Methods for concurrently processing multiple biological chip assays

Abstract

Methods for concurrently processing multiple biological chip assays by providing a biological chip plate comprising a plurality of test wells, each test well having a biological chip having a molecular probe array; introducing samples into the test wells; subjecting the biological chip plate to manipulation by a fluid handling device that automatically performs steps to carry out reactions between target molecules in the samples and probes; and subjecting the biological chip plate to a biological chip plate reader that interrogates the probe arrays to detect any reactions between target molecules and probes.

1 . A method for concurrently processing multiple biological chip assays comprising the steps of: 
 (a) providing a biological chip plate comprising a plurality of probe arrays and, surrounding the probe arrays, material resistant to the flow of liquid, thereby forming a plurality of test wells, each test well defining a space for the introduction of a sample;    (b) introducing into each test well test samples from a plurality of different patients, wherein each test sample contains target molecules;    (c) manipulating the biological chip plate with a fluid handling device that automatically performs steps to carry out reactions between target molecules in the test samples and probes in a plurality of the test wells; and    (d) interrogating the probe arrays of the biological chip plate with a biological chip plate reader to detect reactions between target molecules and probes in a plurality of the test wells to generate assay results.    
     
     
         2 . The method of  claim 1  further comprising the step of processing the results with a computer.  
     
     
         3 . The method of  claim 2  wherein the results are processed into an image with the intensity in each region of the image varying according to the binding affinity between targets and probes.  
     
     
         4 . The method of  claim 1  wherein the probes are DNA or RNA molecules.  
     
     
         5 . The method of  claim 4  wherein 
 (a) the reactions are hybridization of target molecules to probes; and    (b) the results provide information regarding the nucleotide sequence of the target molecule.    
     
     
         6 . The method of  claim 5  wherein the assay is the detection or identification of a pathogenic organism.  
     
     
         7 . The method of  claim 6  wherein the pathogenic organism is HIV.  
     
     
         8 . The method of  claim 5  wherein the assay is the detection or identification of a human nucleic acid.  
     
     
         9 . The method of  claim 8  wherein the assay is the detection of a human gene variant.  
     
     
         10 . The method of  claim 9  wherein the human gene variant indicates the existence of, or predisposition to cystic fibrosis, diabetes, muscular dystrophy or cancer.  
     
     
         11 . The method of  claim 1  further comprising controlling the temperature of the samples in the test wells and adding or removing fluids from the test wells at predetermined times.  
     
     
         12 . The method of  claim 1  wherein the target molecule is tagged with a fluorescent marker, a chemiluminescent marker, a light scattering marker or a radioactive marker.  
     
     
         13 . The method of  claim 12  wherein the marker is a fluorescent marker selected from the group consisting of fluorescein, rhodamine, or cyanine.  
     
     
         14 . The method of  claim 12  wherein the fluid handling device and the biological chip plate reader comprise 
 (a) a confocal detection device having a monochromatic or polychromatic light source;    (b) optics for directing an excitation light from the light source at the substrate;    (c) a temperature controller for controlling temperature of the substrate during a reaction; and    (d) a detector for detecting fluorescence emitted by the targets in response to the excitation light.    
     
     
         15 . The method of  claim 1  wherein the manipulating step comprises robotically controlling pipets for adding or removing fluids from the test wells at predetermined times.  
     
     
         16 . The method of  claim 14  wherein the detector comprises a photomultiplier tube.  
     
     
         17 . The method of  claim 14  wherein the interrogating step comprises focusing the excitation light to a point on the plate and determining the region from which the fluorescence originated.  
     
     
         18 . The method of  claim 14  wherein the target is tagged with a fluorescent marker and the biological chip plate reader comprises a CCD array.  
     
     
         19 . The method of  claim 1  wherein the probe arrays each have at least about 2500 features.  
     
     
         20 . The method of  claim 1  wherein the probe arrays each have at least about 50,000 features.  
     
     
         21 . The method of  claim 1  wherein said chip plate is made by the steps of mating a wafer comprising a plurality of probe arrays to an array of open ended wells.  
     
     
         22 . The method of  claim 1  wherein the interrogating step comprises the steps of: 
 (a) directing excitation light through a bottom surface of said plate; and    (b) detecting where targets bound on said probe arrays.    
     
     
         23 . The method of  claim 1  wherein the interrogating step comprises determining the on- or off-rates of binding between target molecules in a sample and probes.  
     
     
         24 . The method of  claim 1  wherein the probe arrays are produced by light-directed probe synthesis.  
     
     
         25 . The method as recited in  claim 24  wherein said arrays of probes are made by repeating the steps of: 
 (a) selectively directing light at said surface to remove photoremovable protecting groups; and    (b) selectively coupling monomers to said surface.    
     
     
         26 . The method of  claim 24  wherein the chip comprises a contiguous substrate that comprises a contiguous surface a arrays are attached to the contiguous surface.  
     
     
         27 . The method of  claim 1  wherein each probe array is about 0.25 cm 2 .  
     
     
         28 . The method of  claim 1  wherein each probe array is about 1 cm 2 .  
     
     
         29 . The method of  claim 1  wherein the probe arrays comprise features of about 100 microns on a side.  
     
     
         30 . The method of  claim 1  wherein the probe arrays comprise features of about 20 microns on a side.  
     
     
         31 . The method of  claim 1  wherein the chip comprises a contiguous substrate that comprises a contiguous surface and the plurality of probe arrays are attached to the contiguous surface.