Analysis of nucleic acids
First Claim
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1. A method of detecting variations in copy number of a target nucleic acid, the method comprising:
- a. contacting a sample comprising a plurality of polynucleotides with at least one agent, wherein each of one or more of polynucleotides comprises multiple copies of a target nucleic acid;
b. subjecting the sample to conditions that enable the agent to cleave a specifically-selected target site between the multiple copies of the target nucleic acid, thereby separating the multiple copies from one another;
c. separating the sample contacted with the agent into a plurality of droplets;
d. subjecting the target nucleic acid to an amplification reaction in droplets;
e. detecting amplification data for the target nucleic acid from individual droplets;
f. enumerating a number of droplets comprising the target nucleic acid based on the amplification data; and
g. determining a copy number of the target nucleic acid based on the step of enumerating.
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Abstract
Provided herein are improved methods, compositions, and kits for analysis of nucleic acids. The improved methods, compositions, and kits can enable copy number estimation of a nucleic acid in a sample. Also provided herein are methods, compositions, and kits for determining the linkage of two or more copies of a target nucleic acid in a sample (e.g., whether the two or more copies are on the same chromosome or different chromosomes) or for phasing alleles.
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28 Claims
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1. A method of detecting variations in copy number of a target nucleic acid, the method comprising:
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a. contacting a sample comprising a plurality of polynucleotides with at least one agent, wherein each of one or more of polynucleotides comprises multiple copies of a target nucleic acid; b. subjecting the sample to conditions that enable the agent to cleave a specifically-selected target site between the multiple copies of the target nucleic acid, thereby separating the multiple copies from one another; c. separating the sample contacted with the agent into a plurality of droplets; d. subjecting the target nucleic acid to an amplification reaction in droplets; e. detecting amplification data for the target nucleic acid from individual droplets; f. enumerating a number of droplets comprising the target nucleic acid based on the amplification data; and g. determining a copy number of the target nucleic acid based on the step of enumerating. - 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)
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27. A method of detecting variations in copy number of a target nucleic acid comprising:
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a. obtaining a sample comprising (i) a plurality of polynucleotides, wherein at least one of the polynucleotides comprises multiple copies of a target nucleic acid;
(ii) a probe with a fluorescent label to detect the target nucleic acid; and
(iii) reagents to enable a PCR reaction;b. separating the sample into a plurality of spatially-isolated partitions, wherein the spatially-isolated partitions comprise on average less than five copies of the target nucleic acid; c. subjecting the sample to a PCR amplification reaction in order to detect the target nucleic acid; d. detecting the fluorescence intensity of the fluorescent label before any of the reagents for the PCR reaction become limiting; e. enumerating the number of partitions that have a fluorescence intensity above a threshold value indicative of one copy of the target nucleic acid; f. enumerating the number of partitions that have a fluorescence intensity above a threshold value indicative of multiple copies of the target nucleic acid; and g. calculating the copy number of the target nucleic acid based on the numbers obtained in step e and step f. - View Dependent Claims (28)
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Specification