Differential hybridization for relative quantification of variant populations

A method of measuring the relative populations of first and second variants of a target nucleotide sequence of a target genome in a sample, the method comprising the steps of:

• (a) amplifying a region of the target genome containing both the target nucleotide sequence and a control nucleotide sequence to obtain amplified target polynucleotides;
• (b) separating the amplified target polynucleotides into at least a first and second portion;
• (c) contacting the first portion of the amplified target polynucleotide with a first labelled polynucleotide probe complementary to the first variant of the target nucleotide sequence to obtain a first hybridized labelled polynucleotide probe, and contacting the second portion of the amplified target polynucleotide with a second labelled polynucleotide probe complementary to the second variant of the target nucleotide sequence to obtain a second hybridized labelled polynucleotide probe;
• (d) quantifying the amount of the first and second hybridized labelled polynucleotide probes;
• (e) contacting the amplified target polynucleotide with a third labelled polynucleotide probe complementary to the control nucleotide sequence contained in the target genome to obtain a third labelled polynucleotide probe;
• (f) quantifying the amount of the third hybridized labelled polynucleotide probe;
• (g) measuring the relative populations of the first and second variants by determining the relative amounts of the first and second hybridized labelled polynucleotide probes compared to the third hybridized labelled polynucleotide probe.