Automated analysis of multiplexed probe-target interaction patterns: pattern matching and allele identification

Abstract

Disclosed are methods and algorithms (and their implementation) supporting the automated analysis and interactive review and refinement (“redaction”) of the analysis within an integrated software environment, for automated allele assignments. The implementation, preferably with a software system and a program referred to as the Automated Allele Assignment (“AAA”) program, provides a multiplicity of functionalities including: data management by way of an integrated interface to a portable database to permit visualizing, importing, exporting and creating customizable summary reports; system configuration (“Set-up”) including user authorization, training set analysis and probe masking; Pattern Analysis including string matching and probe flipping; and Interactive Redaction combining real-time database computations and “cut-and-paste” editing, generating “warning” statements and supporting annotation. It also includes a thresholding function, a method of setting thresholds, a method of refining thresholds by matching an experimental binary string (“reaction pattern”) setting for that probe, probe masking of signals produced by probes which do not contribute significantly to discriminating among alleles.

1 . A method for allele assignments where assignment is made based on the results of a hybridization assay or capture-mediated elongation assay, or both, and several polymorphic markers are present on each allele, comprising:
 determining the actual reaction pattern generated by a sample subjected to the assay, and making initial allele assignments based on said actual reaction pattern; and   changing said initial allele assignments based on comparing said actual reaction pattern to a predicted reaction pattern which would be generated from targets derived from particular alleles selected form a reference database of alleles, where said particular alleles are selected because they would generate a predicted reaction pattern as similar as possible to said reaction pattern.   
     
     
         2 .- 54 . (canceled)