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US 2013/0172212 A1Published application
Ligation-based detection of genetic variants
AssigneeAriosa Diagnostics, Inc.
InventorsArnold Oliphant, Andrew Sparks, John Stuelpnagel, Ken Song
Life of this patent
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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.
Claims22
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 fixed sequence oligonucleotides to the genetic sample under conditions that allow the fixed sequence oligonucleotides to specifically hybridize to complementary regions in each nucleic acid region of interest, wherein both ends of each fixed sequence oligonucleotide are complementary to a single nucleic acid region of interest, and wherein upon hybridization each fixed sequence oligonucleotide forms a pre-circle oligonucleotide;
- introducing one or more bridging oligonucleotides to the genetic sample under conditions that allow the one or more 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 ends of the fixed sequence oligonucleotides, and wherein the one or more bridging oligonucleotides hybridize continguously between the ends of the fixed sequence oligonucleotides;
- ligating the hybridized oligonucleotides to create circular ligation products, a portion of which is complementary to the nucleic acid region of interest;
- amplifying the circular 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.
4 more elements
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 fixed sequence oligonucleotides to the genetic sample under conditions that allow the fixed sequence oligonucleotides to specifically hybridize to complementary regions in each nucleic acid region of interest, wherein both ends of the fixed sequence oligonucleotides are complementary to a single nucleic acid region of interest, wherein upon hybridization each fixed sequence oligonucleotide forms a pre-circle oligonucleotide and wherein each fixed sequence oligonucleotide comprises a locus index specific for 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 ends of the fixed sequence oligonucleotides, and wherein the one or more bridging oligonucleotides hybridize continguously between the ends of the fixed sequence oligonucleotides;
- ligating the hybridized oligonucleotides to create a circular ligation product, a portion of which is complementary to the nucleic acid region of interest;
- amplifying the circular 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 circular amplification products.
3 more elements
Dependencies are inferred from the claim text.