Patent ID: 7569343

Claim:
A method of determining if a positionally-addressable biopolymer array has a synthesis defect, said method comprising the following steps in the order stated: a) contacting a positionally-addressable biopolymer array with a sample, wherein said positionally addressable biopolymer array comprises a substrate to which is attached a plurality of different biopolymer probes, said different biopolymer probes being situated at different positions on said substrate and being the product of a step-by-step synthesis of said different biopolymer probes on said substrate, said plurality of different biopolymer probes comprising a plurality of quality control probes, each quality control probe in said plurality of quality control probes comprising (i) the same predetermined binding sequence or (ii) a different predetermined binding sequence with the same binding specificity, the synthesis of said predetermined binding sequence in each said quality control probe having been initiated during said step-by-step synthesis at different cycles of synthesis, wherein at least some of said quality control probes further comprise a first sequence contiguous with said predetermined binding sequence, wherein at least some of said quality control probes differ from other of said quality control probes in the length of said first sequence, and wherein said first sequence is a sequence of up to N monomers, where N is a whole number equal to or greater than 1, and wherein said sample comprises a binding partner that binds said predetermined binding sequence; b) detecting or measuring binding between (1) two or more quality control probes of said plurality of quality control probes that differ in the number of said monomers; and (2) said binding partner in the sample; and c) comparing binding of said two or more quality control probes of said plurality of quality control probes; wherein if said binding is similar, the absence of a synthesis defect between said different cycles of synthesis used to synthesize said two or more quality control probes is indicated.