A computer-implemented method for determining whether a male fetus of a pregnant female has an X-linked mutation, wherein the pregnant female is heterozygous for a mutant and a normal allele at a locus on the X chromosome, the method comprising: receiving data from a plurality of reactions, each involving one or more nucleic acid molecules from a biological sample, the biological sample including nucleic acid molecules from the pregnant female and from the male fetus, wherein the data includes: a first set of quantitative data indicating a first amount of the mutant allele at the locus; and a second set of quantitative data indicating a second amount of the normal allele at the locus; determining a parameter from the first amount and the second amount, wherein the parameter represents a relative amount between the first and second amounts; obtaining a percentage Pf of fetal nucleic acid molecules in the biological sample; calculating a first cutoff value for determining whether the fetus has inherited the mutant allele at the locus, wherein the first cutoff value is derived at least from a first proportion of k/(1+k-Pf), where k is a number of mutant alleles on a mutant chromosome of the pregnant female, k being an integer equal to or greater than one; calculating a second cutoff value for determining whether the fetus has inherited the normal allele at the locus, wherein the second cutoff value is derived at least from a second proportion of [k(1-Pf)]/[1+k-kPf)]; and comparing the parameter to at least one of the first and second cutoff values to determine a classification of whether the fetus has inherited the mutant allele or the normal allele. receiving data from a plurality of reactions, each involving one or more nucleic acid molecules from a biological sample, the biological sample including nucleic acid molecules from the pregnant female and from the male fetus, wherein the data includes: a first set of quantitative data indicating a first amount of the mutant allele at the locus; and a second set of quantitative data indicating a second amount of the normal allele at the locus; a first set of quantitative data indicating a first amount of the mutant allele at the locus; and a second set of quantitative data indicating a second amount of the normal allele at the locus; determining a parameter from the first amount and the second amount, wherein the parameter represents a relative amount between the first and second amounts; obtaining a percentage Pf of fetal nucleic acid molecules in the biological sample; calculating a first cutoff value for determining whether the fetus has inherited the mutant allele at the locus, wherein the first cutoff value is derived at least from a first proportion of k/(1+k-Pf), where k is a number of mutant alleles on a mutant chromosome of the pregnant female, k being an integer equal to or greater than one; calculating a second cutoff value for determining whether the fetus has inherited the normal allele at the locus, wherein the second cutoff value is derived at least from a second proportion of [k(1-Pf)]/[1+k-kPf)]; and comparing the parameter to at least one of the first and second cutoff values to determine a classification of whether the fetus has inherited the mutant allele or the normal allele.