Methods of validating snps and compiling libraries of assays

Abstract

Libraries of assays and methods of compiling the libraries are provided. The assays can identify Single Nucleotide Polymorphisms (SNPs). Methods of validating SNPs are provided. Methods of constructing linkage disequilibrium maps using sets or subsets of SNPs are also provided.

1 - 34 . (canceled)  
     
     
         35 . A library that contains a plurality of data sets, corresponding to one or more respective oligonucleotides that can function as a respective assay to hybridize with at least one respective Single Nucleotide Polymorphism (SNP) in a nucleic acid sequence, wherein the library is compiled using a method comprising the steps of: 
 providing a representation of a nucleic acid sequence;    designating a region within at least a part of the nucleic acid sequence;    determining the locations of known SNPs, if any, within the region;    determining the locations of newly identified SNPs, if any, within the region; and    selecting for the library a collection of data sets that corresponds to a collection of the known SNPs and the newly identified SNPs, wherein all of the SNPs of collection are:    (1) spaced less than a specified maximum distance apart from one another along the nucleic acid sequence;    (2) spaced more than a minimum distance apart from one another along the nucleic acid sequence;    (3) spaced apart from one another such that each of the distances between adjacent selected SNPs is from about 75% to about 125% of an average of the distances between the adjacent selected SNPs; or    (4) a combination of (1), (2), and (3).    
     
     
         36 . The library of  claim 35 , wherein the method further comprises the step of designating a specified maximum distance between adjacent selected SNPs that correspond to respective data sets.  
     
     
         37 . The library of  claim 35 , wherein the method further comprises the step of designating a specified minimum distance between adjacent selected SNPs that correspond to respective data sets.  
     
     
         38 . The library of  claim 35 , wherein the method further comprises the step of designating both a specified minimum distance between adjacent selected SNPs that correspond to respective data sets and a specified maximum distance between adjacent selected SNPs that correspond to respective data sets.  
     
     
         39 . The library of  claim 35 , wherein each of the distances between adjacent selected SNPs is from about 75% to about 125% of an average of the distances between the adjacent selected SNPs.