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US 11,959,906 B2Granted
Analysis of measurements of a polymer
AssigneeOxford Nanopore Technologies PLC
InventorsStuart William Reid, James Anthony Clarke, James White, Gavin Harper
Life of this patent
Estimating the term…
Abstract
A time-ordered series of measurements of a polymer made during translocation of the polymer through a Nanopore are analysed. The measurements are dependent on the identity of k-mers in the Nanopore, a k-mer bring k polymer units of the polymer, where k is a positive integer. The method involves deriving, from the series of measurements, a feature vector of time-ordered features representing characteristics of the measurements; and determining similarity between the derived feature vector and at least one other feature vector.
Claims25
A method of estimating an identity of a target polymer, the method comprising:
- making electrical measurements of a polymer during translocation of the polymer through a nanopore to generate a time-ordered series of electrical measurements, wherein the polymer is a polynucleotide comprising at least 1,000 nucleotide pairs, wherein the translocation is controlled by an enzyme molecular motor and wherein each of the electrical measurements is an electrical measurement of respective k polymer units of the polymer, where k is 3 or greater;
- deriving, from the time-ordered series of electrical measurements and using at least one processor, a feature vector of time-ordered features representing characteristics of the time-ordered series of electrical measurements, wherein the features comprise:
- an average of the electrical measurements, a period of the electrical measurements, a variance of the electrical measurements, asymmetry information, confidence information of the electrical measurements, and a distribution of the electrical measurements, wherein the feature vector comprises at least 1000 sets of time-ordered features;
- analyzing, using the at least one processor, the feature vector that comprises the at least 1000 sets of time-ordered features and at least one other feature vector indicative of the target polymer by using an alignment algorithm or a machine learning algorithm;
- and
- estimating, using the at least one processor, the identity of the target polymer using results of analyzing the feature vector comprising the at least 1000 sets of time-ordered features and the at least one other feature vector indicative of the target polymer.
3 more elements
An analysis device, comprising:
- means to make electrical measurements of a polymer during translocation of a polymer through a nanopore to generate a time-ordered series of electrical measurements, wherein the polymer is a polynucleotide comprising at least 1,000 nucleotide pairs, wherein the translocation is controlled by an enzyme molecular motor and wherein each electrical measurement is an electrical measurement of respective k polymer units of the polymer, where k is 3 or greater;
- means for deriving, from the time-ordered series of electrical measurements, a feature vector of time-ordered features representing characteristics of the time-ordered series of electrical measurements, wherein the features comprise:
- an average of the electrical measurements, a period of the electrical measurements, a variance of the electrical measurements, asymmetry information, confidence information of the electrical measurements, and a distribution of the electrical measurements, wherein the feature vector comprises at least 1000 sets of time-ordered features;
- and
- means for analyzing, using at least one processor, the feature vector that comprises the at least 1000 sets of time-ordered features and at least one other feature vector indicative of the target polymer by using an alignment algorithm or a machine learning algorithm;
- means for estimating an identity of the target polymer using results of analyzing the feature vector comprising the at least 1000 sets of time-ordered features and the at least one other feature vector indicative of the target polymer.
3 more elements
An analysis device, comprising:
- a measurement system configured to make electrical measurements of a polymer during translocation of a polymer through a nanopore to generate a time-ordered series of electrical measurements, wherein the polymer is a polynucleotide comprising at least 1,000 nucleotide pairs, wherein the translocation is controlled by an enzyme molecular motor and wherein each of the electrical measurements is an electrical measurement of respective k polymer units of the polymer, where k is 3 or greater;
- at least one processor configured to perform:
- deriving, from the time-ordered series of electrical measurements, a feature vector of time-ordered features representing characteristics of the time-ordered series of electrical measurements, wherein the features comprise:
- an average of the electrical measurements, a period of the electrical measurements, a variance of the electrical measurements, asymmetry information, confidence information of the electrical measurements, and a distribution of the electrical measurements, wherein the feature vector comprises at least 1000 sets of time-ordered features;
- analyzing the feature vector that comprises the at least 1000 sets of time-ordered features and at least one other feature vector indicative of a target polymer by using an alignment algorithm or a machine learning technique;
- and
- estimating an identity of the target polymer using results of analyzing the feature vector comprising the at least 1000 sets of time-ordered features and the at least one other feature vector indicative of the target polymer.
4 more elements
Dependencies are inferred from the claim text.