Method of screening for genetic polymorphism

• US 6,653,077 B1
• Filed: 04/30/2001
• Issued: 11/25/2003
• Est. Priority Date: 09/04/1998
• Status: Expired due to Term

• Current Assignee: Solexa Incorporated (Illumina Incorporated)
• Original Assignee: Lynx Therapeutics, Inc. (Illumina Incorporated)
• Inventors: Brenner, Sydney
• Primary Examiner(s): Myers, Carla J.
• Application Number:
  US09/786,254
• Time in Patent Office: 939 Days
• Field of Search: 435/6, 435/91.2, 435/7.1, 435/91.5, 435/91.1
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 2521/301 Endonuclease
• CPC Class Codes: C12Q 2521/319 Exonuclease
• CPC Class Codes: C12Q 2521/325 Single stranded exonuclease
• CPC Class Codes: C12Q 2531/107 Probe or oligonucleotide ligation
• CPC Class Codes: C12Q 2537/113 Heteroduplex formation
• CPC Class Codes: C12Q 2537/149 Sequential reactions

Abstract

Method and materials are provided for screening for genetic polymorphism in a test population of DNA fragments. Heteroduplexes are formed between members of a test DNA population and their corresponding complements from a reference DNA population. Perfectly matched heteroduplexes are destroyed or separated from those containing mismatched sequences. Preferably, perfectly matched heteroduplexes are digested by a single stranded exonuclease which requires double stranded DNA as a substrate, such as E. coli exonuclease III. Amplicons are formed from mismatched heteroduplexes, preferably by extending the partially digested duplexes after treatment with exonuclease III followed by PCR amplification. The resulting amplicons are inserted into a cloning vector which is used to transform a bacterial host. After host cells are plated and allowed to form colonies, clones are picked and sequenced to identify DNA fragments containing polymorphic sequences.

Claims

1. A method of identifying polymorphic DNA sequences in a test DNA population, the method comprising the steps of:

(a) providing a reference DNA population;

(b) forming a population of heteroduplexes from single stranded DNA of the reference DNA population and single stranded DNA of the test DNA population, said heteroduplexes having at one terminus a region in which both strands are in single stranded form;

(c) treating said heteroduplexes with an exonuclease whose substrate is duplex DNA, such that said exonuclease converts substantially every perfectly matched duplex to single stranded DNA and substantially every mismatched duplex to partially double stranded DNA;

(d) extending said partially double stranded DNA to form double stranded heteroduplexes;

(e) amplifying the double stranded heteroduplexes to form a population of amplicons; and

(f) determining the nucleotide sequence of a portion of each amplicon so that polymorphic DNA sequences of the test DNA population are identified.

2. The method of claim 1, wherein members of said reference DNA population are provided in a first cloning vector, and members of said test DNA population are provided in a second cloning vector, wherein

the first cloning vector has a first primer binding site, a second primer binding site, a third primer binding site, and a cloning site disposed between the second and third primer binding sites,

and the second cloning vector has a fourth primer binding site, a fifth primer binding site, and a cloning site disposed between the fourth primer binding site and the fifth primer binding site, wherein the fifth primer binding site has a nucleotide sequence identical to said third primer binding site, and the sequence of the fourth primer binding site is different from that of any of the other primer binding sites.

3. The method of claim 2, wherein said single stranded DNA of said reference DNA population is generated by amplifying said members of said reference DNA population in a polymerase chain reaction, using a nuclease-resistant primer specific for said first primer binding site and a primer specific for said third primer binding site, to form an amplicon having a single strand with a nuclease-resistant 5′

end, and digesting the amplicon with a 5′

→

3′

exonuclease.

4. The method of claim 3 wherein said single stranded DNA of said test DNA population is generated by amplifying said members of said test DNA population in a polymerase chain reaction using a nuclease-resistant primer specific for said fourth primer binding site and a primer specific for said fifth primer binding site to form an amplicon having a single strand with a nuclease-resistant 5′

end, and digesting the amplicon with a 5′

→

3′

exonuclease.

5. The method of claim 1 wherein said step of forming a population of heteroduplexes includes partitioning said test DNA population into subpopulations and separately forming subpopulations of heteroduplexes from single stranded DNA of said reference DNA population and single stranded DNA from each subpopulation of said test DNA population.

6. The method of claim 5 wherein said subpopulations of said test DNA population and said reference DNA population have complexities which permit at least ninety percent of heteroduplexes of said subpopulations of heteroduplexes to be formed in seventy-two hours or less.