Ligation-based detection of genetic variants
AssigneeAriosa Diagnostics, Inc.
InventorsArnold Oliphant, Andrew Sparks, John Stuelpnagel, Ken Song
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Abstract
The present invention provides assays systems and methods for detection of genetic variants in a sample, including copy number variation and single nucleotide polymorphisms. The invention preferably employs the technique of tandem ligation, i.e. the ligation of two or more fixed sequence oligonucleotides and one or more bridging oligonucleotides complementary to a region between the fixed sequence oligonucleotides.
Claims21
A method for detecting nucleic acid regions of interest in a genetic sample, comprising the steps of:
- providing a genetic sample;
- introducing at least two sets of first and second fixed sequence oligonucleotides to the genetic sample under conditions that allow the sets of fixed sequence oligonucleotides to specifically hybridize to complementary regions in the nucleic acid regions of interest, wherein the first fixed sequence oligonucleotide of at least one set is specific for a polymorphism in a nucleic acid region of interest;
- introducing one or more bridging oligonucleotides to the genetic sample under conditions that allow the bridging oligonucleotides to specifically hybridize to complementary regions in the nucleic acid regions of interest, wherein the one or more bridging oligonucleotides are complementary to a region between the region of the nucleic acid region of interest complementary to the first and second fixed sequence oligonucleotides of a set, and wherein the one or more bridging oligonucleotides hybridize contiguously between the first and second fixed sequence oligonucleotides;
- ligating the hybridized oligonucleotides to create a ligation product complementary to the nucleic acid region of interest;
- amplifying the ligation product to create amplification products that reflect the relative frequency of the nucleic acid regions of interest in the genetic sample;
- and
- detecting and quantifying the amplification products to detect nucleic acid regions of interest in a genetic sample.
A method for detecting nucleic acid regions of interest in a genetic sample, comprising the steps of:
- providing a genetic sample;
- introducing at least two sets of first and second fixed sequence oligonucleotides to the genetic sample under conditions that allow the set of fixed sequence oligonucleotides to specifically hybridize to complementary regions in each nucleic acid region of interest, wherein the first fixed sequence oligonucleotides comprise a locus index and the first fixed sequence oligonucleotide of at least one set is specific for a polymorphism in a nucleic acid region of interest;
- introducing one or more bridging oligonucleotides to the genetic sample under conditions that allow the bridging oligonucleotides to specifically hybridize to complementary regions in the nucleic acid regions of interest, wherein the one or more bridging oligonucleotides are complementary to a region between the region of the nucleic acid region of interest complementary to the first and second fixed sequence oligonucleotides of a set, and wherein the one or more bridging oligonucleotides hybridize contiguously between the first and second fixed sequence oligonucleotides;
- ligating the hybridized oligonucleotides to create a ligation product complementary to the nucleic acid region of interest;
- amplifying the ligation product to create amplification products that reflect the relative frequency of the nucleic acid regions of interest in the genetic sample;
- and
- detecting and quantifying the amplification products to detect nucleic acid regions of interest in a genetic sample.
Dependencies are inferred from the claim text.