Method and system for DNA analysis

Abstract

The present invention pertains to a process for automatically analyzing nucleic acid samples. Specifically, the process comprises the steps of forming electrophoretic data of DNA samples with DNA ladders; comparing these data; transforming the coordinates of the DNA sample's data into DNA length coordinates; and analyzing the DNA sample in length coordinates. This analysis is useful for automating fragment analysis and quality assessment. The automation enables a business model based on usage, since it replaces (rather than assists) labor. This analysis also provides a mechanism whereby data generated on different instruments can be confidently compared. Genetic applications of this invention include gene discovery, genetic diagnosis, and drug discovery. Forensic applications include identifying people and their relatives, catching perpetrators, analyzing DNA mixtures, and exonerating innocent suspects.

1 . A method for analyzing a nucleic acid sample comprised of the steps: 
 (a) forming labeled DNA sample fragments from a nucleic acid sample;    (b) size separating said sample fragments with size standard fragments, and detecting the fragments to form a sample signal and a size standard signal;    (c) transforming the sample signal into size coordinates using the size standard signal; and    (d) analyzing the nucleic acid sample in size coordinates.    
     
     
         2 . A method for analyzing a nucleic acid sample comprised of the steps: 
 (a) forming labeled DNA sample fragments from a nucleic acid sample;    (b) size separating and detecting said sample fragments to form a sample signal;    (c) forming labeled DNA ladder fragments corresponding to molecular lengths;    (d) size separating and detecting said ladder fragments to form a ladder signal;    (e) transforming the sample signal into length coordinates using the ladder signal; and    (f) analyzing the nucleic acid sample signal in length coordinates.    
     
     
         3 . A method as described in  claim 2  wherein after the analyzing step (f) there is the additional step of determining a length or amount of a fragment in the nucleic acid sample.  
     
     
         4 . A method as described in  claim 3  wherein after the determining step there is the additional step of finding a gene by positional cloning.  
     
     
         5 . A method as described in  claim 3  wherein after the determining step there is the additional step of identifying an individual by DNA profiling.  
     
     
         6 . A method for generating-revenue from computer scoring of genetic data comprised of the steps: 
 (a) supplying a software program that automatically scores genetic data;    (b) forming genetic data that can be scored by the software program;    (c) scoring the genetic data using the software program to form a quantity of genetic data; and    (d) generating a revenue from computer scoring of genetic data that is related to the quantity.    
     
     
         7 . A method as described in  claim 6  wherein prior to the step (d) of generating a revenue there are the steps of: 
 (e) defining a labor cost of scoring the quantity of genetic data when not using the software program;    (f) providing a calculating mechanism for estimating the labor cost from the quantity;    (g) determining the labor cost based on the quantity; and    (h) establishing a price for using the software program that is related to the labor cost.    
     
     
         8 . A method as described in  claim 7  wherein the calculating mechanism includes a spreadsheet.  
     
     
         9 . A method as described in  claim 7  wherein the calculating mechanism is provided via the Internet.  
     
     
         10 . A method as described in  claim 7  wherein the calculating mechanism operates interactively via the Internet.  
     
     
         11 . A system for analyzing a nucleic acid sample comprising: 
 (a) means for forming labeled DNA sample fragments from a nucleic acid sample;    (b) means for size separating and detecting said sample fragments to form a sample signal, said separating and detecting means in communication with the sample fragments;    (c) means for forming labeled DNA ladder fragments corresponding to molecular lengths;    (d) means for size separating and detecting said ladder fragments to form a ladder signal, said separating and detecting means in communication with the ladder fragments;    (e) means for transforming the sample signal into length coordinates using the ladder signal, said transforming means in communication with the signals; and    (f) means for analyzing the nucleic acid sample signal in length coordinates, said analyzing means in communication with the transforming means.    
     
     
         12 . A method for producing a nucleic acid analysis comprised of the steps: 
 (a) analyzing a first nucleic acid sample on a first size separation instrument to form a first signal;    (b) analyzing a second nucleic acid sample on a second size separation instrument to form a second signal;    (c) comparing the first signal with the second signal in a computing device with memory to form a comparison; and    (d) producing a nucleic acid analysis of the two samples from the comparison that is independent of the size separation instruments used.    
     
     
         13 . A method as described in  claim 12  wherein the size separation instrument is a DNA sequencer that uses electrophoresis.  
     
     
         14 . A method as described in  claim 12  wherein the nucleic acid analysis characterizes a size or amount of DNA in one of the nucleic acid samples.  
     
     
         15 . A method as described in  claim 12  wherein the nucleic acid analysis finds a gene by positional cloning.  
     
     
         16 . A method as described in  claim 12  wherein the nucleic acid analysis identifies an individual by DNA profiling.  
     
     
         17 . A method for resolving DNA mixtures comprised of the steps: 
 (a) obtaining DNA profile data that include a mixed sample;    (b) representing the data in a linear equation;    (c) deriving a solution from the linear equation; and    (d) resolving the DNA mixture from the solution.    
     
     
         18 . A method as described in  claim 17  wherein the obtaining step (a) includes the step of performing a PCR on an STR locus of an individual.  
     
     
         19 . A method as described in  claim 17  wherein the representing step (b) includes a matrix or vector representation.  
     
     
         20 . A method as described in  claim 17  wherein the deriving step (c) includes an optimization procedure.  
     
     
         21 . A method as described in  claim 17  wherein the deriving step (c) includes a matrix operation.  
     
     
         22 . A method as described in  claim 17  wherein the resolving step (d) produces the genotype of an individual.