Methods of using an array of pooled probes in genetic analysis

Abstract

The invention provides arrays of polynucleotide probes having at least one pooled position. A typical array comprises a support having at least three discrete regions. A first region bears a pool of polynucleotide probes comprising first and second probes. A second region bears the first probe without the second probe and a third region bears the second probe without the first probe. A target nucleic acid having segments complementary to both the first and second probes shows stronger normalized binding to the first region than to the aggregate of binding to the second and third regions due to cooperative binding of pooled probes in the first region. The invention provide methods of using such arrays for e.g., linkage analysis, sequence analysis, and expression monitoring.

1 - 18 . (canceled) 
     
     
         19 . An array, comprising a substrate having a plurality of discrete regions, different regions being attached in a presynthesized form or directly synthesized form by a plurality of different pools of probes, a pool of probes comprising first and second probes complementary to nonoverlapping target segments, wherein the first probe is the same in at least a subset of the plurality of pools and the second probe varies in different pools in the subset. 
     
     
         20 . The array of  claim 19 , wherein the first probe is the same in each of the pools of probes. 
     
     
         21 . The array of  claim 19 , wherein the probes are 1-50 bases long. 
     
     
         22 . The array of  claim 19 , having 10-1,000,000 discrete regions attached by pools of probes. 
     
     
         23 . The array of  claim 19 , having 100-100,000 discrete regions attached by pools of probes. 
     
     
         24 . The array of  claim 19 , wherein the density of the discrete regions is at least 1000 per cm 2 .