Patent ID: 9388459
Filing Date: 2016-07-12
CPC Classification: C12Q

Claim Text:
1. A method for genotyping a plurality of polymorphisms in a nucleic acid sample, where each polymorphism has a first and a second allele, comprising: amplifying the nucleic acid sample using random primers and DNA polymerase in an isothermal amplification reaction to obtain an amplified nucleic acid sample; fragmenting the amplified nucleic acid sample to obtain a fragmented amplified nucleic acid sample; incubating the fragmented, amplified nucleic acid sample with a plurality of beads attached to allele-specific capture probes to allow formation of complexes between target fragments in the fragmented, amplified nucleic acid sample and allele-specific capture probes, wherein the plurality of beads are attached to a collection of allele-specific capture probes comprising at least 5,000different allele-specific capture probes, wherein the allele-specific capture probes comprise: extending the allele-specific capture probes in the presence of labeled nucleotides using the target fragment as template to obtain labeled allele-specific capture probes, wherein extension of the allele-specific capture probes is blocked if there is a mismatch between the polymorphic position and the 3′ end of the allele-specific capture probe; separating the target fragment from the extended labeled allele-specific capture probes; cleaving the extended labeled allele-specific capture probes from the beads to produce released extended labeled allele-specific capture probes; detecting the released extended labeled allele-specific capture probes by hybridization to an array of tag probes of known sequence, wherein no amplification of the released extended labeled allele-specific capture probes occurs between the cleaving and detecting steps, wherein said tag probes are present at known or determinable locations on said array and each tag probe is complementary to a different tag region present in the allele-specific capture probes; and determining the genotype of said plurality of polymorphisms by determining which alleles are present, wherein the presence of hybridized labeled allele-specific capture probes is indicative of the presence of a particular allele in the nucleic acid sample.