Synthetic nucleic acid control molecules

A run control composition, comprising:

• a) a number of copies of a first synthetic DNA fragment, comprising:
• i) a methylation footprint nucleotide sequence of a human gene, the methylation footprint nucleotide sequence in said first synthetic DNA fragment comprising a pattern of cytosines, wherein each of the cytosines within the methylation footprint nucleotide sequence comprises a 5-methyl, and
• ii) a capture footprint nucleotide sequence;
• and
• b) a number of copies of a second synthetic DNA fragment comprising:
• i) the methylation footprint nucleotide sequence of the human gene, the methylation footprint nucleotide sequence in the second synthetic DNA fragment comprising the same number and pattern of cytosines as the methylation footprint nucleotide sequence in the first synthetic DNA fragment, wherein none of the cytosines within the methylation footprint nucleotide sequence in the second synthetic DNA fragment comprises a 5-methyl, and
• ii) the capture footprint nucleotide sequence;
• wherein a ratio of the number of copies of the first synthetic DNA fragment to the number of copies of the second synthetic DNA fragment in the run control composition produces a run control expected result when assayed in a methylation assay.

A method of characterizing a DNA test sample, comprising:

• A) providing a run control composition comprising:
• a) a first synthetic DNA fragment, comprising:
• i) a methylation footprint nucleotide sequence of a human gene, the methylation footprint nucleotide sequence in said first synthetic DNA fragment comprising a pattern of cytosines, wherein each of the cytosines within the methylation footprint nucleotide sequence comprises a 5-methyl, and
• ii) a capture footprint nucleotide sequence;
• and
• b) a second synthetic DNA fragment comprising:
• i) the methylation footprint nucleotide sequence of the human gene, the methylation footprint nucleotide sequence in the second synthetic DNA fragment comprising the same number and pattern of cytosines as the methylation footprint nucleotide sequence in the first synthetic DNA fragment, wherein none of the cytosines within the methylation footprint nucleotide sequence in the second synthetic DNA fragment comprises a 5-methyl, and
• ii) the capture footprint nucleotide sequence;
• wherein a ratio of the number of copies of the first synthetic DNA fragment to the number of copies of the second synthetic DNA fragment in the run control composition produces a run control expected result when assayed in a methylation assay;
• B) providing a DNA test sample isolated from a human subject;
• C) applying the methylation assay to the run control composition to produce run control experimental data;
• D) applying the methylation assay to the DNA test sample to produce test sample experimental data;
• and
• E) classifying the test sample experimental data as valid if the run control experimental data are within a pre-defined acceptable range relative to the run control expected result.
• wherein applying the methylation assay comprises processing the run control composition with a capture reagent comprising a capture probe that hybridizes to the capture footprint nucleotide sequence.