Array-based methods for analysing mixed samples using differently labelled allele-specific probes

A method for analyzing a mixed nucleic acid sample obtained from an organism, comprising:

• obtaining or deriving from an organism a nucleic acid sample containing a mixed nucleic acid population that includes a major subpopulation and a minor subpopulation, wherein the major and minor subpopulations each include a target sequence located in a first nucleic acid locus and containing a polymorphic site, wherein the polymorphic site can include combinations of a first nucleotide variant and a second nucleotide variant;
• genotyping the polymorphic site, wherein the genotyping includes:
• (a) contacting the nucleic acid sample with a pool of linear molecular inversion probes to provide an annealing mixture, wherein portions of the linear molecular inversion probes hybridize to the target sequence;
• (b) dividing the annealing mixture into a first channel composition and a second channel composition;
• (c) adding a mixture of deoxynucleotides to each of the first and second channel composition, wherein the mixture of deoxynucleotides added to the first channel composition is different from the mixture of deoxynucleotides added to the second channel composition;
• (d) contacting the first and second channel compositions with a ligase to form first and second circularized probe compositions from the linear molecular inversion probes:
• (e) cleaving the first and second circularized probe compositions to form first and second linearized probe compositions;
• (f) combining the first and second linearized probe compositions;
• (g) hybridizing the first and second linearized probe compositions to an oligonucleotide probe of an oligonucleotide array;
• and
• (h) detecting from the oligonucleotide array, using a detector, a first signal indicating the presence or absence of the first nucleotide variant (“A signal”) corresponding to a first allelic variant and a second signal indicating the presence or absence of the second nucleotide variant (“B signal”) corresponding to a second allelic variant.