samples per day in a consistent and reliable manner.

FTAÔ has been shown to be amenable to most forms of investigation that incorporate PCR amplification or RFLP-based assays. FTAÔ has been utilized in a number of diverse genetic disciplines and applications, including but not limited to: Human genetic research, paternity testing, population genetics, cancer screening, tissue typing, neonatal screening (both DNA and non-DNA-based), epidemeological studies, mitochondrial characterizations, human genomic disease screening and diagnostics, veterinary genetic research and diagnostics, bacterial identification, food contaminant testing, agricultural genetics, environmental testing. forensic science DNA identification which includes, of course, a ‘hard’ back-up for criminal/repeat offender databases (CODIS).

It should be pointed out that routine, non-DNA-based tests, such as those performed in neonate screening programs, often employ enzymes and/or antibodies to detect trace metabolites in blood and other body fluids. Although FTAÔ will inactivate and denature these assay agents, this ‘FTAÔ effect’ can be very simply and conveniently neutralized, making the FTAÔ matrix agreeable for use with otherwise sensitive test-antibodies or test-enzymes. (Patent pending- Dr. Burgoyne)

This analysis considered the following areas: sample procurement, transport, storage and processing. A cost-comparison of the FTAÔ Gene Guard System versus the traditional blood vacuum-tubes was performed for each category. The most conservative estimates were used to assure the least-biased result possible. Each item was carefully researched between vendors to find the best cost. The most cost-effective materials were considered for this analysis, and bulk rates were used. The following scenario was assumed for both traditional methods and for the FTAÔ Gene Guard procedures. Alternative scenarios do exist, however, and may differ from one institution to another.

Sample Storage. Estimates for sample storage were based on direct and indirect costs, or "hidden costs". Direct costs for the storage of whole blood included estimates for a 20.2 cu. ft., -80°C upright freezer unit (VWR S Plainfield, NJ.). The interior dimensions were considered to determine the number of racks (hold 16 boxes) and the number of storage boxes (hold 100 tubes) necessary to hold 5,000 samples. Hidden costs for the large refrigeration unit were also calculated. These include maintenance agreements, warranties, and protection systems. Other hidden costs may include the amount of electricity used by the refrigeration unit per year, as well as the value of the square footage the unit occupies. Although these particular costs were not included in the overall cost analysis, they should not be overlooked.

Sample Collection – Peripheral Blood. Blood can be applied directly, from a finger-puncture, to a FTAÔ treated stain card or, if desired, the FTAÔ paper can be loaded from liquid-blood in a tube, using a syringe or pipette. In either case, the ‘spotted’ card is then left to dry on a workbench. The drying time can be accelerated by placing cards in a 60°C incubator or a laminar flow hood. Upon drying, the FTAÔ cards is then placed in a Multi Barrier Pouch (with or without dessicant), which is then inserted into a flat chipboard mailer for transport.

Sample Collection & Transport – Buccal Epithelial. Buccal epithelial cells can be collected using an un-treated foam tipped swab, which is then pressed onto an FTAÔ card. The saliva absorbed into the swab facilitates cell transfer onto the paper. The card is then dried and prepared for transport as described above.

Components used for sample collection with the FTAÔ stain card included a FTAÔ card, Multi-Barrier pouch, lancets, adhesive bandages, and alcohol swabs (alternatively, a foam-tipped applicator). Transport consisted of a chip board mailer (US postal approved), desiccant, and postal rates for five FTAÔ cards (representative of five different people).

Sample Processing. Sample processing is achieved using the FTAÔ reagent and a Harris 2.0mm diameter punch. This analysis was based on the number of samples processed per 500 ml bottle (833 samples). The number of bottles necessary to process 5000 samples were considered in the estimate as well as the cost for the reagents to make TE-4 Buffer. In addition to the materials, personnel time was estimated for sample procurement and processing for both the FTAÔ Gene Guard System and traditional methods. This estimate was based on the actual time to log in 20 samples, as well as aliquot the blood from vaccutainer tubes to cryo-tubes, labeling, protocol time and any additional times not recorded by the manufacturer. Twenty samples were chosen for this time estimate simply because the centrifuge available only holds 20 tubes at one time

The over-all analysis was divided into three parts: sample procurement, sample storage, and sample processing. Table 1 shows the cost assumptions used in the decision analysis-procurement. This table is divided into two parts; direct material costs and transportation costs. Upon first look at sample collection, there is not much of a difference between whole blood collection and FTAÔ blood-stain collection. This is primarily due to the up front cost for the blood stain card. However, this card is then utilized as a storage unit, as well as a technical tool for processing the DNA. Table 2 shows the cost assumptions used in the decision analysis for storage. As expected, the majority of the costs were in the refrigeration units. The estimate of 5,000 samples can be translated into one tube per person. Therefore, if 5 ml of whole blood is collected, and 1.5 ml is used for storage, then there is 3.5 ml to dispose of. If additional tubes per individual are desired for storage, then the amount of materials should be increased proportionally. The amount of space required should also increase. Table 3 shows the cost of sample processing. This estimate was based solely on the cost of the kits, and not consumables.

Although labor was considered in the analysis, it was not directly included in the analysis. Considerations were based on the number of hours a technician spends collecting, logging in the sample, aliquoting the sample, labeling the sample, and then processing. The analysis was estimated based on twenty samples. This number was chosen based on the number of samples a centrifuge would hold. In addition to the time required for sample procurement, the actual processing time of the 20 samples was established. In addition to time claimed by the manufacturer for processing a sample, additional time was taken into consideration. For example, although it is claimed that the column based format is under one hour, the total time to process 20 samples was over 2 hours. This is directly due to the amount of time to add reagents, switch tubes, and even let the centrifuge ramp to a braking stop. These times may not seem that important if processing a small number of samples, however, an extra hour per 20 samples may require hiring another technician for 5,000 CODIS samples. Over all it was estimated when using the column format, the average technician would spend 61 percent of his/her time in extractions, while the same technician could spend 16% isolation, using FTAÔ Gene Guard System. When the cost for materials is considered and the cost for labor is estimated, the average laboratory can save over 50% using the FTAÔ Gene Guard System.

FTAÔ technology will have a significant impact on the cost of sample, transport, processing, and storage. FTAÔ represents a better than 48% reduction in processing time when compared to conventional methods. Similar savings are realized in the transport of samples collected on FTAÔ versus vaccutainer tubes. The most substantial savings are reflected in the ambient storage conditions, eliminating the enormous cost of freezers and freezer maintenance.

Table 1: Cost Assumptions used in the Decision Analysis-Procurement

Table 2: Cost Assumptions used in the Decision Analysis-Storage

Table 3: Cost Assumptions for the Cost Analysis of Processing Samples

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