Methods and compositions for whole genome amplification and genotyping

• US 9,045,796 B2
• Filed: 06/17/2004
• Issued: 06/02/2015
• Est. Priority Date: 06/20/2003
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Gunderson, Kevin, Steemers, Frank
• Primary Examiner(s): Pande, Suchira
• Application Number:
  US10/871,513
• Publication Number:
  US 20050037393A1
• Time in Patent Office: 4,002 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/682 Signal amplification
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6848 characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
• CPC Class Codes: C12Q 2522/101 Single or double stranded nucleic acid binding proteins
• CPC Class Codes: C12Q 2525/301 Hairpin oligonucleotides
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2537/163 blocking probe
• CPC Class Codes: C12Q 2565/513 characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: C12Q 2565/537 characterised by the capture oligonucleotide acting as a primer
• CPC Class Codes: C12Q 2565/549 characterised by the capture oligonucleotide being a reporter labelled capture oligonucleotide

Abstract

This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.

Claims

1. A method for indicating the presence of single nucleotide polymorphisms (SNPs) of interest in typable loci of a genome, comprising the steps of:

(a) providing an array of at least 1,000 different immobilized nucleic acid probes that are attached to a surface for flow-through sample analysis, wherein said at least 1,000 different immobilized nucleic acid probes comprise a region of at most 100 nucleotides in length that are complementary to at least 1,000 different typable loci of a genome;

(b) contacting said array with a population of genome fragments representing 1.7 Gigabases or more of genomic sequence under conditions wherein probe-fragment hybrids are formed;

(c) contacting said probe-fragment hybrids with a polymerase and a nucleotide analog comprising a label under conditions whereby if the typable locus of a fragment contains a SNP of interest, the hybridized probe is modified by incorporation of the nucleotide analog to obtain a labeled probe; and

(d) detecting the labeled probe, thereby indicating the presence of said single nucleotide polymorphisms of interest at typable loci of said genome.

2. The method of claim 1, wherein said population of genome fragments is obtained by amplification under isothermal conditions and is amplified at least 10-fold.

3. The method of claim 1, wherein said population of genome fragments is obtained by denaturing said genome prior to step (b).

4. The method of claim 3, wherein said denaturing comprises heat denaturing.

5. The method of claim 1, wherein said immobilized nucleic acid probes are attached to particles.

6. The method of claim 5, wherein each of said particles is attached to a single type of nucleic acid probe.

7. The method of claim 1, wherein the surface is a flat or planar substrate upon which said immobilized nucleic acid probes are attached.

8. The method of claim 1, wherein at least 100,000 of said different nucleic acid probes hybridize with genome fragments to form probe-fragment hybrids.

9. The method of claim 1, wherein said population of genome fragments is obtained by random primer amplification.

10. The method of claim 1, wherein said population of genome fragments is obtained using a polymerase having low processivity.

11. The method of claim 1, further comprising exposing said probe-fragment hybrids to denaturing conditions after step (c), thereby removing said genome fragments.

12. The method of claim 1, wherein the label is an affinity ligand, thereby forming affinity ligand-labeled probes.

13. The method of claim 12, further comprising contacting said affinity ligand-labeled probes with a receptor and an amplification reagent, wherein said receptor has one or more sites capable of binding said ligand, and wherein said amplification reagent has affinity for said receptor, whereby multimeric complexes form between said affinity ligand-labeled probes, said receptor and said amplification reagent.

14. The method of claim 13, wherein said detecting comprises detecting said multimeric complexes.

15. The method of claim 1, wherein said probes are 25 to 60 nucleotides in length.

16. The method of claim 1, wherein the population of genome fragments represent 2.7 Gigabases or more of genomic sequence.

17. The method of claim 1, wherein the genome fragments are at most 0.6 kb in length.

18. The method of claim 1, wherein said genome fragments are concatenated DNA produced by ligating fragmented genomic DNA.

19. The method of claim 1, wherein at least 30 copies and at most 10,000 copies of said genome are representationally amplified.

20. The method of claim 1, further comprising the step of

(b1) after step (b), contacting the plurality of nucleic acid probes with an ectopic extension inhibitor (EE1) under conditions wherein probe-EE1 hybrids are formed;

whereby step (c) detects probe-fragment hybrids selectively compared to probe-EE1 hybrids.

21. The method of claim 20, wherein the EE1 is a single-stranded nucleic acid binding protein (SSB).

22. The method of claim 20, wherein the EE1 is a blocking oligonucleotide that is complementary to the 3′

-end of a nucleic acid probe.

23. The method of claim 1, wherein at least one of the plurality of different nucleic acid probes comprises a first region and a second region, wherein the second region is complementary to the first region, whereby a probe that does not form a probe-fragment hybrid forms a hairpin structure that is not capable of addition of a nucleotide or nucleotide analog by a polymerase.

24. The method of claim 23, wherein the first and second regions of the nucleic acid probe do not substantially anneal at temperatures used during probe-fragment hybridization, but anneal to form hairpin structures at temperatures used during polymerase addition.

25. The method of claim 1, wherein the addition by a polymerase is a single nucleotide analog.

26. The method of claim 1, wherein the addition by a polymerase is more than one nucleotide analog.

27. The method of claim 1, wherein said immobilized nucleic acid probes are configured as an array of arrays, having a plurality of individual arrays configured to allow processing of multiple samples.

28. The method of claim 1, wherein the nucleotide analog in step (c) comprises a native nucleotide and a detection label.

29. The method of claim 1, wherein the nucleotide analog in step (c) comprises a non-native nucleotide and a detection label.

30. The method of claim 2, wherein said population of genome fragments is obtained by random primer amplification.