Compounds and method for representational selection of nucleic acids from complex mixtures using hybridization

• US 10,538,759 B2
• Filed: 11/20/2017
• Issued: 01/21/2020
• Est. Priority Date: 10/10/2006
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Stuelpnagel, John R., Barker, David L., Velarde, Jorge, Barnard, Steven M., Graige, Michael
• Primary Examiner(s): Martinell, James
• Application Number:
  US15/818,712
• Publication Number:
  US 20180073016A1
• Time in Patent Office: 792 Days
• Field of Search: None
• CPC Class Codes: C12N 15/1072 Differential gene expression library synthesis, e.g. subtracted libraries, differential screening
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2565/515 characterised by the interaction between or sequential use of two or more arrays

Abstract

The invention provides a method of selecting a representational sample of nucleic acid sequences from a complex mixture. The method includes: (a) contacting a complex mixture of nucleic acids under conditions sufficient for hybridization with a population of capture probes complementary to one or more nucleic acids comprising a predetermined portion of the sequence collectively present in the complex mixture to form hybridization complexes of the one or more nucleic acids with the population of probes, the population of capture probes being attached to a solid support, and (b) removing unhybridized nucleic acids to select a representational sample of nucleic acids having a complexity of less than 10% but more than 0.001% of the complex mixture, wherein the representational sample comprises a nucleic acid copy having a proportion of each sequence in the copy relative to all other sequences in the copy substantially the same as the proportions of the sequences in the predetermined portion of one or more nucleic acids within the complex mixture. A method of selecting a representational sample of genomic sequences from a complete genome also is provided. The invention further provides a nucleic acid population that includes a representational sample having a complexity of less than 10% but more than 0.001% of a complex mixture, the representational sample comprising a nucleic acid copy having a proportion of each sequence in the copy relative to all other sequences in the copy substantially the same as the proportions of sequences in a predetermined portion of a sequence collectively present in one or more nucleic acids within the complex mixture.

Claims

1. A method of selecting a representational sample of nucleic acid sequences from a mixture of nucleic acids, comprising:

(a) obtaining a complex mixture of nucleic acids;

(b) providing a population of capture probes comprising nucleic acids complementary to nucleic acids comprising a predetermined portion of the nucleic acid sequences collectively present in the complex mixture of nucleic acids;

(c) contacting the complex mixture of nucleic acids with the capture probes under conditions sufficient for hybridization of the nucleic acids with the capture probes;

(d) removing unhybridized nucleic acids to separate desired sequences from undesired sequences within the mixture, thereby selecting a representational sample of nucleic acids, wherein the proportion of each sequence in the representational sample relative to all other sequences in the representational sample is substantially the same as the proportions of the sequences in the complex mixture;

(e) amplifying the nucleic acids in the representational sample to generate an amplified representational sample; and

(f) performing a sequence analysis of the amplified representational sample.

2. The method of claim 1, wherein the capture probes are attached to a solid support.

3. The method of claim 2, wherein the solid support comprises microspheres or a chip.

4. The method of claim 1, wherein the amplifying is on the solid support.

5. The method of claim 1, wherein the complex mixture of nucleic acids comprises genomic DNA sequence having a complexity of at least 1.7 Gbp.

6. The method of claim 1, wherein the representational sample of nucleic acids has a complexity of at least 0.001% and at most 49% of the mixture.

7. The method of claim 1, wherein the genomic DNA comprises human genomic DNA.

8. The method of claim 1, wherein the predetermined portion comprises one or more nucleic acid sequences selected from the group consisting of a low copy number gene, a rare mutation, and a mutation indicative of cancer.

9. The method of claim 1, wherein the complex mixture of nucleic acids is derived from a mixed cell population.

10. The method of claim 1, wherein the complex mixture of nucleic acids is obtained from a paraffin embedded sample, blood, saliva, a biopsy sample, a fixed archival cell sample, or a tissue sample.

11. The method of claim 1, wherein the complex mixture of nucleic acids is isolated from one or more cells, bodily fluids, or tissues.

12. The method of claim 1, wherein the predetermined portion comprises a plurality of exon sequences, a plurality of gene sequences, or a plurality of intron sequences.

13. The method of claim 1, wherein the copy number of each sequence in the representational sample of nucleic acid sequences substantially correlates with the copy number for each the sequence in the predetermined portion.

14. The method of claim 1, wherein the population of capture probes comprises oligonucleotides having a length of at least about 35 nucleotides.

15. The method of claim 1, wherein the population of capture probes consists essentially of oligonucleotides having substantially similar melting temperatures (Tm).

16. The method of claim 1, wherein the population of capture probes comprise an amount in molar excess compared to complementary sequences within the predetermined portion of nucleic acids.

17. A method of analyzing a complex mixture of nucleic acids comprising:

(a) contacting a complex mixture of nucleic acids with a population of capture probes comprising nucleic acids complementary to nucleic acids comprising a predetermined portion of the nucleic acid sequences collectively present in the complex mixture of nucleic acids, under conditions sufficient for hybridization of the nucleic acids with the capture probes;

(b) removing unhybridized nucleic acids to separate desired sequences from undesired sequences within the mixture, thereby selecting a representational sample of nucleic acids, wherein the proportion of each sequence in the representational sample relative to all other sequences in the representational sample is substantially the same as the proportions of the sequences in the complex mixture;

(c) detecting individual nucleic acids in the representational sample to determine a sequence characteristic of the predetermined portion of the sequence collectively present in the complex mixture.

18. The method of claim 17, wherein the sequence characteristic comprises one or more of:

(i) the nucleotide sequence for the predetermined portion of the sequence collectively present in the complex mixture;

(ii) the copy number for sequences in the predetermined portion of the sequence collectively present in the complex mixture;

(iii) loss of heterozygosity in the predetermined portion of the sequence collectively present in the complex mixture;

(iv) genotype for the predetermined portion of the sequence collectively present in the complex mixture;

or

(v) methylation analysis for the predetermined portion of the sequence collectively present in the complex mixture.

19. The method of claim 17, wherein step (c) comprises amplifying the representational sample and detecting targets in an amplified population of the representational sample, thereby detecting individual nucleic acids in the representational sample to determine a sequence characteristic of the predetermined portion of the sequence collectively present in the complex mixture.

20. The method of claim 17, wherein the capture probes are attached to a solid support.