A method for identifying the presence or absence of a sex chromosome aneuploidy in a fetus, comprising: (a) obtaining counts of sequence reads mapped to sections of a human reference genome, which sequence reads are reads of circulating cell-free nucleic acid from a test sample from a human pregnant female bearing a fetus, wherein the sections of the reference genome include sex chromosome genomic sections; (b) determining a guanine and cytosine bias coefficient for each of the sections of the reference genome for multiple samples from a fitted relation for each sample between (i) the counts of the sequence reads mapped to each of the sections of the reference genome, and (ii) GC content for each of the sections; (c) calculating a genomic section level L i for each of the sections of the reference genome for test sample i according to Equation α: L i = m i − G i S I − 1 wherein: I is the intercept from a fitted linear relation between the GC bias coefficient for each of the sections and the counts of the sequence reads mapped to each of the sections of the reference genome for the multiple samples, S is the slope of the fitted linear relation between the GC bias coefficient for each of the sections and the counts of the sequence reads mapped to each of the sections of the reference genome for the multiple samples, G i is the GC bias coefficient for the test sample i, m i is measured counts mapped to each section for the test sample i, thereby providing calculated genomic section levels; and (d) identifying the presence or absence of a sex chromosome aneuploidy for the fetus according to the calculated genomic section levels. (a) obtaining counts of sequence reads mapped to sections of a human reference genome, which sequence reads are reads of circulating cell-free nucleic acid from a test sample from a human pregnant female bearing a fetus, wherein the sections of the reference genome include sex chromosome genomic sections; (b) determining a guanine and cytosine bias coefficient for each of the sections of the reference genome for multiple samples from a fitted relation for each sample between (i) the counts of the sequence reads mapped to each of the sections of the reference genome, and (ii) GC content for each of the sections; (c) calculating a genomic section level L i for each of the sections of the reference genome for test sample i according to Equation α: L i = m i − G i S I − 1 wherein: I is the intercept from a fitted linear relation between the GC bias coefficient for each of the sections and the counts of the sequence reads mapped to each of the sections of the reference genome for the multiple samples, S is the slope of the fitted linear relation between the GC bias coefficient for each of the sections and the counts of the sequence reads mapped to each of the sections of the reference genome for the multiple samples, G i is the GC bias coefficient for the test sample i, m i is measured counts mapped to each section for the test sample i, thereby providing calculated genomic section levels; and I is the intercept from a fitted linear relation between the GC bias coefficient for each of the sections and the counts of the sequence reads mapped to each of the sections of the reference genome for the multiple samples, S is the slope of the fitted linear relation between the GC bias coefficient for each of the sections and the counts of the sequence reads mapped to each of the sections of the reference genome for the multiple samples, G i is the GC bias coefficient for the test sample i, m i is measured counts mapped to each section for the test sample i, thereby providing calculated genomic section levels; and (d) identifying the presence or absence of a sex chromosome aneuploidy for the fetus according to the calculated genomic section levels.