Methods of Analysis of Methylation

a methylation and analysis method technology, applied in the field of methods of analysis of methylation, can solve the problems of genomic instability and alterations in the normal methylation process, and achieve the effects of reducing the risk of methylation instability

Inactive Publication Date: 2008-05-08
AFFYMETRIX INC
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  • Abstract
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  • Application Information

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Benefits of technology

[0012] The multiplex methods of the present invention may include at least 10 templates of distinct sequence, at least 100 templates of distinct sequence, at least 1000 templates o...

Problems solved by technology

Alterations in the normal methylation process have also bee...

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General

[0034] The present invention has many preferred embodiments and relies on many patents, applications and other references for details known to those of the art. Therefore, when a patent, application, or other reference is cited or repeated below, it should be understood that it is incorporated by reference in its entirety for all purposes as well as for the proposition that is recited.

[0035] As used in this application, the singular form “a,”“an,” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “an agent” includes a plurality of agents, including mixtures thereof.

[0036] An individual is not limited to a human being, but may also include other organisms including but not limited to mammals, plants, fungi, bacteria or cells derived from any of the above.

[0037] Throughout this disclosure, various aspects of this invention can be presented in a range format. It should be understood that the description in range format ...

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Abstract

Methods for determining the methylation status of a plurality of cytosines are disclosed. In some aspects genomic DNA target sequences containing CpGs are targeted for analysis by multiplex amplification using target specific probes that can be specifically degraded prior to amplification. The targets may be modified with bisulfite prior to amplification. In another aspect targets are cut with methylation sensitive or insensitive restriction enzymes and marked with a tag using the target specific probes. The presence or absence of methylation may be determined using methylation sensitive restriction enzyme or bisulfite treatment. Detection in many embodiments employs hybridization to tag arrays, genotyping arrays or resequencing arrays.

Description

RELATED APPLICATIONS [0001] The present application claims priority to U.S. application No. 60 / 862,735 filed Oct. 24, 2006, the disclosure of which is incorporated herein by reference in its entirety.BACKGROUND OF THE INVENTION [0002] The genomes of higher eukaryotes contain the modified nucleoside 5-methyl cytosine (5-meC). This modification is usually found as part of the dinucleotide CpG. [0003] Cytosine is converted to 5-methylcytosine in a reaction that involves flipping a target cytosine out of an intact double helix and transfer of a methyl group from S-adenosylmethionine by a methyltransferase enzyme (Klimasauskas et al. Cell 76:357-369, 1994). This enzymatic conversion is the only epigenetic modification of DNA known to exist in vertebrates and is essential for normal embryonic development (Bird, Cell 70:5-8, 1992; Laird and Jaenisch, Human Mol. Genet. 3:1487-1495, 1994; and Li et al. Cell 69:915-926, 1992). [0004] The frequency of the CpG dinucleotide in the human genome i...

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Application Information

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IPC IPC(8): C12Q1/68
CPCC12Q1/6813C12Q2600/154C12Q2521/331C12Q2523/125C12Q1/6853C12Q1/6806C12Q1/683
Inventor NAUTIYAL, SHIVANIFAHAM, MALEK
Owner AFFYMETRIX INC
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