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US 2013/0210640 A1Published application
Assay systems for genetic analysis
AssigneeAriosa Diagnostics, Inc.
InventorsAndrew Sparks, Arnold Oliphant, Jacob Zahn, John Stuelpnagel, Ken Song
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Abstract
The present invention provides assay systems and methods for detection of copy number variation at one or more loci and polymorphism detection at one or more loci in a mixed sample from an individual.
Claims28
A method for detecting a presence or absence of copy number variations of one or more nucleic acid regions of interest and the presence of absence of polymorphisms in one or more nucleic acid regions of interest in a single assay, comprising the steps of:
- providing a genetic sample;
- introducing at least two first sets of first and second fixed sequence oligonucleotides to the genetic sample under conditions that allow the first sets of fixed sequence oligonucleotides to specifically hybridize to complementary regions in nucleic acid regions of interest;
- introducing at least two second sets of first and second fixed sequence oligonucleotides to the genetic sample under conditions that allow the second sets of fixed sequence oligonucleotides to specifically hybridize to complementary regions in nucleic acid regions of interest, wherein the first fixed sequence oligonucleotides of the second sets of fixed sequence oligonucleotides are complementary to alternative sequences of a polymorphism of interest in the nucleic acid regions of interest;
- extending the region between the first fixed sequence oligonucleotides of the first and second sets and the second fixed sequence oligonucleotides of the first and second sets with a polymerase and dNTPs to create adjacently-hybridized oligonucleotides in each set in the nucleic acid regions of interest;
- ligating the adjacently-hybridized oligonucleotides to create ligation products complementary to the nucleic acid regions of interest;
- amplifying the ligation products to create amplification products that are representative of the original content of the nucleic acid regions of interest in the genetic sample;
- and
- detecting and quantifying the amplification products from the first sets of fixed sequence oligonucleotides to detect the presence or absence of copy number variations in the nucleic acid regions of interest and detecting and quantifying the amplification products from the second sets of fixed sequence oligonucleotides to detect the presence of absence of polymorphisms in the nucleic acid regions of interest.
5 more elements
A method for detecting a presence or absence of copy number variations of one or more nucleic acid regions of interest and the presence of absence of polymorphisms in one or more nucleic acid regions of interest in a single assay, comprising the steps of:
- providing a genetic sample;
- introducing at least two first sets of first and second fixed sequence oligonucleotides to the genetic sample under conditions that allow the first sets of fixed sequence oligonucleotides to specifically hybridize to adjacent complementary regions in nucleic acid regions of interest;
- introducing at least two second sets of first and second fixed sequence oligonucleotides to the genetic sample under conditions that allow the second sets of fixed sequence oligonucleotides to specifically hybridize to adjacent complementary regions in nucleic acid regions of interest to create adjacently-hybridized oligonucleotides, wherein the first fixed sequence oligonucleotides of the second sets of fixed sequence oligonucleotides are complementary to alternative sequences of a polymorphism of interest in the nucleic acid regions of interest;
- ligating the adjacently-hybridized oligonucleotides to create ligation products complementary to the nucleic acid regions of interest;
- amplifying the ligation products to create amplification products that are representative of the original content of the nucleic acid regions of interest in the genetic sample;
- and
- detecting and quantifying the amplification products from the first sets of fixed sequence oligonucleotides to detect the presence or absence of copy number variations in the nucleic acid regions of interest and detecting and quantifying the amplification products from the second sets of fixed sequence oligonucleotides to detect the presence of absence of polymorphisms in the nucleic acid regions of interest.
4 more elements
Dependencies are inferred from the claim text.