Single-particle analysis of particle populations
First Claim
1. A method of producing a data set comprising a plurality of parameters for single particles in a plurality of particles, wherein each of said single particles comprises one or more target nucleic acids, said method comprising:
- capturing particles of said plurality of particles in separate compartments of a microfluidic device, thereby producing a plurality of separate reaction volumes in the separate compartments of the microfluidic device such that at least 35% of said separate reaction volumes comprise only a single particle of said plurality of particles, the separate compartments being arranged as an array defined by rows and columns;
determining which of said separate reaction volumes comprise only a single particle of said plurality of particles by microscopy and/or using a stain, dye, or label;
performing a plurality of reactions in each of said separate reaction volumes, thereby producing a plurality of reaction products in each of said separate reaction volumes, wherein at least one reaction of the plurality of reactions in each of said separate reaction volumes comprises a nucleic acid amplification reaction that produces at least one amplicon in each of said separate reaction volumes,wherein the at least one amplicon in each of said separate reaction volumes is produced using amplification primers, wherein each of at least two of the amplification primers comprises a barcode nucleotide sequence, the at least one amplicon comprising a combination of the barcode nucleotide sequence from each of the at least two of the amplification primers,wherein the combination of the barcode nucleotide sequence from each of the at least two amplification primers in the at least one amplicon in each of said separate reaction volumes identifies the row and column of a compartment of the separate compartments of the microfluidic device and thereby identifies the source of the at least one amplicon;
recovering the reaction products, comprising the at least one amplicon from each of said separate reaction volumes by pooling the reaction products from each of the separate reaction compartments, thereby producing pooled reaction products;
obtaining analysis results by analyzing the pooled reaction products;
generating analysis results for the single particles in the plurality of particles by disregarding the analysis results from said separate reaction volumes that contain no particle of said plurality of particles or contain more than one single particle of said plurality of particles; and
producing the data set comprising the plurality of parameters for the single particles in the plurality of particles by associating the analysis results for the single particles in the plurality of particles with each of said separate reaction volumes that comprise only a single particle of the plurality of particles.
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Abstract
In certain embodiments, the invention provides methods and devices for assaying single particles in a population of particles, wherein at least two parameters are measured for each particle. One or more parameters can be measured while the particles are in the separate reaction volumes. Alternatively or in addition, one or more parameters can be measured in a later analytic step, e.g., where reactions are carried out in the separate reaction volumes and the reaction products are recovered and analyzed. In particular embodiments, one or more parameter measurements are carried out “in parallel,” i.e., essentially simultaneously in the separate reaction volumes.
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Citations
46 Claims
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1. A method of producing a data set comprising a plurality of parameters for single particles in a plurality of particles, wherein each of said single particles comprises one or more target nucleic acids, said method comprising:
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capturing particles of said plurality of particles in separate compartments of a microfluidic device, thereby producing a plurality of separate reaction volumes in the separate compartments of the microfluidic device such that at least 35% of said separate reaction volumes comprise only a single particle of said plurality of particles, the separate compartments being arranged as an array defined by rows and columns; determining which of said separate reaction volumes comprise only a single particle of said plurality of particles by microscopy and/or using a stain, dye, or label; performing a plurality of reactions in each of said separate reaction volumes, thereby producing a plurality of reaction products in each of said separate reaction volumes, wherein at least one reaction of the plurality of reactions in each of said separate reaction volumes comprises a nucleic acid amplification reaction that produces at least one amplicon in each of said separate reaction volumes, wherein the at least one amplicon in each of said separate reaction volumes is produced using amplification primers, wherein each of at least two of the amplification primers comprises a barcode nucleotide sequence, the at least one amplicon comprising a combination of the barcode nucleotide sequence from each of the at least two of the amplification primers, wherein the combination of the barcode nucleotide sequence from each of the at least two amplification primers in the at least one amplicon in each of said separate reaction volumes identifies the row and column of a compartment of the separate compartments of the microfluidic device and thereby identifies the source of the at least one amplicon; recovering the reaction products, comprising the at least one amplicon from each of said separate reaction volumes by pooling the reaction products from each of the separate reaction compartments, thereby producing pooled reaction products; obtaining analysis results by analyzing the pooled reaction products; generating analysis results for the single particles in the plurality of particles by disregarding the analysis results from said separate reaction volumes that contain no particle of said plurality of particles or contain more than one single particle of said plurality of particles; and producing the data set comprising the plurality of parameters for the single particles in the plurality of particles by associating the analysis results for the single particles in the plurality of particles with each of said separate reaction volumes that comprise only a single particle of the plurality of particles. - 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)
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Specification