Compositions and methods for the amplification of nucleic acids

• US 10,870,099 B2
• Filed: 02/21/2013
• Issued: 12/22/2020
• Est. Priority Date: 07/26/2012
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Fan, Jian-Bing, Gunderson, Kevin L., Steemers, Frank J., Pokholok, Dmitry K., Kaper, Fiona
• Primary Examiner(s): Havlin, Robert H
• Application Number:
  US14/416,563
• Publication Number:
  US 20150360193A1
• Time in Patent Office: 2,861 Days
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions

Abstract

The present disclosure relates to systems and methods for the amplification of nucleic acids, including, but not limited to, the amplification of nucleic acid libraries and whole genome amplification.

Claims

1. A method of creating a nucleic acid library with reduced amplification bias from a nucleic acid sample comprising genomic DNA, the method comprising:

a) providing a set of amplification primers to the nucleic acid sample comprising;

(i) a plurality of random primers comprising primers selected from the group consisting of;

(A) a set of variable-length random amplification primers, wherein each primer comprises a random 3′

portion and a degenerate 5′

tail that is proportional in length to the A/T content of the random 3′

portion of the primer,

(B) a first set of random amplification primers, wherein each primer comprises a random 3′

portion that comprises RNA and a constant 5′

priming portion, and

(C) a second set of random amplification primers, wherein each primer comprises a random 3′

portion and a constant 5′

priming portion, wherein the random 3′

portion comprises at least one non-natural base selected from the group consisting of 2-thio-dT and 2-amino-dA;

(ii) a plurality of locus specific primers configured to amplify at least 100 predetermined genomic regions of the nucleic acids of the nucleic acid sample; and

(iii) a plurality of blocked primers complementary to regions of a genome comprising repetitive sequences;

wherein each plurality in the set of amplification primers is a mixture of primers; and

b) amplifying the nucleic acid sample using the set of amplification primers thereby creating a nucleic acid library, wherein the amplifying provides more homogeneous amplification of the nucleic acid sample as compared to amplifying in the absence of the plurality of locus specific primers.

2. The method of claim 1, wherein the random primers are from 5 to 18 nucleotides in length.

3. The method of claim 2, wherein the random primers are 9 nucleotides in length.

4. The method of claim 1, wherein the plurality of blocked primers comprise a 3′

blocking group.

5. The method of claim 1, wherein the plurality of blocked primers lack a 3′

OH.

6. The method of claim 1, wherein said locus specific primers comprise sequences specific to one or more repetitive regions of a genome.

7. The method of claim 1, wherein said locus specific primers comprise exonuclease-resistant primers, and wherein the amplifying comprises amplifying in the presence of a polymerase with exonuclease activity.

8. The method of claim 1, wherein said plurality of random primers are in greater abundance compared to said plurality of locus specific primers.

9. The method of claim 1, wherein the amplification primers comprise a set of Tm-normalized primers, wherein said primer set of Tm-normalized amplification primers comprises one or more base analogs selected from the group consisting of 2-thio-dT, 2-amino-dA, N4-Et-dC, and 7-deaza-G.

10. The method of claim 1, wherein the plurality of random primers comprise primers selected from the group consisting of:

an AT-rich set of random amplification primers;

a set of random amplification primers comprising AT-rich 5′

tails;

the set of variable-length random amplification primers, wherein each primer comprises a random 3′

portion and a degenerate 5′

tail that is proportional in length to the A/T content of the random 3′

portion of the primer;

a set of T_m-normalized amplification primers, wherein each primer of said set comprises one or more base analogs that normalize the T_m of each primer to the T_m of other primers in the set of primers;

a set of random amplification primers, wherein each primer comprises a random 3′

portion and a constant 5′

priming portion;

the first set of random amplification primers, wherein each primer comprises a random 3′

portion that comprises RNA and a constant 5′

priming portion;

the second set of random amplification primers, wherein each primer comprises a random 3′

portion and a constant 5′

priming portion, wherein the random 3′

portion comprises at least one non-natural base selected from the group consisting of 2-thio-dT and 2-amino-dA; and

any combination of the foregoing sets of primers.

11. The method of claim 1, wherein the plurality of locus specific primers are configured to hybridize to non-repetitive sequences in the human genome.

12. The method of claim 1, wherein the plurality of locus specific primers is configured to amplify at least 1000 predetermined genomic regions of the nucleic acid sample.

13. The method of claim 1, wherein the nucleic acid sample is a single cell.

14. The method of claim 1, wherein the plurality of locus specific primers is configured to amplify sequences that are distributed across the genomic DNA.

15. The method of claim 1, wherein the at least 100 predetermined genomic regions comprise regions distributed evenly along the length of at least a portion of a genome.

16. The method of claim 1, wherein the concentration of a first locus specific primer of the plurality of locus specific primers is different from the concentration of a second locus specific primer of the plurality of locus specific primers.

17. The method of claim 1, wherein the plurality of random primers comprises the set of variable-length random amplification primers, wherein each primer comprises a random 3′

portion and a degenerate 5′

tail that is proportional in length to the A/T content of the random 3′

portion of the primer.

18. The method of claim 1, wherein the at least 100 predetermined genomic regions comprise single nucleotide polymorphic (SNP) sites.