Patent Document ID: 9212394
Application ID: 14603323
Patent Flag: 1

Claim One:
1. A method of detecting trisomy in a fetus of a pregnant human subject, comprising contacting first and second probe sets to a cell-free DNA sample from the pregnant human subject, wherein the first probe set comprises a first labeling probe and a first tagging probe, the second probe set comprises a second labeling probe and a second tagging probe, the first and second tagging probes comprise a common tagging nucleotide sequence, hybridizing at least parts of the first and second probe sets to nucleotide molecules located in first and second chromosomes present in the cell-free DNA sample, respectively, ligating at least parts of the first probe set by ligating the first labeling probe and the first tagging probe to form a first ligated probe set, ligating at least parts of the second probe set by ligating the second labeling probe and the second tagging probe to form a second ligated probe set, amplifying (i) the first ligated probe set with first forward and reverse primers, wherein at least one of the first forward and reverse primers comprises a first label and hybridizes to the first labeling probe of the first ligated probe set, and (ii) the second ligated probe set with second forward and reverse primers, wherein at least one of the second forward and reverse primers comprises a second label and hybridizes to the second labeling probe of the second ligated probe set, to form amplified first and second ligated probe sets comprising (i) the first and second labels, respectively, and (ii) an amplified common tagging nucleotide sequence amplified from said common tagging nucleotide sequence, wherein the first and second labels are different, immobilizing by hybridizing at least a part of the amplified common tagging nucleotide sequence to affinity nucleotide tags immobilized on a substrate, at a density in which the first and second labels of the amplified first and second ligated probe sets are optically resolvable after immobilization, wherein the affinity nucleotide tags comprise a complementary sequence of the at least a part of the amplified common tagging nucleotide sequence, reading the first and second labels on the substrate in first and second imaging channels that correspond to the first and second labels, respectively, producing one or more images of the substrate, wherein the first and second labels are optically resolvable in the one or more images, distinguishing a first optical signal from a single first label from the rest of the optical signals from background and/or multiple first labels by calculating a relative signal and/or signal-to-noise intensity of the first optical signal compared to an intensity of an optical signal from a single first label, and determining whether the optical signal is from a single label, distinguishing a second optical signal from a single second label from the rest of the optical signals from background and/or multiple second labels by calculating a relative signal and/or signal-to-noise intensity of the second optical signal compared to an intensity of an optical signal from a single second label, and determining whether the optical signal is from a single label, counting (i) a first number of the first label from said first optical signal from the single first label, wherein the first number corresponds to a number of the amplified first ligated probe set immobilized to the substrate, and (ii) a second number of the second label from said second optical signal from the single second label, wherein the second number corresponds to a number of the amplified second ligated probe set immobilized to the substrate, and comparing the first and second numbers to determine whether a copy number of the first chromosome is greater than a copy number of the second chromosome, wherein the copy number of the first chromosome greater than the copy number of the second chromosome indicates the presence of trisomy of the first chromosome in the fetus.