A computer-implemented method for calculating with reduced bias genomic section levels for a test sample, comprising: (a) obtaining counts of sequence reads mapped to portions of a reference genome, which sequence reads are reads of circulating cell-free nucleic acid from a test sample; (b) determining a guanine and cytosine (GC) bias for each of the portions of the reference genome for multiple samples from a fitted linear relation for each sample between (i) the counts of the sequence reads mapped to each of the portions of the reference genome, and (ii) GC content for each of the portions, wherein each GC bias is a GC bias coefficient, which GC bias coefficient is the slope of the linear relationship between (i) the counts of the sequence reads mapped to each of the portions of the reference genome, and (ii) the GC content for each of the portions; and (c) calculating a genomic section level for each of the portions of the reference genome from a fitted linear relation between (i) the GC bias and (ii) the counts of the sequence reads mapped to each of the portions of the reference genome, thereby providing calculated genomic section levels, wherein the genomic section level L i is determined for each of the portions of the reference genome according to Equation α: L i = m i − G i S I − 1 wherein G i is the GC bias, I is the intercept of the fitted relation in (c), S is the slope of the relation in (c), m i is measured counts mapped to each portion of the reference genome and i is a sample, whereby bias in the counts of the sequence reads mapped to each of the portions of the reference genome is reduced in the calculated genomic section levels. (a) obtaining counts of sequence reads mapped to portions of a reference genome, which sequence reads are reads of circulating cell-free nucleic acid from a test sample; (b) determining a guanine and cytosine (GC) bias for each of the portions of the reference genome for multiple samples from a fitted linear relation for each sample between (i) the counts of the sequence reads mapped to each of the portions of the reference genome, and (ii) GC content for each of the portions, wherein each GC bias is a GC bias coefficient, which GC bias coefficient is the slope of the linear relationship between (i) the counts of the sequence reads mapped to each of the portions of the reference genome, and (ii) the GC content for each of the portions; and (c) calculating a genomic section level for each of the portions of the reference genome from a fitted linear relation between (i) the GC bias and (ii) the counts of the sequence reads mapped to each of the portions of the reference genome, thereby providing calculated genomic section levels, wherein the genomic section level L i is determined for each of the portions of the reference genome according to Equation α: L i = m i − G i S I − 1 wherein G i is the GC bias, I is the intercept of the fitted relation in (c), S is the slope of the relation in (c), m i is measured counts mapped to each portion of the reference genome and i is a sample, whereby bias in the counts of the sequence reads mapped to each of the portions of the reference genome is reduced in the calculated genomic section levels. <EOS>