Patent ID: 11866772
Assignee: ROCHE MOLECULAR SYSTEMS, INC.
Field: Computer technology (Electrical engineering)
Classification: CPC C  G | IPC C  G

Claim 0:
1. A computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system to determine settings for a digital PCR (dPCR) experiment involving pre-amplification of DNA molecules in a plasma sample from a female pregnant with a fetus, the dPCR experiment for the detection of a chromosomal aneuploidy, the instructions comprising:
receiving data, the data including:
a number of loci on each of a test chromosome and a control chromosome from which DNA molecules in the plasma sample is to be amplified in a pre-amplification procedure;
a fetal DNA fraction measured in the plasma sample, the fetal DNA fraction relating to a percentage of DNA molecules in the plasma sample that is fetal in origin;
a pre-specified fetal DNA fraction error tolerance in a measurement of the fetal DNA fraction;
a pre-specified error control number that controls a probability that a relative error between an unknown expected fetal DNA fraction and the measured fetal DNA fraction from the plasma sample is within the fetal DNA fraction error tolerance;
a degree of the chromosomal aneuploidy being tested;
a pre-specified portion constraint that specifies a portion of DNA molecules resulting from the pre-amplification procedure to be input to the dPCR experiment;
data about PCR efficiencies for the pre-amplification procedure; and
pre-specified error rate criteria for the dPCR experiment including a false positive rate and a false negative rate;

determining a minimal input number of control chromosome molecules for the dPCR experiment based on the pre-specified error rate criteria, the determined fetal DNA fraction, the data about PCR efficiencies, and the degree of chromosomal aneuploidy;
determining a minimal number of control chromosome molecules for the pre-amplification procedure based on the determined fetal DNA fraction, the pre-specified fetal DNA fraction error tolerance, and the pre-specified error control number;
estimating a number of PCR cycles in the pre-amplification procedure based on the minimal input number of control chromosome molecules for the dPCR experiment, the minimal number of control chromosome molecules for the pre-amplification procedure, the data about PCR efficiencies for the pre-amplification procedure, the number of loci for the pre-amplification procedure, and the pre-specified portion constraint;
causing a PCR amplification device to perform the pre-amplification procedure using the determined minimal number of control chromosome molecules for the estimated number of PCR cycles; and
causing a dPCR device to perform the dPCR experiment to detect the chromosomal aneuploidy in the fetal DNA molecules in the plasma sample using the determined minimal input number of control chromosome molecules.