Methods to detect cross-contamination between samples contacted with a multi-array substrate

Abstract

Methods and compositions for detecting cross-contamination between samples contacted with different arrays of a multi-array substrate are provided. The methods involve contacting sample to arrays of a multi-array substrate that contains cross-contamination probes in each of its arrays, and evaluating the resultant sample contacted arrays for cross-contamination between the samples. In many embodiments, the arrays of the multi-array substrate contain a set of cross-contamination probes for a corresponding set of cross-contamination targets in the sample(s). Kits and systems are provided for performing the invention. The subject methods may be used in a variety of different applications, such as gene expression analysis, DNA sequencing, mutation detection, as well as other genomics and proteomics applications.

1 - 15 . (canceled)  
   
   
       16 . A composition comprising: 
 a substrate comprising at least two separate arrays, each array containing a set of cross-contamination probes.    
   
   
       17 . The composition of  claim 16 , wherein said set of cross-contamination probes is identical in said at least two separate arrays.  
   
   
       18 . The composition of  claim 16 , wherein said substrate comprises 2, 4, 6, 8,16, 24, 48, 96 or 384 or more arrays.  
   
   
       19 - 28 . (canceled)  
   
   
       29 . A kit comprising: 
 a set of cross-contamination targets; and    a set of corresponding cross-contamination probes.    
   
   
       30 . The kit of  claim 29 , further comprising instructions for determining if cross-contamination between samples contacted with different arrays of a substrate has occurred.  
   
   
       31 . The kit of  claim 29 , wherein the cross-contamination probe set is present on the surface of a substrate.  
   
   
       32 . A system for detecting cross-contamination, said system comprising: 
 an substrate comprising at least two separate arrays, each array containing a set of cross-contamination probes; and    a set of cross-contamination targets for said probes.    
   
   
       33 . (canceled)  
   
   
       34 . The composition of  claim 16 , wherein the number of cross-contamination probes in said set of cross-contamination probes is equal to a number of arrays of said substrate.  
   
   
       35 . The kit of  claim 29 , wherein the number of sets of cross-contamination probes is identical to the number of cross-contamination targets in said set of cross-contamination targets.  
   
   
       36 . The system of  claim 32 , wherein the number of sets of cross-contamination probes is identical to the number of cross-contamination targets in said set of cross-contamination targets.  
   
   
       37 . The system of  claim 32 , wherein the number of cross-contamination probes in said set of cross-contamination probes is equal to a number of arrays of said substrate.  
   
   
       38 . The system of  claim 37 , wherein said set of cross-contamination probes is identical in said at least two separate arrays.  
   
   
       39 . The system of  claim 37 , wherein said substrate comprises 2, 4, 6, 8, 16, 24, 48, 96 or 384 or more arrays.