Ligation-based detection of genetic variants

A method for detecting a fetal aneuploidy and alleles at polymorphic loci in a maternal plasma or serum sample, comprising the steps of:

• providing a maternal plasma or serum sample;
• introducing between 48 and 2000 first sets of first and second fixed sequence oligonucleotides to the maternal plasma or serum sample under conditions that allow the sets of fixed sequence oligonucleotides to specifically hybridize to non-polymorphic regions on a first chromosome of interest, wherein each first set comprises a binding region that binds selectively to a first array feature and a region that binds to a first label;
• introducing between 48 and 2000 second sets of first and second fixed sequence oligonucleotides to the maternal plasma or serum sample under conditions that allow the sets of fixed sequence oligonucleotides to specifically hybridize to non-polymorphic regions on a second chromosome of interest, wherein each second set comprises a binding region that binds selectively to the first array feature and a region that binds to a second label that is different from the first label;
• introducing between 48 and 2000 third sets of first, second and third fixed sequence oligonucleotides to the maternal plasma or serum sample under conditions that allow the sets of fixed sequence oligonucleotides to specifically hybridize to polymorphic regions of interest, wherein each third set comprises a first fixed sequence oligonucleotide specific for a first allele and a third label, a second fixed sequence oligonucleotide specific for a second allele and a fourth label different from the third label, a binding region that binds selectively to an array feature, and wherein there is a different binding region and a different array feature for each polymorphic region;
• hybridizing the sets of fixed sequence oligonucleotides to nucleic acids in the maternal plasma or serum sample;
• ligating the hybridized fixed sequence oligonucleotides to create contiguous ligation products complementary to the non-polymorphic and polymorphic regions of interest;
• introducing the contiguous ligation products to an array comprising array features complementary to binding regions in the contiguous ligation products;
• detecting hybridization of the contiguous ligation products from the first and second sets of fixed sequence oligonucleotides to the array by detection of the first and second labels at the first array feature;
• determining a frequency of the first and second chromosomes of interest based on the level of hybridization of the first and second sets of fixed sequence oligonucleotides;
• detecting a fetal aneuploidy based on the frequency of the first and second chromosomes of interest;
• detecting hybridization of the contiguous ligation products from the third sets of fixed sequence oligonucleotides to the array by detecting the third and fourth labels at the other array features;
• and
• determining a frequency of the first and second alleles at each polymorphic locus based on level of hybridization of the third sets of fixed sequence oligonucleotides comprising the third and fourth labels at the other array features.