Back to results
US 2014/0349859 A1Published application
Detection of target nucleic acids using hybridization
AssigneeAriosa Diagnostics, Inc.
InventorsArnold Oliphant, Jacob Zahn, Kara Juneau, Patrick Bogard, Stephanie Huang
Life of this patent
Estimating the term…
Abstract
The present invention provides detection systems and methods for detection of loci and genomic regions in a sample, including mixed samples, using hybridization to an array.
Claims20
An assay method for providing a statistical likelihood of a fetal copy number variation comprising:
- providing a maternal sample comprising maternal and fetal cell free DNA;
- interrogating two or more loci from a first target genomic region using synthetic oligonucleotides comprising a region complementary to a locus in the first target genomic region and a capture region;
- interrogating two or more loci from a second target genomic region using synthetic oligonucleotides comprising a region complementary to a locus in the second target genomic region and a capture region;
- detecting the interrogated loci from the first and second target genomic region via hybridization of the capture regions of the synthetic oligonucleotides to an array comprising capture probes complementary to the capture regions;
- quantifying the capture regions of the synthetic oligonucleotides to determine a relative frequency of the interrogated loci;
- estimating the relative frequency of the first and second target genomic regions based on the quantified interrogated loci;
- interrogating polymorphic loci from at least one target genomic region different from the first and second target genomic regions using allele-specific oligonucleotides;
- detecting alleles of the polymorphic loci;
- quantifying the alleles of the polymorphic loci to determine the fraction of fetal DNA in the sample;
- and
- calculating a statistical likelihood of a fetal copy number variation in the maternal sample using the estimated relative frequency of the first and second genomic regions in the sample and the fraction of fetal DNA.
8 more elements
An assay method for determining a likelihood of a fetal aneuploidy comprising the steps of:
- providing a maternal sample comprising maternal and fetal cell free DNA;
- introducing at least a first set of two or more fixed sequence oligonucleotides complementary to a locus in a first target genomic region in the maternal sample under conditions that allow a complementary region of each fixed sequence oligonucleotide to specifically hybridize to the locus, wherein at least one of the fixed sequence oligonucleotides of each set comprises a universal primer site and a capture region;
- introducing at least a second set of two or more fixed sequence oligonucleotides complementary to a locus in a second target genomic region in the maternal sample under conditions that allow a complementary region of each fixed sequence oligonucleotide to specifically hybridize to the locus, wherein at least one of the fixed sequence oligonucleotides of each set comprises a universal primer site and a capture region;
- extending at least one of the hybridized fixed sequence oligonucleotides of the first and second sets to form adjacently hybridized fixed sequence oligonucleotides;
- ligating the hybridized first and second fixed sequence oligonucleotides of the first and second set to create ligation products corresponding to the loci;
- amplifying the ligation products using the universal primer sites;
- applying the amplified ligation products to an array, wherein the array comprises capture probes complementary to the capture regions on the ligation products;
- quantifying a relative frequency of ligation products corresponding to loci from the first target genomic region and a relative frequency of ligation products corresponding to loci from the second target genomic region;
- and
- computing a likelihood of fetal aneuploidy using the relative frequency of ligation products corresponding to loci from the first and second target genomic regions to determine the likelihood of a fetal aneuploidy.
7 more elements
An assay method for determining a likelihood of a fetal aneuploidy comprising the steps of:
- providing a maternal sample comprising maternal and fetal cell free DNA;
- introducing at least a first set of two or more fixed sequence oligonucleotides complementary to a locus in a first target genomic region in the maternal sample under conditions that allow a complementary region of each fixed sequence oligonucleotide to specifically hybridize to the locus, wherein at least one of the fixed sequence oligonucleotides of each set comprises a universal primer site and a capture region;
- introducing at least a second set of two or more fixed sequence oligonucleotides complementary to a locus in a second target genomic region in the maternal sample under conditions that allow a complementary region of each fixed sequence oligonucleotide to specifically hybridize to the locus, wherein at least one of the fixed sequence oligonucleotides of each set comprises a universal primer site and a capture region;
- introducing two or more third sets of two or more fixed sequence oligonucleotides complementary to a set of polymorphic loci in the maternal sample under conditions that allow a complementary region of each fixed sequence oligonucleotide to specifically hybridize to a polymorphic locus, wherein at least one of the two fixed sequence oligonucleotides of each set comprises a universal primer site and a capture region;
- extending at least one of the hybridized fixed sequence oligonucleotides of the first and second sets to form adjacently hybridized fixed sequence oligonucleotides;
- ligating the adjacent hybridized first and second fixed sequence oligonucleotides from the first and second sets to create ligation products corresponding to the loci;
- amplifying the ligation products using the universal primer sites;
- applying the amplified ligation products to an array, wherein the array comprises capture probes complementary to the capture regions on the ligation products;
- quantifying a relative frequency of each allele from the polymorphic loci to determine a percent fetal cell-free DNA in the sample;
- quantifying a relative frequency of ligation products corresponding to loci from the first target genomic region and a relative frequency of ligation products corresponding to loci from the second target genomic region;
- and
- computing a likelihood of a fetal aneuploidy using the relative frequency of ligation products corresponding to loci from the first and second target genomic regions and the percent fetal cell-free DNA.
9 more elements
Dependencies are inferred from the claim text.