Polynucleotide sequence detection assays and analysis
AssigneeApplera Corporation
InventorsBarnett Rosenblum, David Holden, Yuandan Lou, Ryan Koehler, Srinivasa Ramachandra
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Abstract
Methods and software for associating mobility probes with target macromolecules are discussed. By encoding the identities of macromolecules of interest with a universal set of tag portions complementary to a universal set of mobility probes, reactions varying in their input starting material may be identified using the same universal set of mobility probes. This allows the universal collection of mobility probes to be used in a target macromolecule-independent manner. Software is used to decode the associations between the mobility probes and a given target macromolecular identity.
Claims27
A method for determining the presence or absence of a target biochemical or biochemical complex in a sample, comprising:
- (i) receiving mobility data from an analysis of one or more released mobility probes using a mobility dependent analysis technique;
- (ii) extracting at least one feature or feature set from the mobility data;
- (iii) receiving information for associating the at least one feature or feature set to the one or more released mobility probes;
- (iv) associating one of the one or more released mobility probes with a respective target biochemical or biochemical complex;
- and
- (v) determining the presence or absence of the target biochemical or biochemical complex.
A method for determining the presence or absence of a target biochemical or biochemical complex in a sample, comprising:
- (i) receiving mobility data from an analysis of a plurality of released mobility probes using a mobility dependent analysis technique;
- (ii) extracting a feature set from the mobility data;
- (iii) receiving information for associating the feature set to the plurality of released mobility probes;
- (iv) associating a released mobility probe with a respective target biochemical or biochemical complex;
- (v) determining the presence or absence of the target biochemical or biochemical complex.
A program storage device readable by a machine, embodying a program of instructions executable by the machine to perform method steps for analysis of a target biochemical or biochemical complex in a sample, said method steps comprising:
- (i) receiving mobility data from an analysis of one or more released mobility probes using a mobility dependent analysis technique;
- (ii) extracting at least one feature or feature set from the mobility data;
- (iii) receiving information for associating the at least one feature or feature set to the one or more released mobility probes;
- (iv) associating one of the one or more released mobility probes with a respective target biochemical or biochemical complex;
- and
- (v) determining the presence or absence of the target biochemical or biochemical complex.
A method for genetic analysis, comprising:
- analyzing a plurality of samples on an electrophoresis instrument, with each sample representing an individual of a population, whereby mobility data is generated for each sample;
- receiving said mobility data, represented as fluorescence intensity over time;
- associating the mobility data with the presence or absence of one or more target biochemicals or biochemical complexes in the samples;
- transforming the mobility data to a different feature space;
- assigning a class to each sample based on said transforming;
- and
- determining a genoptypic characteristic of each sample or the population based the class assignment.
A program storage device readable by a machine, embodying a program of instructions executable by the machine to perform genetic analysis, said method steps comprising:
- receiving mobility data, represented as fluorescence intensity over time, generated by electrophoresis of a plurality of samples, with each sample representing an individual of a population;
- associating the mobility data with the presence or absence of one or more target biochemicals or biochemical complexes in the samples;
- transforming the mobility data to a different feature space;
- and
- assigning a class to each sample based on said transforming.
A method for determining a target biochemical or biochemical complex, comprising:
- (i) receiving mobility-dependent data representing the output of a mobility-dependent analysis technique;
- (ii) receiving data for associating the mobility-dependent data with a mobility probe;
- (iii) receiving data for associating the mobility probe with a tag or a complimentary tag sequence;
- (iv) receiving data for associating the tag or complimentary tag sequence with a target;
- and, using the data from (ii), (iii), and (iv):
- (v) associating the mobility-dependent data with a corresponding mobility probe;
- (vi) associating the mobility probe from (v) with a corresponding tag or complimentary tag sequence;
- (vii) associating the tag or complimentary tag sequence from (vi) with a corresponding target;
- and
- (viii) reporting the detection of the target from (vii).
A method for determining a target biochemical or biochemical complex, comprising:
- (i) receiving mobility-dependent data representing the output of a mobility- dependent analysis technique;
- (ii) receiving data for associating the mobility-dependent data with a plurality of mobility probes;
- (iii) receiving data for associating each of the mobility probes with a respective tag or complimentary tag sequence;
- (iv) receiving data for associating the tag or complimentary tag sequence from (iii) with a respective target;
- and, using the data from (ii), (iii), and (iv):
- (v) associating the mobility-dependent data with the plurality of mobility probes;
- (vi) associating each of the plurality of mobility probes with a corresponding tag or complimentary tag sequence;
- (vii) associating each tag or complimentary tag sequence from (vi) with a corresponding target;
- and
- (viii) reporting the detection of each target from (vii).
A program storage device readable by a machine, embodying a program of instructions executable by the machine for determining a target biochemical or biochemical complex, said method steps comprising:
- (i) receiving mobility-dependent data representing the output of a mobility-dependent analysis technique;
- (ii) receiving data for associating the mobility-dependent data with a mobility probe;
- (iii) receiving data for associating the mobility probe with a tag or a complimentary tag sequence;
- (iv) receiving data for associating the tag or complimentary tag sequence with a target;
- and, using the data from (ii), (iii), and (iv):
- (v) associating the mobility-dependent data with a corresponding mobility probe;
- (vi) associating the mobility probe from (v) with a corresponding tag or complimentary tag sequence;
- (vii) associating the tag or complimentary tag sequence from (vi) with a corresponding target;
- and
- (viii) reporting the detection of the target from (vii).
A program storage device readable by a machine, embodying a program of instructions executable by the machine for determining one or more target biochemicals or biochemical complexes, said method steps comprising:
- (i) receiving mobility-dependent data representing the output of a mobility- dependent analysis technique;
- (ii) receiving data for associating the mobility-dependent data with a plurality of mobility probes;
- (iii) receiving data for associating each of the plurality of mobility probes with a respective target biochemical or biochemical complex;
- and, using the data from (ii) and (iii):
- (iv) associating the mobility-dependent data with the mobility probes;
- (v) associating each of the mobility probes from (iv) with a corresponding target;
- and
- (vi) reporting the detection of the target from (v).
A method for genetic analysis, comprising:
- receiving electropherogram data;
- extracting peaks from the electropherogram data;
- associating the peaks with respective released mobility probes;
- associating the released mobility probes with respective targets;
- analyzing the peaks against selected criteria to filter out peaks not indicative of targets;
- and
- reporting the detection of targets.
Dependencies are inferred from the claim text.