A method of selecting a defined subset of CpG loci in a marker nucleic acid for use in a nucleic acid detection assay detecting coordinate methylation of the defined subset of CpG loci, wherein coordinate methylation of the defined subset of CpG loci is indicative of adenoma or cancer, the method comprising: a) determining the methylation status of a plurality of CpG loci in each of a plurality of individual copies of a marker nucleic acid from a plurality of normal samples; b) determining the methylation status of said plurality of CpG loci in each of a plurality of individual copies of said marker nucleic acid from a plurality of non-normal samples from subjects having adenoma or cancer; wherein the plurality of individual copies of said marker nucleic acid analysed in each of said normal samples and said adenoma samples or said cancer samples comprises at least 1,000; c) determining methylation ratios for each CpG locus in said plurality of said CpG loci in said marker nucleic acid, wherein determining said methylation ratios comprises determining the ratio between the mean methylation at each of said plurality of CpG loci in said normal samples to the mean methylation at each corresponding CpG locus in said plurality of CpG loci in said non-normal samples; d) selecting a defined set of CpG loci in said marker nucleic acid, wherein said defined set of CpG loci comprises at least three CpG loci having advantageous methylation ratios correlating with adenoma or cancer; and e) selecting a defined subset of CpG loci from within said defined set, wherein said defined subset of CpG loci comprises at least three CpG loci, and wherein said defined subset is selected such that the percentage of individual copies of said marker nucleic acid from said plurality of normal samples that are methylated at all of said at least three CpG loci in said defined subset is less than the percentage of individual copies of said marker nucleic acid from said plurality of non-normal samples from subjects having adenoma or cancer that are methylated at all of said at least three CpG loci in said defined subset. a) determining the methylation status of a plurality of CpG loci in each of a plurality of individual copies of a marker nucleic acid from a plurality of normal samples; b) determining the methylation status of said plurality of CpG loci in each of a plurality of individual copies of said marker nucleic acid from a plurality of non-normal samples from subjects having adenoma or cancer; wherein the plurality of individual copies of said marker nucleic acid analysed in each of said normal samples and said adenoma samples or said cancer samples comprises at least 1,000; c) determining methylation ratios for each CpG locus in said plurality of said CpG loci in said marker nucleic acid, wherein determining said methylation ratios comprises determining the ratio between the mean methylation at each of said plurality of CpG loci in said normal samples to the mean methylation at each corresponding CpG locus in said plurality of CpG loci in said non-normal samples; d) selecting a defined set of CpG loci in said marker nucleic acid, wherein said defined set of CpG loci comprises at least three CpG loci having advantageous methylation ratios correlating with adenoma or cancer; and e) selecting a defined subset of CpG loci from within said defined set, wherein said defined subset of CpG loci comprises at least three CpG loci, and wherein said defined subset is selected such that the percentage of individual copies of said marker nucleic acid from said plurality of normal samples that are methylated at all of said at least three CpG loci in said defined subset is less than the percentage of individual copies of said marker nucleic acid from said plurality of non-normal samples from subjects having adenoma or cancer that are methylated at all of said at least three CpG loci in said defined subset.