Polymorphism detection utilizing clustering analysis
AssigneeAffymetrix, Inc.
InventorAnthony J. Berno
Life of this patent
Estimating the term…
Abstract
Systems and methods for detecting differences in sample polymers, such as nucleic acid sequences, are provided. Hybridization affinity information for the sample polymers is clustered so that the differences, if any, between or among the sample polymers can be readily identified. By clustering the hybridization affinity information of the sample polymers, differences in the sample polymers can be accurately achieved even in the presence of random and systematic errors.
Claims42
A method of detecting differences in sample polymers, comprising:
- inputting a plurality of sets of hybridization affinity information, each set of hybridization affinity information including hybridization affinities between a sample polymer and polymer probes;
- clustering the plurality of sets of hybridization affinity information into a plurality of clusters such that all sets of hybridization affinity information in each cluster are more similar to each other than to the sets of hybridization affinity information in another cluster;
- and
- analyzing the plurality of clusters to determine a number of clusters, such that the number of clusters indicates if there are differences in the sample polymers.
A computer program product that detects differences in sample polymers, comprising:
- computer code that receives a plurality of sets of hybridization affinity information, each set of hybridization affinity information including hybridization affinities between a sample polymer and polymer probes;
- computer code that clusters the plurality of sets of hybridization affinity information into a plurality of clusters such that all sets of hybridization affinity information in each cluster are more similar to each other than to the sets of hybridization affinity information in another cluster;
- computer code that analyzes the plurality of clusters to determine a number of clusters, such that the number of clusters indicates if there are differences in the sample polymers;
- and
- a computer readable medium that stores the computer codes.
A method of detecting polymorphisms in sample nucleic acid sequences, comprising:
- inputting a plurality of sets of hybridization affinity information, each set of hybridization affinity information including hybridization affinities between a sample nucleic acid sequence and nucleic acid probes;
- hierarchically clustering the plurality of sets of hybridization affinity information into a plurality of clusters such that all sets of hybridization affinity information in each cluster are more similar to each other than to the sets of hybridization affinity information in another cluster;
- and
- analyzing the plurality of clusters to determine a number of clusters, such that the number of clusters indicates if there are polymorphisms in the sample polymers.
A computer program product that detects polymorphisms in sample nucleic acid sequences, comprising:
- computer code that receives a plurality of sets of hybridization affinity information, each set of hybridization affinity information including hybridization affinities between a sample nucleic acid sequence and nucleic acid probes;
- computer code that hierarchically clusters the plurality of sets of hybridization affinity information into a plurality of clusters such that all sets of hybridization affinity information in each cluster are more similar to each other than to the sets of hybridization affinity information in another cluster;
- computer code that analyzes the plurality of clusters to determine a number of clusters, such that the number of clusters indicates if there are polymorphisms in the sample polymers;
- and
- a computer readable medium that stores the computer codes.
Dependencies are inferred from the claim text.