Spotting pattern for placement of compounds in an array
First Claim
1. An array of n unique materials, each of which appears in the array at least two times and which has a plurality of neighboring materials, wherein for each of the n materials in the array, the neighboring materials in one occurrence of the material are different from the neighboring materials of all other occurrences of the material, wherein n is greater than 25:
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Accused Products
Abstract
A plurality of samples of different substances are tested for their ability to enhance or inhibit a biological process. The samples are deposited on a supporting surface, such as a ChemCard, in an array comprising at least two dots of each sample, wherein at least one of the dots of each sample is at least a predetermined distance from at least one of the dots of each of the plurality of samples. One or more assay reagents in a gel sheet, for example, are then brought in contact with the compounds and reactions with certain of the compounds are evident as the active compounds diffuse into the one or more assay reagents. The concept of having unique neighbors for each occurrence of a dot allows the definitive correlation of active compounds with the dot (and the compound) that caused the biological activity.
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Citations
50 Claims
- 1. An array of n unique materials, each of which appears in the array at least two times and which has a plurality of neighboring materials, wherein for each of the n materials in the array, the neighboring materials in one occurrence of the material are different from the neighboring materials of all other occurrences of the material, wherein n is greater than 25:
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17. A method of testing a plurality of samples of different substances for their ability to enhance or inhibit a biological process, the method comprising:
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providing an array of at least two dots of each of said samples on a planar matrix such that each of said at least two dots is centered at its own distinct site, wherein at least one of said at least two dots of each of said samples is at least a predetermined distance from at least one of said dots of each of said plurality of samples;
transferring the array from the planar matrix into a uniformly dispersed assay reagent; and
observing the interaction of each of said substances with said assay reagent and correlating said interaction with an ability of each of said substances to enhance or inhibit said biological process. - View Dependent Claims (18, 19, 20, 21, 22)
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23. A method of testing a plurality of samples of different substances for their ability to enhance or inhibit a biological process, the method comprising:
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depositing in an array at least one dot of each of said samples onto a plurality of planar matrixes such that each of said at least one dot is centered at its own distinct site, wherein at least one of said dots of each of said samples is at least a predetermined distance from at least one of said dots of each of said plurality of samples;
transferring the array of samples from the plurality of planar matrixes into a uniformly dispersed assay reagent; and
observing the interaction of each of said substances with said assay reagent and correlating said interaction with an ability of each of said substances to enhance or inhibit said biological process.
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24. A system for creating an array of sample compounds comprising:
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a relatively flat carrier configured to support a plurality of samples; and
a dispensing mechanism configured to dispense at least two dots of each of said plurality of samples of different compounds on said flat carrier such that each of said at least two dots of each of said plurality of samples has a different set of neighboring compounds within a predetermined distance. - View Dependent Claims (25, 26, 27, 28, 29, 30)
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31. An array of samples in which each sample appears at least twice and there are at least 768 dispenses of groups of 12 samples.
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32. An array of samples in which each sample appears at least twice and there are at least 4608 samples, wherein the array comprises 144 columns and 64 rows and the samples are arranged substantially according to the relative coordinates shown in Table 1.
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33. A method for performing an assay, comprising:
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providing a substantially planar substrate having an array of at least two dots of each of a plurality of test materials, wherein each of said dots has a plurality of neighboring test materials and is placed such that the neighboring materials in one occurrence of the material are different from the neighboring materials of all other occurrences of the material; and
transferring the array of test materials into a uniformly-dispersed assay reagent that participates in indicating which of the test materials are active in the assay while maintaining the relative positioning of the test materials vis-a-vis each other. - View Dependent Claims (34, 35, 36, 37, 38)
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39. An algorithm for formulating an array S having A elements (SA), wherein the value of each element SA represents a dispense position on a card, wherein a dispensing mechanism dispenses a plurality of compounds at each dispense position, the algorithm comprising:
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(a) setting each of the A elements of the array S to a random, non-repeating value from 1- A, wherein each SA is set to a preliminary dispense position;
(b) providing an array C having A elements (CA), wherein each of said A elements of the array C comprises J representations of compounds;
(c) setting a counter x to zero;
(d) incrementing x by 2;
(e) determining whether each of said J compounds in CX satisfy a placement constraint with respect to certain other compounds in the array C;
(f) if step (e) determines that there in a constraint violation with one or more of said J compounds in Cx;
(1) decrementing x by 2;
(2) determining if there are remaining dispense positions that have not been tested in SX against the constraints of step (e);
(3) if step (2) determines that there are no remaining dispense positions that have not been tested in SX against the constraints of step (e), repeating steps (1) and (2);
(4) changing the value of SX to a remaining dispense position that has not been tested in SX against the constraints of step (e);
(5) return to step (e);
(g) if step (e) determines that there is not a constraint violation with any of said J compounds in CX, return to step (d). - View Dependent Claims (40)
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41. A method for creating an array of a plurality of materials, each material occurring at least twice within the array and having different neighboring materials in each occurrence, the method comprising:
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(a) creating a candidate arrangement of materials containing pairs of n said materials in a spatial relationship;
(b) testing whether a first occurrence and a second occurrence of each of said materials have different neighbors;
(c) if the criteria of (b) is not satisfied, changing said spatial relationship of at least some of n said materials; and
(d) repeating steps (b) and (c) until the criteria of (b) is satisfied. - View Dependent Claims (42, 43, 44)
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45. A method for formulating an array S having A elements (SA), wherein the value of each element of SA represents a dispense position for one or more materials on a substrate, wherein each material occurs at least two times (C1 and C2) in SA, with the constraint that when the distance from one of C1 and C2 to any occurrence of any other material is less than or equal to a minimum value D, then the distance from the other of C1 and C2 to any occurrence of such other material is greater than D, comprising:
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tentatively assigning a plurality of elements to SA;
for each first occurrence of a material, determining a set of Q materials that are within a distance of D;
for each second occurrence of a material, ascertaining whether each of the Q materials are within a distance of D and, if so, changing the location of at least one material.
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46. A method for formulating an array containing pairs of materials, wherein each member of the pair has different neighboring materials than the other member of the pair, comprising:
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(a) tentatively assigning a plurality of materials to array locations;
(b) testing to ascertain whether a first member of a pair has different neighboring materials than a second member of a pair, and if not, then (c) sequentially repeating step (a) with at least one altered material location and repeating step (b), until each member of each pair has different neighboring materials. - View Dependent Claims (47, 48, 49)
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50. A method of creating an array of sample compounds comprising:
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providing a relatively flat carrier configured to support a plurality of samples; and
dispensing at least two dots of each of said plurality of samples of different compounds on said flat carrier such that each of said at least two dots of each of said plurality of samples has a different set of neighboring compounds within a predetermined distance.
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Specification