System and method for multidimensional evaluation of combinations of compositions
First Claim
1. A method for evaluating an activity of each member of a set of combined compositions, each member of the set being a combination of a common plurality of constituent compositions, the method comprising:
- providing, for each constituent composition, a constituent array of locations, each location associated with a specific concentration of such constituent composition, the arrays having a number corresponding to the plurality of constituent compositions;
providing an assay array of locations, each location of the assay array corresponding to a member of the set and being associated with a designated aliquot from each of the constituent arrays, wherein each aliquot is one of zero and non-zero; and
evaluating the activity of the combined composition at each location of the assay array.
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Abstract
Embodiments of the invention are directed toward methods and devices for constructing assay arrays including a combination of constituent compositions from constituent arrays. The combined compositions are evaluated, in some embodiments of the invention, to identify combinations with a combination effect. Other embodiments of the invention are directed toward constructing constituent arrays in various configurations to facilitate the production of assay arrays. Such embodiments include: constructing constituent arrays and assay arrays with corresponding composition and assay control sets; constructing constituent arrays with a unique set of origin locations and corresponding sets of derivative locations; varying the concentrations utilized for a constituent composition; and composing assay arrays corresponding to a virtual sparse assay array. Other embodiments of the invention are directed towards systems and method of evaluating the activity of combined compositions in an assay array.
40 Citations
151 Claims
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1. A method for evaluating an activity of each member of a set of combined compositions, each member of the set being a combination of a common plurality of constituent compositions, the method comprising:
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providing, for each constituent composition, a constituent array of locations, each location associated with a specific concentration of such constituent composition, the arrays having a number corresponding to the plurality of constituent compositions;
providing an assay array of locations, each location of the assay array corresponding to a member of the set and being associated with a designated aliquot from each of the constituent arrays, wherein each aliquot is one of zero and non-zero; and
evaluating the activity of the combined composition at each location of the assay array. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98)
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99. A method of evaluating the activity of a set of compositions in an array, the method comprising:
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determining a measured value for each location of a set of compositions, for each of a plurality of sets of the array, pertinent to the activity thereof, wherein each set of the array includes substantially the same set of compositions arranged in corresponding locations;
for each of the locations of the sets of the array, determining predicted values of activity according to each of a plurality of models; and
determining the activity of the set of compositions based upon the measured values and predicted values using at least one statistical method. - View Dependent Claims (100, 101, 102, 103, 104, 105, 106, 107)
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108. An assay array having a set of combined compositions, each member of the set being a combination of a common plurality of constituent compositions, the assay array comprising:
an array of locations, each location corresponding to a member of the set and being associated with a designated aliquot from each of a plurality of constituent arrays, each constituent array having locations holding a specific concentration of a constituent composition, the constituent arrays having a number corresponding to the plurality of constituent compositions, each aliquot is one of zero and non-zero.
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109. An assay array having a set of combined compositions, each member of the set being a combination of a common plurality of constituent compositions, the assay array comprising:
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an array of locations, each location corresponding to a member of the set and being associated with a designated aliquot from of a specific concentration of a constituent composition, each aliquot is one of zero and non-zero, wherein a particular concentration of at least one constituent composition in the assay array is designated based upon activity data of the at least one constituent composition. - View Dependent Claims (110, 111, 112, 113, 114, 115, 116, 117, 118)
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119. An assay array having a set of combined compositions, each member of the set being a combination of a common plurality of constituent compositions, the assay array comprising:
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an array of locations, each location corresponding to a member of the set and being associated with a designated aliquot from of a specific concentration of a constituent composition, each aliquot is one of zero and non-zero, wherein at least one concentration of a particular constituent composition in the assay array is not combined with every concentration of a different constituent composition in the assay array. - View Dependent Claims (120)
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121. A plurality of arrays for evaluating an activity of each member of a set of combined compositions, each member of the set being a combination of a common plurality of constituent compositions, the plurality of arrays comprising:
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for each constituent composition, a constituent array of locations, each location associated with a specific concentration of such constituent composition, the constituent arrays having a number corresponding to the plurality of constituent compositions, each location of any constituent array having a corresponding location in any of the other constituent arrays;
an assay array of locations, each location of the assay array corresponding to a member of the set and being associated with a designated aliquot from each of the constituent arrays, each aliquot is one of zero and non-zero; and
an assay control in each location of an assay control set of the assay array, wherein each location of the assay control set has a corresponding location in each constituent array. - View Dependent Claims (122, 123, 124)
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125. A plurality of constituent arrays for producing an assay array, each constituent array comprising:
an array of locations for holding a constituent composition, each location associated with a specific concentration of such constituent composition, the constituent arrays having a number corresponding to the plurality of constituent compositions, each constituent array including;
(i) an origin set of unique locations, each origin set location associated with a quantity of constituent composition associated with such array; and
(ii) for each location of the origin set, a derivative set of unique locations, each location of a specific derivative set having a portion of constituent composition obtained from a location of the origin set. - View Dependent Claims (126, 127, 128, 129, 130, 131, 132, 133)
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134. A plurality of arrays for evaluating an activity of each member of a set of combined compositions, each member of the set being a combination of a common plurality of constituent compositions, the plurality of arrays comprising:
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for each constituent composition, a constituent array of locations, each location associated with a specific concentration of such constituent composition, the constituent arrays having a number corresponding to the plurality of constituent compositions, each location of any constituent array having a corresponding location in any of the other constituent arrays;
an assay array of locations, each location of the assay array corresponding to a member of the set and being associated with a designated aliquot from each of the constituent arrays, each aliquot is one of zero and non-zero; and
a composition control in each location of a composition control set, wherein the composition control set of each constituent array is disposed so that all locations of the composition control set of a given constituent array are distinct from any locations of such constituent array that correspond to locations of the composition control set in any other constituent array, the locations of all composition control sets having a corresponding location in the assay array. - View Dependent Claims (135, 136, 137, 138, 139, 140)
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141. A computer program product for use on a computer system for evaluating a combination effect in a plurality of locations of an assay array, the computer readable program code including:
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(a) a module for collecting an evaluated activity in the plurality of locations of the assay array;
(b) program code for providing a measure value in the plurality of locations of the assay array, the measure values based upon the evaluated activity in the plurality of locations;
(c) program code for providing a predicted value for each of the plurality of locations of the assay array, the predicted values based upon a model; and
(d) program code for evaluating a combination effect for each of the plurality of locations of the assay array, the evaluation based upon the measured values and predicted values. - View Dependent Claims (142, 143, 144, 145, 146, 147, 148, 149, 150, 151)
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Specification