A single assay method for calculation of source contribution by a major and a minor source and detection of the presence or absence of copy number variation in one or more genomic regions in a mixed sample, the mixed sample being a maternal sample comprising both maternal and fetal DNA, the assay comprising the steps of: introducing a first set of fixed sequence oligonucleotides to the mixed sample in a vessel under conditions that allow the fixed sequence oligonucleotides to specifically hybridize to complementary regions on one or more loci in or associated with a genomic region, wherein at least one of the fixed sequence oligonucleotides comprises a universal primer region; introducing a second set of fixed sequence oligonucleotides to the mixed sample in the vessel under conditions that allow the fixed sequence oligonucleotides to specifically hybridize to complementary regions on two or more informative loci, wherein at least one of the fixed sequence oligonucleotides comprises a universal primer region; wherein the number of loci measured is less than 2000 per chromosome; ligating the hybridized oligonucleotides to create contiguous ligation products; amplifying the contiguous ligation products using the universal primer region to create amplification products; wherein unhybridized fixed sequence oligonucleotides are removed prior to amplification of the contiguous ligation products; detecting the sequence of the amplification products using high throughput sequencing, wherein each locus is measured on average at least 100 times; calculating the source contribution by determining the percentage of fetal DNA in the mixed sample, wherein the percentage fetal DNA detected by informative loci corresponds to the proportion of reads derived from non-maternal versus maternal alleles at loci where such a distinction can be made; and using the relative frequencies of the loci to determine the presence or absence of a copy number variation. introducing a first set of fixed sequence oligonucleotides to the mixed sample in a vessel under conditions that allow the fixed sequence oligonucleotides to specifically hybridize to complementary regions on one or more loci in or associated with a genomic region, wherein at least one of the fixed sequence oligonucleotides comprises a universal primer region; introducing a second set of fixed sequence oligonucleotides to the mixed sample in the vessel under conditions that allow the fixed sequence oligonucleotides to specifically hybridize to complementary regions on two or more informative loci, wherein at least one of the fixed sequence oligonucleotides comprises a universal primer region; wherein the number of loci measured is less than 2000 per chromosome; ligating the hybridized oligonucleotides to create contiguous ligation products; amplifying the contiguous ligation products using the universal primer region to create amplification products; wherein unhybridized fixed sequence oligonucleotides are removed prior to amplification of the contiguous ligation products; detecting the sequence of the amplification products using high throughput sequencing, wherein each locus is measured on average at least 100 times; calculating the source contribution by determining the percentage of fetal DNA in the mixed sample, wherein the percentage fetal DNA detected by informative loci corresponds to the proportion of reads derived from non-maternal versus maternal alleles at loci where such a distinction can be made; and using the relative frequencies of the loci to determine the presence or absence of a copy number variation.