Patent Document ID: 20130325360
Application ID: 13797930
Patent Flag: 0

Claim One:
1. A method for determining the presence or absence of a complex genetic variation comprising: (a) obtaining counts of nucleic acid sequence reads mapped to portions of a reference genome, which sequence reads are reads of circulating cell-free nucleic acid from a sample from a pregnant female; (b) determining a guanine and cytosine (GC) bias for each of the portions 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 portions of the reference genome, and (ii) GC content for each of the portions; (c) calculating a genomic section level for each of the portions of the reference genome from a fitted 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, 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; and (d) determining the presence or absence of a complex genetic variation for the sample from the pregnant female according to the calculated genomic section levels, wherein the complex genetic variation comprises two or more genetic variations chosen from a whole chromosome aneuploidy, a microduplication and a microdeletion, and wherein the determination is generated from the nucleic acid sequence reads.