A method for analyzing a maternal sample obtained from a pregnant woman to facilitate prenatal determination of the presence of a genetic disorder, the method comprising: • adding, to the maternal sample, a set of quality control template molecules associated with the genetic disorder, the set of QCT molecules comprising: • target-associated regions with sequence similarity to a target sequence region of endogenous target molecules, and • variation regions with sequence dissimilarity to a sequence region of the endogenous target molecules, wherein the variation regions comprise an embedded molecular identifier region having a unique nucleotide sequence; • generating a co-amplified mixture based on co-amplifying the set of QCT molecules and nucleic acid molecules comprising the target sequence region of the endogenous target molecules; • sequencing the co-amplified mixture; • computationally determining a unique number of the set of QCT molecules, based on a number of distinct variation regions of the set of QCT molecules that are detected from QCT molecule sequence reads identified during sequencing, wherein the QCT molecule sequence reads correspond to the set of QCT molecules; • calculating the average QCT sequencing depth based on dividing a number of the QCT molecule sequence reads by the unique number of QCT molecules; • determining an absolute count of the endogenous target molecules based on dividing a total read count for the endogenous target molecules by the average QCT sequencing depth; • determining an absolute count of endogenous reference molecules based on dividing a total read count for the endogenous reference molecules by the average QCT sequencing depth; and • facilitating the prenatal determination of the presence of the genetic disorder based on a comparison between the absolute count of endogenous target sequences and the absolute count of endogenous reference sequences. • adding, to the maternal sample, a set of quality control template molecules associated with the genetic disorder, the set of QCT molecules comprising: • target-associated regions with sequence similarity to a target sequence region of endogenous target molecules, and • variation regions with sequence dissimilarity to a sequence region of the endogenous target molecules, wherein the variation regions comprise an embedded molecular identifier region having a unique nucleotide sequence; • target-associated regions with sequence similarity to a target sequence region of endogenous target molecules, and • variation regions with sequence dissimilarity to a sequence region of the endogenous target molecules, wherein the variation regions comprise an embedded molecular identifier region having a unique nucleotide sequence; • generating a co-amplified mixture based on co-amplifying the set of QCT molecules and nucleic acid molecules comprising the target sequence region of the endogenous target molecules; • sequencing the co-amplified mixture; • computationally determining a unique number of the set of QCT molecules, based on a number of distinct variation regions of the set of QCT molecules that are detected from QCT molecule sequence reads identified during sequencing, wherein the QCT molecule sequence reads correspond to the set of QCT molecules; • calculating the average QCT sequencing depth based on dividing a number of the QCT molecule sequence reads by the unique number of QCT molecules; • determining an absolute count of the endogenous target molecules based on dividing a total read count for the endogenous target molecules by the average QCT sequencing depth; • determining an absolute count of endogenous reference molecules based on dividing a total read count for the endogenous reference molecules by the average QCT sequencing depth; and • facilitating the prenatal determination of the presence of the genetic disorder based on a comparison between the absolute count of endogenous target sequences and the absolute count of endogenous reference sequences.