Chemical apparatus and process disinfecting – deodorizing – preser – Control element responsive to a sensed operating condition
Reexamination Certificate
1999-09-08
2002-03-26
Warden, Jill (Department: 1743)
Chemical apparatus and process disinfecting, deodorizing, preser
Control element responsive to a sensed operating condition
C422S091000, C422S105000, C436S043000, C436S047000, C436S063000
Reexamination Certificate
active
06361745
ABSTRACT:
This invention relates to the automatic quantitative scanning of microarrays. It relates more particularly to a microarray storage device for use in an automated microarray handling system.
BACKGROUND OF THE INVENTION
Microarrays are arrays of very small samples of purified DNA or protein target material arranged as small spots, usually in the order of 100-200 microns in diameter, on a solid substrate. The spots in the array are exposed to complimentary genetic or protein probe samples derived from cells that have been tagged with fluorescent dyes. The probe material binds selectively to target spots only where complimentary bonding sites occur from a process called hybridization. In other words, probe molecules with a similar sequence to the target will bind or hybridize to the target molecules. Dissimilar probe molecules will not bind to the target molecules and will be washed away in a subsequent rinsing process. By measuring the quantity of bound probe molecules, a researcher can determine the likeness between the probe and the target molecules. This technique is used to measure a variety of biological characteristics including gene expression, genotype and gene sequence.
Hybridization experiments must be conducted in large quantities in order to be generally useful. For example, there are approximately one hundred thousand genes in the human genome, several thousand of which are considered in a typical study. Technologies have been developed to allow massively parallel hybridization experiments to be performed on DNA on a very large number of samples comprising a microarray.
In a typical hybridization experiment, the reference DNA is spotted onto a substrate, typically a glass slide similar to a microscope slide. The DNA is mixed with a liquid buffer to form a solution that is laid down on the substrate in droplets. The surface of the substrate is treated to control the size of the spots resulting from the drops and to chemically bind the DNA to the substrate. When the microarray dries, it is left with an ordered array of reference DNA samples bound to its surface.
Such spotting is accomplished by using an instrument called an arrayer which is a robotic device that can spot forty to a hundred microarrays on a substrate or slide in an automated fashion. Typical spotting times are in the range of eight minutes per slide, the substrates or slides being manually loaded and removed from the arrayer.
The next step in the microarray process is to introduce the fluorescently labeled probe DNA. The DNA is mixed in a buffer solution and placed onto the surface of the microarray. A thin piece of glass is then used to sandwich the probe between it and the substrate or slide which causes the probe DNA to spread across the region of the microarray that contains the target DNA.
Next the target and probe are hybridized by putting the microarray into a humid, thermally controlled environment and baking at temperatures ranging from 40-60° C. for periods ranging from thirty minutes to twelve hours depending on the nature of the experiment. During this stage, target and probe molecules with similar structures bind.
After hybridization, the glass cover is removed and the microarray is rinsed to wash away any probe DNA that did not bind to the target DNA.
Finally, the microarray is imaged. For this, the microarray is manually loaded into an imager or scanner where the probe DNA is illuminated by light which excites the fluors in the probe DNA causing the fluors to fluoresce. The brightness of each specimen or spot in the microarray is a function of the fluor density in that specimen or spot. The fluor density is, in turn, a function of the binding affinity or likeness of the probe molecule to the target molecule for each spot. Therefore, the brightness of each spot can be mapped to the degree of similarity between the probe DNA and the target DNA in that spot or sample. In a typical microarray, up to tens of thousands of experiments can be performed simultaneously on the probe DNA allowing for a detailed characterization of complex molecules.
As can be appreciated, performing the above described microarray process manually is costly and time consuming. A researcher or technician is required to handle each microarray at every step in the process, i.e. spotting, hybridization, washing and imaging. The imaging process is particularly labor intensive because each slide is inserted by hand into the imager for single slide imaging while the user waits to load the next slide. The situation becomes acute for high volume users which process several hundred microarrays a day. They will need to hire several technicians just to keep up with the imaging. Thus, there is a need to reduce the amount of handling required to process microarrays and indeed, to process the microarrays in batches.
Also microarrays are susceptible to damage if they are not stored properly. Everything from dust to light can affect the data that is gleaned from the microarrays. Therefore, there is a need for a way to properly store microarrays so that they are not degraded or damaged over time.
We should mention that there do exist mechanisms for loading microscope slides bearing biomedical samples, such as Pap smears, into microscopes; see e.g., U.S. Pat. Nos. 4,367,915 and 5,690,892.
The former patent describes a system which uses two separate mechanisms for loading slides into, and unloading them from, a cassette or magazine. The magazine is indexed to position each specimen slide for access by a horizontal feed mechanism which transfers the specimen slide onto a microscope stage which has controllable X,Y and Z axes to move the specimen slide into the optical viewing field of the microscope. A duplicate mechanism on the other side of the microscope returns the slide to the magazine.
The latter patent describes a system wherein specimen slides are removed from a magazine or cassette by a shuttle which reaches under each slide and lifts up to engage the slide using a complex motion. The weight of the slide is used to keep it in place on the shuttle mechanism, limiting the acceleration that can be applied and the friction forces that can be overcome when transferring the slide to another mechanism. The slides are then passed to a second mechanism which changes the direction of motion of travel into and out of an associated microscope.
Aside from being designed for use with biomedical samples instead of fluorescent microarrays, those prior loading/unloading mechanisms exhibit a great deal of complexity which results in increased size, decreased reliability and increased cost.
There also exist automated microarray scanning or imaging apparatus which use substrate storage cassettes or magazines. Such apparatus do include mechanisms for holding multiple microarrays. However, they invariably require that each substrate or slide be placed in a metal sub-frame or clip prior to loading it into the storage mechanism or magazine. Both the substrate and the frame are then moved into the scanning field of the apparatus and subsequently scanned. However, as throughput demands increase for microarray processing, this sub-frame approach becomes limiting because of the added manual labor required to place each microarray into a sub-frame. Further, the user needs to gather multiple sub-frames to process a batch of microarrays. The sub-frames also increase the amount of space required by each microarray in the magazine or cassette placing an upper limit on the number of microarrays that can be stored in a magazine of reasonable size.
Currently there are no microarray magazines or cassettes that can be used both as a common interface for different types of microarray processing equipment and as a storage device for a batch of microarrays allowing a user to queue batches of microarrays in such storage devices and protect them when they are stored.
SUMMARY OF THE INVENTION
Thus, an object of the invention is to provide a microarray storage device for use with an automated microarray handling system which can be used as a common platform microarray stor
Doane Sean R.
Gyorke, Jr. George
Milkowski Robert T.
Regan Donald T.
St. Cyr Paul L.
Cesari and McKenna LLP
Gakh Yelena
Packard Instrument Company Inc.
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