Probes for variance detection

A method for determining if two nucleotide mismatches are located on the same strand of DNA in a nucleic acid sample, said method comprising the steps of:

• (a) providing a first nucleic acid probe derived from a hemizygous cell, said first nucleic acid probe having a first unique sequence;
• (b) forming a first duplex between said nucleic acid sample and said first nucleic acid probe;
• (c) contacting said first duplex with a compound that cleaves a duplex containing a nucleotide mismatch under conditions which allow said compound to cleave said first duplex to produce a cleavage product if said first duplex contains a nucleotide mismatch;
• (d) providing a second nucleic acid probe derived from a hemizygous cell, said second nucleic acid probe having a second unique sequence;
• (e) forming a second duplex between the product of step (c) and said second nucleic acid probe;
• (f) contacting said second duplex with said compound under conditions which allow said compound to cleave said second duplex to produce a second cleavage product if said second duplex contains a nucleotide mismatch;
• and
• (g) comparing the cleavage product of step (c) with the second cleavage product of step (f), a reduction in the size of said second cleavage product of step (f) compared to said cleavage product of step (c) indicating that both said nucleotide mismatches are located on the same strand of DNA in said nucleic acid sample.