Polymorphic DNA fragments and uses thereof

• US 20060199198A1
• Filed: 01/13/2006
• Published: 09/07/2006
• Est. Priority Date: 02/22/1999
• Status: Abandoned Application

• Current Assignee: Solexa Incorporated (Illumina Incorporated)
• Original Assignee: Solexa Incorporated (Illumina Incorporated)
• Inventors: Brenner, Sydney
• Application Number:
  US11/331,661
• Publication Number:
  US 20060199198A1
• Time in Patent Office: Days
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/683 involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence

Abstract

The invention provides methods and materials for generating a reference library of restriction fragments from pooled nucleic acids that contain a sequence polymorphism. Preferably, such a library is formed by digesting genomic DNA from a pool of individuals with a first and a second restriction endonuclease to form a population of restriction fragments; isolating restriction fragments of the population digested by both the first and second restriction endonucleases and forming a first single stranded fragment population therefrom; separately isolating restriction fragments from the population digested by the first restriction endonuclease but not the second restriction endonuclease and forming a second single stranded fragment population therefrom; hybridizing the first and second single stranded fragment populations to form a population of duplexes; and isolating the population of duplexes to form a reference library of restriction fragments that contain sequence polymorphism. An important aspect of the invention is the use of the reference population of restriction fragments to compare the frequencies of polymorphic sequences between different population pools. Such comparisons may be accomplished by competively hybridizing DNA from the respective pools which has been enriched for the presence of a restriction site polymorphism with DNA from the reference population. Preferably, such competitive hybridization reactions are carried out the reference library attached to one or more solid phase supports. Most preferably, members of the reference library are attached to individual microparticles so that each microparticle has a unique fragment attached. After competitive hybridization, the microparticles may be analyzed and sorted for identifying those microparticles carrying sequences for which the pools being compared exhibit different polymorphic frequencies.

Claims

1. A method of making a reference library comprising a mixture of heterogeneous nucleic acid fragments, comprising:

digesting pooled nucleic acid from a plurality of individuals, comprising first restriction sites s, with a first restriction endonuclease S, to produce a mixture of restriction fragments;

forming a first population of single stranded nucleic DNA fragments from a first subpopulation of said restriction fragments, wherein said first subpopulation of restriction fragments comprises a second restriction site t which is different from said first restriction site;

forming a second population of single stranded DNA fragments from a second subpopulation of said restriction fragments, wherein said second subpopulation of said restriction fragments do not contain said second restriction site, and wherein said first single stranded DNA fragments are complementary to said second single stranded DNA fragments when said single stranded DNA fragments are derived from the same restriction fragment;

hybridizing the first and second populations of single stranded DNA fragments to form a population of duplexes; and

isolating said duplexes to form a reference population of restriction fragments.

2. The method of claim 1, further comprising the step of pretreating said pooled nucleic acid to enrich for non-repetitive sequences.

3. The method of claim 1, wherein forming said first population comprises:

(a) attaching a Q adaptor, containing a primer binding site, to a sample of said mixture of restriction fragments, to produce fragment-adaptor complexes;

(b) digesting said fragment-adaptor complexes with a second restriction endonuclease T, which cleaves at said second restriction site t, to produce a population containing (i) fragments which lack said restriction site t and (ii) fragments having a Q adaptor at one end and a protruding strand resulting from cleavage of t at the other end;

(c) attaching to the protruding strands of fragments (ii), an M adaptor, itself having a 3′

protruding strand at the end distal to the fragment to which it is attached, and a primer binding site;

thereby producing a mixture containing fragments having a Q adaptor at each end, designated Q-Q fragments, and fragments having a Q adaptor at one end and an M adaptor at the other end, designated Q-M fragments;

(d) digesting said mixture with a 3′

-exonuclease, to produce a further mixture containing a full length single stranded fragment from each Q-M fragment and two half-length single stranded fragments from each Q-Q fragment;

(e) annealing an M-specific primer to said primer binding site of the M adaptors in said further mixture;

extending said primer to give double stranded Q-M fragments; and

amplifying said double stranded fragments, using an M-specific primer and a Q-specific primer;

(f) cleaving said amplified double stranded fragments with restriction endonuclease S; and

(g) digesting the cleaved fragments with a 5→

3′

exonuclease, to give single stranded fragments.

4. The method of claim 1, wherein forming said second population comprises:

(a) attaching an N adaptor to a sample of said mixture of restriction fragments, to produce fragment-adaptor complexes;

(b) cleaving said complexes with a second restriction endonuclease T, which cleaves at said second restriction site t, to produce a population containing (i) fragments which lack said restriction site t and (ii) fragments having an N adaptor at one end and a protruding strand resulting from cleavage of t at the other end;

(c) amplifying said fragments having an N adaptor, using an N-specific primer; and

(d) digesting the amplified fragments with a 3′

exonuclease, to give partially single stranded fragments.

5. The method of claim 1, wherein the frequency of restriction site t in said pooled nucleic acid is greater than that of restriction sites.