Patent ID: 8507197
Filing Date: 2013-08-13
Classification: C12Q

Abstract:
1. A method for identifying poor quality oligonucleotides on a solid support, comprising: (a) preparing an array of test oligonucleotides on the solid support, whereas each of said test oligonucleotides is anchored at the 5′ end and occupies a predetermined location on said solid support, and whereas test oligonucleotides from each allele of a multi-allelic locus occupies a separate location and the last base at the 3′ end is unique to said allele of the multi-allelic locus; (b) synthesizing probe oligonucleotides for each arrayed test oligonucleotide, said probe oligonucleotides being a complement of the arrayed test oligonucleotide and contain one additional base at the 5′ end; (c) pooling said probe oligonucleotides into at most four groups, wherein probe oligonucleotides representing each allele of a multi-allelic locus is separated into a different group; (d) mixing one group of pooled probe oligonucleotides with said arrayed test oligonucleotides to allow hybridization of probe and test oligonucleotides on said solid support; (e) performing single base extension reaction with labeled dideoxynucleotides, wherein extension occurs only for those test oligonucleotides having a 3′ base that hybridizes with a probe oligonucleotide; (f) washing off dideoxynucleotides not incorporated into test oligonucleotides; (g) detecting labels on extended test oligonucleotides and their location; (h) repeating steps step (d) through step (g) for each additional group of pooled probe oligonucleotides; (i) predicting locations of each labeled test oligonucleotide of interest, based on pooling information and probe oligonucleotide sequence information; and (j) comparing said detected labels and location information from step (h) with the predicted test oligonucleotide location information from step (i), whereas any non-match is indicative of a poor quality of the test oligonucleotide at that location; wherein all the probe oligonucleotides within each group contain the same said additional base such that only a single type of labeled dideoxynucleotide is added for the single nucleotide extension reaction.