Molecule detection system on a solid support

Abstract

Disclosed herein are compositions and methods used for detecting different types of molecules associated with a site on a solid support.

What is claimed is: 
     
         1 . A method of detecting molecules, said method comprising the steps of:
 (a) providing a solid support comprising molecules associated with a site on the solid support such that the molecules are detected in aggregate during a detection step, wherein the site comprises at least two different types of molecules;   (b) detecting a signal corresponding to the aggregate of molecules at the site;   (c) estimating the fraction of different types of molecules at the site or estimating the amount of signal corresponding to different types of molecules at the site;   (d) calculating the amount of signal corresponding to different types of molecules at the site using the fraction estimate, thereby obtaining a signal estimate or calculating the fraction of different types of molecules at the site using the signal estimate, thereby obtaining a fraction estimate; and   (e) iteratively updating the fraction estimate and signal estimate until the estimates converge, thereby detecting molecules associated with the site.   
     
     
         2 . The method of  claim 1 , wherein the providing step further comprises attaching the molecules at the site. 
     
     
         3 . The method of  claim 1 , wherein the estimating step is performed by guessing the fraction of different types of molecules at the site or guessing the amount of signal corresponding to different types of molecules at the site. 
     
     
         4 . The method of  claim 1 , wherein the providing step further comprises associating the molecules with the site. 
     
     
         5 . The method of  claim 1 , wherein the estimating step comprises performing a principal component analysis (PCA). 
     
     
         6 . The method of  claim 1 , wherein the updating step comprises performing a numerical optimization algorithm. 
     
     
         7 . The method of  claim 6 , wherein the numerical optimization algorithm is based on an iterative map search. 
     
     
         8 . The method of  claim 7 , wherein the numerical optimization algorithm is based on Fienup's iteration map. 
     
     
         9 . The method of  claim 1 , wherein sequence data is obtained for one or more molecules. 
     
     
         10 . The method of  claim 10 , wherein sequence data is obtained by a sequencing-by-synthesis process. 
     
     
         11 . The method of  claim 1 , wherein about 1,000 to about 10,000 molecules are associated with the site. 
     
     
         12 . The method of  claim 1 , wherein the molecules comprise nucleic acids. 
     
     
         13 . The method of  claim 12 , wherein the nucleic acids comprise a first subpopulation of nucleic acids and a second subpopulation of nucleic acids, said nucleic acids of the first subpopulation each having an identical target region and the nucleic acids of the second subpopulation each having an identical region that is a variant of the target region. 
     
     
         14 . The method of  claim 12 , wherein the nucleotide sequence of said target region of the nucleic acids of the first subpopulation has at least 3 nucleotides that are different as compared to the nucleotide sequence of said variant of the target region of the nucleic acids of the second subpopulation. 
     
     
         15 . The method of  claim 12 , wherein the nucleic acids comprise alleles of a genetic locus from a polyploid organism. 
     
     
         16 . The method of  claim 12 , wherein the nucleic acids comprise alternative splicing forms of a nucleic acid. 
     
     
         17 . The method of  claim 12 , the nucleic acids comprises alleles of a genetic locus from a diploid organism. 
     
     
         18 . A molecule detection system comprising:
 a solid support comprising molecules associated with a site on the solid support such that the molecules are detected in aggregate, wherein the molecules comprise at least two different types of molecules; and   a detector configured to detect said molecules associated with said site.   
     
     
         19 . A method of identifying a target region of a nucleic acid, said method comprising:
 (a) associating a first subpopulation of nucleic acids with a site on a solid support, wherein nucleic acids of said first subpopulation comprise an identical target region;   (b) associating a second subpopulation of nucleic acids with the site on the solid support, wherein nucleic acids of said second subpopulation comprise an identical target region that is a variant of the target region of the nucleic acids of said first subpopulation;   (c) detecting a signal corresponding to one or more nucleotides of the target region of first subpopulation nucleic acids and one or more nucleotides of the variant of the target region of second subpopulation nucleic acids;   (d) estimating the fraction of first subpopulation nucleic acids and second subpopulation nucleic acids associated with the site or estimating the amount of signal corresponding to first subpopulation nucleic acids and second subpopulation nucleic acids associated with the site;   (e) calculating the amount of signal corresponding to first subpopulation nucleic acids and second subpopulation nucleic acids associated with the site using the fraction estimate, or calculating the fraction of first subpopulation nucleic acids and second subpopulation nucleic acids associated with the site using the signal estimate; and   (f) iteratively updating the fraction estimate and signal estimate until the estimates converge, thereby identifying a target region of a nucleic acid.   
     
     
         20 . A method for identifying a biosignature, said method comprising the steps of:
 (a) providing samples obtained from a plurality of subjects, wherein the samples comprise molecules;   (b) tagging molecules from the samples so as to identify the subject from which each sample originated;   (c) associating molecules from the samples with a site on a solid support such that the molecules are detected in aggregate during a detection step, wherein the site comprises at least two different types of molecules;   (d) obtaining a biosignature for molecules associated with the site by:
 i) detecting a signal corresponding to the aggregate of the molecules at the site; 
 ii) estimating the fraction of different types of molecules at the site or the amount of signal corresponding to different types of molecules at the site; 
 iii) calculating the amount of signal corresponding to different types of molecules at the site using the fraction estimate, or calculating the fraction of different types of molecules at the site using the signal estimate; and 
 iv) iteratively updating the fraction estimate and signal estimate until the estimates converge, thereby obtaining a biosignature for molecules at the site; and 
   (e) comparing the biosignature obtained in step (d) to a reference biosignature, thereby identifying said bio signature.