Radiant energy – Luminophor irradiation
Reexamination Certificate
1998-08-07
2001-05-01
Hannaher, Constantine (Department: 2878)
Radiant energy
Luminophor irradiation
C250S374000
Reexamination Certificate
active
06225635
ABSTRACT:
BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention relates generally to systems and methods for locating microchannel positions, and more particularly for optically locating microchannel positions as part of a scanning DeoxyriboNucleic Acid (DNA) sequencer.
2. Discussion of Background Art
DNA sequencing is a technique used in conjunction with a national plan to decode the human genome in as little time as possible. The human genome is a very complex structure containing about three billion nucleic acid “base-pairs.” Current DNA sequencing techniques involve placing DNA fragments onto a slab gel and separating the fragments so that base-pair information can be determined. Electrophoresis is a common technique used to separate the base-pair fragments from each other. The base-pairs can then be identified by various optical techniques that involve collecting a series of data points across the slab gel.
In efforts to speed up base-pair identification glass plates, having a set of microchannels, enable separation of several groups of DNA fragments in parallel. This technique requires collection of a very large number of optical measurement. Twelve-hundred to three-thousand data points may be taken during a single scan across such glass plates. A total amount of data taken for the entire glass plate may run in the one to eight gigabyte range.
Due to the large amount of data involved, modern DNA sequencers employ scanning devices and computers to collect the data. However, when the microchannel plates are not placed in their holders the same way each time, or plates with different microchannel formats are used, the computer controlled scanning devices will not work as intended. Furthermore, motors which drive the sequencer scanning devices often vary in speed and suffer from hysteresis, preventing accurate motor positioning during a scan. All of these effects hinder test result reproducibility, and limit efforts to reduce the amount of data collected.
In response to the concerns discussed above, what is needed is a system and method for optically locating a microchannel position that overcomes the problems of the prior art.
SUMMARY OF THE INVENTION
The present invention is a system and method for optically locating microchannel positions. Within the system of the present invention, a laser source generates a primary laser beam which is directed at a microchannel plate. The microchannel plates include microchannels at various locations. A back-reflectance beam detector receives a back-reflected beam from the plate. The back-reflected beam is generated when the primary beam reflects off of the plate. A photodiode circuit generates a trigger signal when the back-reflected beam exceeds a predetermined threshold, indicating a presence of a microchannel.
In another aspect of the invention, the photodiode circuit generates the trigger signal when the back-reflected beam exceeds a level corresponding to a gel-glass interface and falls below a level corresponding to an air-glass interface.
In another aspect of the invention, the photodiode circuit generates the trigger signal when the back-reflected beam exceeds a level corresponding to a glass-glass interface and falls below a level corresponding to a gel-glass interface.
And, in yet another aspect of the invention, the system collects and stores an entire set of back-reflectance beam data. A computer then analyzes the stored data to determine microchannel positions, using one or more of the techniques described above for generating trigger signals.
The method of the present invention includes the steps of generating a primary beam, directing the primary beam to a plate containing a microchannel, receiving from the plate a back-reflected beam generated in response to the primary beam, and generating a trigger signal when the back-reflected beam exceeds a predetermined threshold which corresponds to a presence of the microchannel.
In another aspect of the invention, the method further includes the steps of setting the predetermined threshold level below a back-reflected beam generated from an air-glass interface, and above a back-reflected beam generated from a gel-glass interface.
In another aspect of the invention, the method further includes the steps of setting the predetermined threshold level below a back-reflected beam generated from a gel-glass interface, and above a back-reflected beam generated from a glass-glass interface.
In another aspect of the invention, the method further includes the steps of receiving from the plate a fluorescence beam generated in response to the primary beam, and collecting a predetermined amount of fluorescence beam data in response to the trigger signal.
In a second embodiment of the invention, the method includes the steps of generating a primary beam, directing the primary beam to a plate containing a microchannel, receiving from the plate a back-reflected beam generated in response to the primary beam, collecting a predetermined amount of back-reflected beam data, and determining a position of the microchannel by analyzing the back-reflected beam data.
In the second embodiment of the invention, the method further includes the steps of receiving from the plate a fluorescence beam generated in response to the primary beam, collecting a predetermined amount of fluorescence beam data, and analyzing those fluorescence beam data points near the position of the microchannel.
The system and method of the present invention are particularly advantageous over the prior art because fluorescence data need only be taken when an optical detector of a DNA sequencer is positioned over the microchannels. This can reduce an amount of data that needs to be collected to perform DNA sequencing. Hysteresis and scanning velocity variation effects on data collection are also reduced. With the present invention, the position of the microchannels may be located even if the microchannel plate is not always placed in a same location.
These and other aspects of the invention will be recognized by those skilled in the art upon review of the detailed description, drawings, and claims set forth below.
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Balch Joseph
Brewer Laurence R.
Davidson J. Courtney
Kimbrough Joseph
Dakin, Jr. Lloyd E.
Gabor Otilia
Hannaher Constantine
Horgan Christopher J.
The Regents of the University of California
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