Identification of chemically modified polymers
OwnerHarold R. Garner, John D. Minna +2inventors
InventorsHarold R. Garner, John D. Minna, Kevin J. Luebke, Robert P. Balog
Life of this patent
Estimating the term…
Abstract
The present invention provides a high-throughput method for the parallel analysis of many potential sites of chemical modification (e.g., methylation) in DNA. It makes use of chemical treatment of the DNA to alter its sequence in a way that depends upon the modification of interest and subsequent analysis of the resulting sequence by hybridization to an array of probes. A device, comprising the array of probes, is provided by the invention, and principles and methods for its design and fabrication are also provided.
Claims71
A method for the analysis of chemical modification of DNA comprising the steps of:
- obtaining a sample of DNA to be analyzed;
- treating the DNA with one or more chemical reagents that result in different base sequences depending upon the presence or absence of the modification of interest;
- and
- determining a portion of the base sequence of the resulting DNA.
An array of one or more probes synthesized on a solid support wherein the probes are controlled for methylation state and detect one or more sites of methylation in a sample.
A method for generating DNA probe sequences comprising the steps:
- inputing a nucleic acid sequence in the 3-prime to 5-prime direction;
- converting the sequence to account for chemical modification;
- generating the complimentary sequence to the converted sequence in the 3-prime to 5-prime direction;
- generating a first parent probe by choosing a first starting position on the complementary sequence and an first ending position on the complementary sequence;
- generating a second parent probe by moving the first starting and first ending position one base unit in the same direction.
A method for generating DNA probe sequences comprising the steps:
- inputing a nucleic acid sequence in the 3-prime to 5-prime direction;
- converting the sequence to account for chemical modification;
- generating the complimentary sequence to the converted sequence in the 3-prime to 5-prime direction;
- locating one or more CpG dinucleotide regions within the complementary sequence;
- generating one or more first probes by identifying sequences that have at least one nucleic acid on each end of the CpG dinucleotide regions.
A method of preparing a probe for the analysis of chemical modifications of DNA comprising the steps of:
- inputing a sample sequence as a sequence file into a computer;
- converting the sequence file;
- and
- generating a complementary sequence of the converted sequence file.
Dependencies are inferred from the claim text.