US 7,587,279 B2
Method for quantitative PCR data analysis system (QDAS)
Xitong Li, Mountain View, Calif. (US); and Kenneth Stineman, San Jose, Calif. (US)
Assigned to Genomic Health, Redwood City, Calif. (US)
Filed on Jul. 06, 2004, as Appl. No. 10/886,501.
Prior Publication US 2006/0008809 A1, Jan. 12, 2006
Int. Cl. G01N 33/48 (2006.01); C12P 19/34 (2006.01)
U.S. Cl. 702—17  [435/91.2] 78 Claims
 
1. A method of determining a classification of amplification data resulting from an amplification of nucleic acid molecules in a sample, the method comprising:
receiving, at a computing system, the amplification data, wherein the amplification data is derived from a signal measured from the sample at a plurality of time points, wherein the time points include numbers corresponding to cycles of a reaction of the sample;
determining, with the computing system, a quality score of the amplification data, wherein the quality score is a maximum of a group of one or more local quality values (LQVs), wherein an LQV is proportional to a slope of a respective window region containing a plurality of the amplification data points;
determining a fractional cycle number (Ct) where a function approximating at least a portion of the amplification data intersects a Ct threshold value;
generating, with the computing system, a status classification of the amplification data based on a numerical value of the quality score and based on Ct;
determining a quality lower limit function (Qlimit) as a function of cycle number, wherein the Qlimit:
is a first constant value for cycle numbers less than a lower cycle number (CtL);
decreases from the first constant value to a second constant value, wherein the decrease occurs from CtL to a higher cycle number (CtH); and
is the second constant value for cycles higher than the CtH value,
wherein generating the status classification includes identifying a distance between a point of {Ct, quality score} and Qlimit.