Methods for quantifying nucleic acid variations

1. A method of analyzing a sample comprising a nucleic acid target, the method comprising:

a) providing a sample comprising nucleic acid target, wherein said nucleic acid target comprises at least one copy of a non-variant form of said nucleic acid target and/or at least one copy of a variant form of said nucleic acid target,

b) providing reagents for an amplification reaction comprising a polymerase chain reaction and an invasive cleavage detection assay, wherein said reagents comprise concentrations of oligonucleotides comprising forward primers and reverse primers complementary to portions of said variant and non-variant forms of said nucleic acid target, FRET cassettes, and flap probes, said flap probes comprising a portion complementary to a region of a nucleic acid target and a flap portion complementary to a region of a FRET cassette,

wherein the concentrations of said oligonucleotides in said reagents produce quantitative amplification data in said amplification reaction from said variant form and said non-variant form of nucleic acid target, said data having the same known slope S for each form, wherein S=the slope of the linear regression of reaction efficiency; and having previously determined C p 0 and C p off values, wherein C p 0 is the intercept of the y axis when log copy number=0 and C p off is an offset between regression lines of crossing thresholds of quantitative amplification data from standard curves for said variant and non-variant forms of nucleic acid target;

wherein in said amplification reaction, non-variant and/or variant nucleic acid target is amplified, and wherein amplified nucleic acid is detected by invasive cleavage to produce quantitative amplification data from said non-variant form and said variant form of said nucleic acid target, and wherein said quantitative amplification data correlates to amplification cycle numbers for said non-variant and variant forms of said nucleic acid target present in said sample;

c) amplifying said nucleic acid target using the reagents of step b) to produce quantitative amplification data from said non-variant form and said variant form of said nucleic acid target, wherein said amplifying comprises subjecting a mixture of said nucleic acid target and the reagents of step b) to the following thermal cycling conditions:

a first set of 5-15 cycles of:

i) a first temperature of at least 90° C.;

ii) a second temperature in the range of 60° C. to 75° C.;

iii) a third temperature in the range of 65° C. to 75° C.;

followed by:

a second set of 20-50 cycles of:

i) a fourth temperature of at least 90° C.;

ii) a fifth temperature that is at least 10° C. lower than said second temperature;

iii) a sixth temperature in the range of 65° C. to 75° C.;

wherein no additional reagents are added to said reaction between said first and second sets of cycles and, in each cycle of said second set of cycles, cleavage of a flap probe is measured;

d) determining a first crossing threshold indicative of variant copies of said nucleic acid target (C p v);

e) determining a second crossing threshold indicative of non-variant copies of said nucleic acid target (C p nv);

f) calculating a ratio R=10 (Cpv−Cpnv+Cpoff)/−S) , and

g) calculating the percentage of nucleic acid target present in said sample that is variant form, wherein the percentage of nucleic acid target in said sample that is variant form is calculated as percent variant=100×(R/(R+1)).

2. The method of claim 1 , wherein the value used for S is greater than or equal to about 2.7.

3. The method of claim 1 , wherein the value used for S is less than or equal to about 3.3.

4. The method of claim 1 , wherein the value used for S is 3.

5. The method of claim 1 , wherein said variant nucleic acid is methylated DNA and said non-variant nucleic acid is unmethylated DNA.

6. The method of claim 1 , wherein said variant nucleic acid is nucleic acid containing a mutation and said non-variant nucleic acid is wild type nucleic acid.