Abstract: Methods and compositions are provided for determining the presence of a wild type or variant nucleotide at a position in a nucleic acid molecule of interest.

Abstract: Described herein are methods for increasing the annealing specificity of an amplification reaction using Iso-base Amplification Primers (“IAPs”). IAPs containing an iso-region are capable of regulating sequence-specific annealing thereby enhancing primer-template hybridization for sequence-specific amplification of nucleotides.

Abstract: This disclosure includes an inventive method for nucleic acid array design, in which the array contains individual nucleic acid sequences or portions thereof, and in which the method comprises: (a) providing at least two discrete oligos per nucleic acid sequence or portions thereof; (b) printing the array with the oligos; and (c) using the array in genetic analysis. In a preferred embodiment, two or three oligos are advantageously provided per target nucleic acid sequence or portions thereof on the array. This disclosure further includes an inventive method for genetic analysis, in which the method comprises: (a) generating labeled nucleic acids from a sample nucleic acid population using probe matched target primers; (b) hybridizing the labeled nucleic acids to an array; and (c) analyzing the array.