Dna sequence analysis

• US 20060246449A1
• Filed: 02/26/2004
• Published: 11/02/2006
• Est. Priority Date: 02/26/2003
• Status: Active Grant

• Current Assignee: Solexa Ltd. (Illumina Incorporated)
• Original Assignee: Solexa Ltd. (Illumina Incorporated)
• Inventors: Durbin, Richard Michael, Todd, John Andrew, Swerdlow, Harold Philip, Barnes, Colin
• Granted Patent: US 7,351,532 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 2525/301 Hairpin oligonucleotides
• CPC Class Codes: C12Q 2561/125 Ligase Detection Reaction [LDR]

Abstract

There is disclosed a method for determining the identity of one or more mutations or single nucleotide polymorphisms (SNPs) in a genome, comprising: a contacting a sample genome, under conditions which permit template dependant oligonucleotide ligation, with a plurality of different oligonucleotide molecules which comprise (i) a first set of oligonucleotides each comprising a sequence of nucleotides that is complementary to a region on said genome that includes a known SNP site and which oligonucleotides are complementary to said region other than at a base at or near the 5′ end of said oligonucleotides that is to be tested for complementarity to a base at the SNP site, each of said oligonucleotides comprising a unique label to identify both the base to be tested and the position of the SNP to be scored, (ii) a second set of oligonucleotides each comprising a sequence of nucleotides complementary to a region on said target genome for hybridisation with said target genome adjacent the 5′ end of an oligonucleotide of said first oligonucleotide set, and a surface capture moiety, a phosphate moiety being located at any of either the 5′ end of said first set of oligonucleotides or the 3′ end of said second set of oligonucleotides, any resulting ligated oligonucleotide being immobilised on a solid support via the surface capture moiety, b. analysing said solid support for the identity of one or more of said unique labels and comparing the defined bases in any of said immobilised oligonucleotides to those of the reference one or more SNPs.

Claims

5-1. A method according to claim 1 wherein said label is a unique coding sequence of nucleotides in said first oligonucleotide set.

20. A method according to claim 4 wherein said label is a unique coding sequence of nucleotides in said first oligonucleotide set.