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US 2004/0166493 A1Published application
Methods for variation detection
AssigneeNoga Porat
InventorsNoga Porat, Boaz Porat
Life of this patent
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Abstract
The present invention relates to methods for identifying variations that occur in the genome of an organism. In particular, the present invention relates to identifying variations without the need for specialized oligonucleotides complementary to each SNP and without a priori knowledge of the sequence or position of the variants.
Claims29
A method of analyzing variants in DNA samples comprising:
- obtaining the DNA samples;
- denaturing and renaturing the DNA samples to produce a heteroduplex;
- recognizing mismatched base pairs in the heteroduplex;
- cleaving the mismatched bases to produce abasic residues;
- cleaving a sugar-phosphate backbone of the heteroduplex 5′ and/or 3′ to the abasic residues;
- removing the abasic residues;
- generating a 3′-OH and a 5′-P site in the sugar-phosphate backbone;
- inserting a dNTP or a strand terminator at the 3′-OH site of the sugar-phosphate backbone;
- ligating the heteroduplex at the site of the sugar-phosphate backbone where a dNTP was inserted;
- terminating the heteroduplex at the site of the sugar-phosphate backbone where a strand terminator was inserted;
- and
- analyzing the heteroduplexes.
9 more elements
A method of analyzing variants in a DNA sample comprising:
- obtaining the DNA sample;
- recognizing modified nucleotides in the DNA sample;
- cleaving the modified nucleotides to produce abasic residues;
- cleaving a sugar-phosphate backbone of the DNA sample 5′ and/or 3′ to the abasic residues;
- removing the abasic residues;
- generating a 3′-OH and a 5′-P site in the sugar-phosphate backbone;
- inserting a dNTP or strand terminator at the 3′-OH site of the sugar-phosphate backbone;
- ligating the heteroduplex at the site of the sugar-phosphate backbone where a dNTP was inserted;
- terminating the heteroduplex at the site of the sugar-phosphate backbone where a strand terminator was inserted;
- and
- analyzing the heteroduplexes.
8 more elements
A method of analyzing SNPs in DNA samples comprising:
- obtaining the DNA samples;
- adding Mut Y to recognize modified nucleotides in the DNA sample, cleave the modified nucleotides to produce abasic residues, cleave a sugar-phosphate backbone of the DNA sample, remove the abasic residues, and generate a 3′-OH and a 5′-P site in the sugar-phosphate backbone;
- adding Klenow exo-, dCTP and ddCTP to insert a dCTP or ddCTP at the 3′-OH site of the sugar-phosphate backbone;
- adding DNA ligase to ligate the heteroduplex at the site of the sugar-phosphate backbone where a dNTP was inserted;
- terminating the heteroduplex at the site of the sugar-phosphate backbone where a strand terminator was inserted;
- and
- analyzing the heteroduplexes.
4 more elements
Dependencies are inferred from the claim text.