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Universal methylation profiling methods

a technology of methylation profiling and profiling methods, applied in the field of universal methylation profiling methods, can solve the problems of difficult to discern abnormality of genomic methylation patterns found in human diseases

Inactive Publication Date: 2011-07-21
THE TRUSTEES OF COLUMBIA UNIV IN THE CITY OF NEW YORK
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

While the normal function of the mammalian genome clearly depends on genomic methylation patterns, the abnormalities of genomic methylation patterns found in human disease have been difficult to discern because of the lack of methods for the methylation profiling of the entire genome.

Method used

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  • Universal methylation profiling methods
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Terms

[0056]As used herein, and unless stated otherwise, each of the following terms shall have the definition set forth below.

A—Adenine;

C—Cytosine;

[0057]DNA—Deoxyribonucleic acid;

G—Guanine;

[0058]RNA—Ribonucleic acid;

T—Thymine; and

U—Uracil.

[0059]“Nucleic acid” shall mean any nucleic acid molecule, including, without limitation, DNA, RNA and hybrids thereof. The nucleic acid bases that form nucleic acid molecules can be the bases A, C, G, T and U, as well as derivatives thereof. Derivatives of these bases are well known in the art, and are exemplified in PCR Systems, Reagents and Consumables (Perkin Elmer Catalogue 1996-1997, Roche Molecular Systems, Inc., Branchburg, N.J., USA).

[0060]“Type” of nucleotide refers to A, G, C, T or U. “Type” of base refers to adenine, guanine, cytosine, uracil or thymine.

[0061]“Mass tag” shall mean a molecular entity of a predetermined size which is capable of being attached by a cleavable bond to another entity.

[0062]“Solid substrates” shall mean any su...

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Abstract

This invention provides methods of derivatizing a double-stranded DNA comprising contacting double-stranded DNA with a CpG methyltransferase and an s-adenosylmethionine analog. This invention also provides methods of sequencing DNA to determine methylation patterns. This invention also provides neobases and methods of sequencing for methylation patterns using neobases.

Description

[0001]Throughout this application, various publications are referenced in parentheses. Full citations for these references may be found at the end of the specification immediately preceding the claims. The disclosures of these publications in their entireties are hereby incorporated by reference into this application to more fully describe the state of the art to which this invention pertains.BACKGROUND OF THE INVENTION[0002]The mammalian genome contains ˜28 million CpG sites, about 60% of which are methylated at the 5 position of the cytosine (Rollins et al., 2006). Methylation of relatively CpG-rich promoters causes very strong transcriptional repression (Stein et al., 1982, Lorincz et al., 2002); promoter methylation largely restricted to imprinted genes, transposon promoters, and to CpG islands on the inactive X chromosome. Many experiments have demonstrated faithful inheritance of methylation patterns over many cell divisions in somatic cells (Wigler et al., 1981; Lorincz et al...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12Q1/68C07H19/167C12N9/96C12P19/34C07H21/04C07H19/23
CPCC07H19/23C12Q1/6827C12Q1/6874C12Q2521/125C12Q2527/125C12Q2537/164C12Q1/6806
Inventor BESTOR, TIMOTHY H.EDWARDS, JOHN R.JU, JINGYUELI, XIAOXU
Owner THE TRUSTEES OF COLUMBIA UNIV IN THE CITY OF NEW YORK
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