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(12) United States Patent
Kureshy et al.
(io) Patent No.: (45) Date of Patent:
US 7,776,195 B2 Aug. 17, 2010
(54) INTEGRATED SAMPLE PROCESSING PLATFORM
(75) Inventors: Fareed Kureshy, Del Mar, CA (US);
Vijay K. Mahant, Murrieta, CA (US);
Shailendra Singh, Carlsbad, CA (US)
(73) Assignee: Autogenomics, Inc., Carlsbad, CA (US)
( * ) Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 U.S.C. 154(b) by 1017 days.
(21) Appl.No.: 10/513,459
(22) PCT Filed: May 28, 2003
(86) PCT No.: PCT/US03/16905
§ 371 (c)(1),
(2), (4) Date: Nov. 2, 2004
(87) PCT Pub. No.: WO03/100380 PCT Pub. Date: Dec. 4, 2003
(65) Prior Publication Data
US 2005/0233437 Al Oct. 20, 2005
Related U.S. Application Data
(60) Provisional application No. 60/383,896, filed on May 28, 2002.
(51) Int. CI.
G01N 27/26 (2006.01)
(52) U.S. CI 204/435; 435/6
(58) Field of Classification Search None
See application file for complete search history.
(56) References Cited
U.S. PATENT DOCUMENTS
6,150,173 A 11/2000 Schubert
6,207,031 Bl* 3/2001 Adourian et al 204/451
6,355,423 Bl * 3/2002 Rothberg et al 435/6
6,511,849 Bl* 1/2003 Wang 436/47
6,838,051 B2* 1/2005 Marquissetal 422/63
6,875,619 B2* 4/2005 Blackburn 506/9
2003/0186228 Al * 10/2003 McDevittetal 435/6
FOREIGN PATENT DOCUMENTS
WO 00/66269 11/2000
* cited by examiner
Primary Examiner—Jeffrey S. Lundgren
(74) Attorney, Agent, or Firm—Fish & Associates, PC
An integrated desktop analytic device comprises a fluidics station coupled to a confocal microscope detector, and a biochip is moved from the fluidics station to the detector without manual intervention of an operator.
9 Claims, 2 Drawing Sheets
INTEGRATED SAMPLE PROCESSING
This application is a 35 USC 371 application of international patent application with the Ser. No. PCT/US03/16905, filed May 28, 2003, which claims the benefit of U.S. provisional patent application with the Ser. No. 60/383,896, filed May 28, 2002, and which further claims the benefit of international patent application with the Ser. No. PCT/US02/ 17006, filed May 29, 2002, both of which are incorporated herein by reference.
FIELD OF THE INVENTION
The field of the invention is automated desktop analytic 15 devices, especially for use in high-throughput screening.
BACKGROUND OF THE INVENTION
Recent advances in genomics and proteomics made a vast 20 number of nucleotide and peptide sequences available for analysis, and high-throughput screening of samples for the presence and/or quantity of numerous known genes or polypeptides has gained considerable interest in recent years. While all or almost all of the individual steps or processes in 25 high-throughput screening are well known in the art, integration of such steps or processes into a single analytic device remains a challenge. Among other difficulties and depending on the particular detection method employed, handling requirements for fluid management (e.g., sample application, 30 hybridization, stringency washing) and detection (e.g., electronic or optical detection) are often incompatible where a single platform is employed.
For example, where binding of an analyte is electronically detected, (e.g., Nanogen's Nanochip®) various steps, includ- 35 ing capture probe loading, analyte binding, and washing of the chip are performed in one station (e.g., Nanochip® Loader), while binding analysis is performed in a separate detector station (e.g., Nanochip® Reader). Electronic detection often allows multiple reuse of a biochip, and typically 40 exhibits significantly accelerated analyte binding. However, due to the separation of the fluidics station and the detection station, the operator must manually transfer the chip from one station to the other, requiring proper insertion and operator control to commence detection, which at least somewhat 45 defies the concept of automated high-throughput analysis.
Similarly, where binding of an analyte is optically detected, various biochips are commercially available as arrays of capture probes disposed on a microscope glass slide. Detection of labeled analytes that are bound to the capture 50 probes is then performed with a flatbed scanner that typically acquires fluorescence data from the array on the surface of the slide. High-throughput analysis of such arrays is often relatively inexpensive. However, various disadvantages remain. Among other things, true signals are frequently not acquired 55 where the surface of the glass slide is uneven. Moreover, manual operation of such slides may result in inadvertent damage to the array. Still further, fluidics management (e.g., hybridization, washing, etc.) is generally performed in one or more devices that are separate from the detector, and there- 60 fore again require user manual intervention.
To circumvent at least some of the problems associated with arrays on a glass slide, binding of the analyte may be optically detected in a chip that is disposed in a housing (e.g., Genechip by Affymetrix). A housing advantageously protects 65 the biochip from inadvertent damage, and may further control flow of fluids (e.g., volume and/or flow control). However,
such systems generally require processing the chip in a fluidics/hybridization station for binding and washing of an analyte that is bound to the capture probes, while analyte binding is detected in a separate detector. Again, an operator 5 needs to manually insert the chip into the detector and select the suitable detection protocol prior to analysis. Furthermore, as is the case with the microscopy slide arrays, detection of the signal typically requires that fluids be completely removed from the chip to prevent quenching of the signal or 10 other undesirable optical effects.
In another approach for high-throughput screening, multiwell plates may be used in a robotic station that automatically transfers a multi-well plate from a fluidics station to a plate reader station (see e.g., robotic stations from Beckman, Hudson, Hamilton, Gilson, Perkin Elmer, or Quiagen). Such robotic stations often integrate fluidics and detection, and employ relatively inexpensive multi-well plates. Moreover, customization of multi-well plates is generally relatively simple and can often be done using the same robotic station. However, robotic stations for multi-well plates generally have a relatively large footprint, especially where several thousand samples per day are processed. Smaller modular systems are also commercially available, however, typically fail to provide integrated sample analysis. Still further, detection of analytes in multi-well based systems is generally limited to microplate readers, which often provide limited accuracy and only perform well in assays where optical detection is not critically impaired by variations in focal depth.
Thus, although various systems for high-throughput screening are known in the art, numerous problems still remain. Therefore, there is still a need for an improved methods and systems for high-throughput screening.
SUMMARY OF THE INVENTION
The present invention is directed to an desktop analytic device for a biochip, wherein fluidics management and confocal microscope signal detection are integrated using a sample processing platform, wherein the platform serves as a basis for fluidics management, and wherein the biochip is moved along the x- and/or y-coordinate from the platform to the detector without manual user intervention.
In one aspect of the inventive subject matter, the desktop analytic device includes a substantially horizontal sample processing platform that receives a biochip that is at least partially enclosed in a housing, wherein the biochip is at least partially immersed by a fluid that is retained by the housing, wherein the biochip binds an analyte from the fluid, and wherein the fluid further comprises a non-analyte. An energy source (e.g., heater, cooling element, or ultrasound source) is functionally coupled to the platform and delivers energy to the fluid in the biochip, and a confocal microscope detector is coupled to the platform such that a substantially horizontal transport path is formed between the detector and the platform, wherein the biochip is moved in a sliding motion from the platform to the detector using the transport path. It should be especially noted that in such devices the biochip is moved within the desktop analytic device without manual intervention of an operator from the platform to the detector while the analyte is bound to the biochip, and that the sample processing platform and the detector are enclosed in the desktop analytic device.
In particularly preferred devices, movement of the biochip from the platform to the detector is caused by an actuator that pushes the biochip along at least one of an x-coordinate and a y-coordinate, and it is still further preferred that the biochip is further transported from a multi-biochip magazine to the