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Assay systems for genetic analysis

a technology of genetic analysis and assay system, which is applied in the direction of biochemical apparatus and processes, specific use of bioreactors/fermenters, and after-treatment of biomass, etc., can solve the problem of limited amplification before detection, and achieve the effect of reducing the number of amplification

Inactive Publication Date: 2013-02-14
TANDEM DIAGNOSTICS
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

The invention provides a method for detecting copy number variations and chromosomal abnormalities in a mixed nucleic acid sample using selected loci. The method allows for amplification of the selected loci using various detection techniques such as hybridization, digital PCR, and high throughput sequencing. The method can be used with any type of mixed sample, such as cell-free DNA, and can be performed using a single set of fixed sequence oligonucleotides. The method provides a reliable and accurate way to detect copy number variations and chromosomal abnormalities in mixed samples.

Problems solved by technology

Although amplification of the mixed sample prior to the identification and quantification of the selection nucleic acids regions is not mandatory, limited amplification prior to detection can be performed, in particular if the initial amounts of nucleic acid are limited.

Method used

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  • Assay systems for genetic analysis
  • Assay systems for genetic analysis
  • Assay systems for genetic analysis

Examples

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example 1

General Aspects of the Assay Systems of the Invention

[0246]A number of assay formats were tested to demonstrate the ability to perform selective amplification and detection of independent loci to demonstrate multiplexed, ligation-based detection of a large number (e.g., 96 or more) of loci of interest. These loci included loci that were indicative of the presence of a particular chromosome or the presence or absence of a mutation or polymorphism in a particular allele.

[0247]These assays were designed based on human genomic sequences, and each interrogation consisted of two fixed sequence oligos per selected locus interrogated in the assay. The first oligo, complementary to the 3′ region of a genomic region, comprised the following sequential (5′ to 3′) oligo elements: a universal PCR priming sequence common to all assays: TACACCGGCGTTATGCGTCGAGAC (SEQ ID NO:1); a nine nucleotide identification index specific to the selected locus; a 9 base locus- or locus / allele-specific sequence th...

example 2

Preparation of DNA for Use in Tandem Ligation Procedures

[0252]Genomic DNA from a Caucasian male (NA12801) or a Caucasian female (NA11995) was obtained from Coriell Cell Repositories (Camden, N.J.) and fragmented by acoustic shearing (Covaris, Woburn, Mass.) to a mean fragment size of approximately 200 bp.

[0253]The Coriell DNA was biotinylated using standard procedures. Briefly, the Covaris fragmented DNA was end-repaired by generating the following reaction in a 1.5 ml microtube: 5 μg DNA, 12 μl 10× T4 ligase buffer (Enzymatics, Beverly Mass.), 50 U T4 polynucleotide kinase (Enzymatics, Beverly Mass.), and H20 to 120 μl. This was incubated at 37° C. for 30 minutes. The DNA was diluted using 10 mM Tris 1 mM EDTA pH 8.5 to desired final concentration of ˜2 ng / μl.

[0254]5 μl DNA was placed in each well of a 96-well plate, and the plate sealed with an adhesive plate sealer and spun for 10 seconds at 250×g. The plate was then incubated at 95° C. for 3 minutes, cooled to 25° C., and spun a...

example 3

Exemplary Assay Formats Using Tandem Ligation

[0256]Numerous tandem ligation assay formats using the biotinylated DNA were tested to illustrate proof of concept for the assay systems of the invention, and demonstrated the ability to perform highly multiplexed, targeted detection of a large number of independent loci using the series of different assay formats. The exemplary assay systems of the invention were designed to comprise 96 or more interrogations per loci in a genetic sample, and in cases where SNPs were detected the assay formats utilized 192 or more separate interrogations, each utilizing the detection of different alleles per 96 loci in genetic samples. The examples described for each assay format utilized two different sets of fixed sequence oligonucleotides and / or bridging oligos (as described in Example 1), comprising a total 96 or 192 interrogation reactions for the selected loci depending upon whether or not SNPs were identified.

[0257]A first exemplary assay format u...

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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.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]The present application claims priority to U.S. Ser. No. 13 / 013,732, filed Jan. 25, 2011, which claims priority to U.S. Ser. No. 61 / 371,605, filed Aug. 6, 2010, which is herein incorporated by reference.FIELD OF THE INVENTION[0002]This invention relates to the detection and quantification of genetic variation in mixed samples in a single assay.BACKGROUND OF THE INVENTION[0003]In the following discussion certain articles and methods will be described for background and introductory purposes. Nothing contained herein is to be construed as an “admission” of prior art. Applicant expressly reserves the right to demonstrate, where appropriate, that the articles and methods referenced herein do not constitute prior art under the applicable statutory provisions.[0004]Genetic abnormalities account for a wide number of pathologies, including pathologies caused by chromosomal aneuploidy (e.g., Down syndrome), germline mutations in specific genes (e....

Claims

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Application Information

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IPC IPC(8): C12M1/34
CPCC12Q1/6827C12Q1/6869C12Q1/6883C12Q1/6858C12Q2525/155C12Q2533/107C12Q2537/16C12Q2600/156C12Q2600/158
Inventor SPARKS, ANDREWOLIPHANT, ARNOLDZAHN, JACOBSONG, KENSTUELPNAGEL, JOHN
Owner TANDEM DIAGNOSTICS
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