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Last Updated: October 17, 2019

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Claims for Patent: 8,916,350

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Summary for Patent: 8,916,350
Title:Compositions and methods for representational selection of nucleic acids from complex mixtures using hybridization
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.
Inventor(s): Stuelpnagel; John R. (San Diego, CA), Barker; David L. (Del Mar, CA), Velarde, Jr.; Jorge (San Diego, CA), Barnard; Steven M. (San Diego, CA), Graige; Michael (Cardiff by the Sea, CA)
Assignee: Illumina, Inc. (San Diego, CA)
Application Number:14/046,859
Patent Claims:1. A method of selecting a representational sample of nucleic acid sequences from a complex mixture, comprising: (a) providing a complex mixture of nucleic acids comprising genomic DNA sequence having a complexity of at least 1.7 Gbp; (b) providing a population of solid support-attached capture probes, said population comprising nucleic acids complementary to nucleic acids comprising a predetermined portion of the nucleic acid sequences collectively present in said complex mixture; (c) contacting said complex mixture of nucleic acids with said population of solid support-attached capture probes under conditions sufficient for hybridization of said nucleic acids with said capture probes, wherein the capture probes are randomly located on the solid support; (d) removing unhybridized nucleic acids from the solid support to separate desired sequences from undesired sequences within the complex mixture; thereby selecting a representational sample of nucleic acids having a complexity of at least 0.001% and at most 49% of said complex mixture, wherein the proportion of each sequence in said representational sample relative to all other sequences in said representational sample is substantially the same as the proportions of the sequences in said 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 performing a sequence analysis comprises sequencing by hybridization.

3. The method of claim 1, wherein performing a sequence analysis comprises sequencing by ligation.

4. The method of claim 1, wherein performing a sequence analysis comprises pyrosequencing.

5. The method of claim 1, wherein performing a sequence analysis comprises hybridizing a primer to a nucleic acid in the amplified representational sample and monitoring the extension of the primer by a polymerase.

6. The method of claim 1, wherein said predetermined portion comprises at least 100 kb of genomic DNA sequence.

7. The method of claim 1, wherein said predetermined portion comprises a region of genomic DNA selected from a chromosomal arm, a chromosome or a complete genome.

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

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

10. The method of claim 1, wherein said solid support comprises microspheres.

11. The method of claim 1, wherein said solid support comprises a planar surface.

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

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

14. The method of claim 1, wherein said population of capture probes comprise sequences having complementarity to both strands of said genomic DNA.

15. A method of analyzing a complex mixture of nucleic acids comprising: (a) providing a complex mixture of nucleic acids comprising genomic DNA sequence having a complexity of at least 1.7 Gbp; (b) providing a population of solid support-attached capture probes, said population comprising nucleic acids complementary to nucleic acids comprising a predetermined portion of the nucleic acid sequences collectively present in said complex mixture; (c) contacting said complex mixture of nucleic acids with said population of solid support-attached capture probes under conditions sufficient for hybridization of said nucleic acids with said capture probes, wherein the capture probes are randomly located on the solid support, (d) removing unhybridized nucleic acids from the solid support to separate desired sequences from undesired sequences within the complex mixture; thereby selecting a representational sample of nucleic acids having a complexity of at least 0.001% and at most 49% of said complex mixture, wherein the proportion of each sequence in said representational sample relative to all other sequences in said representational sample is substantially the same as the proportions of the sequences in said complex mixture; (e) amplifying the nucleic acids in the representational sample to generate an amplified representational sample; and (f) detecting individual nucleic acids in said amplified representational sample to determine a sequence characteristic of said predetermined portion of the nucleic acid sequences collectively present in said complex mixture.

16. The method of claim 15, wherein said sequence characteristic comprises the nucleotide sequence for said predetermined portion of the nucleic acid sequences collectively present in said complex mixture.

17. The method of claim 15, wherein said sequence characteristic comprises the copy number for sequences in said predetermined portion of the nucleic acid sequences collectively present in said complex mixture.

18. The method of claim 15, wherein said sequence characteristic comprises loss of heterozygosity in said predetermined portion of the nucleic acid sequences collectively present in said complex mixture.

19. The method of claim 15, wherein said sequence characteristic comprises the genotype of said predetermined portion of the nucleic acid sequences collectively present in said complex mixture.

20. The method of claim 15, wherein said sequence characteristic comprises the methylation status of said predetermined portion of the nucleic acid sequences collectively present in said complex mixture.

Details for Patent 8,916,350

Applicant Tradename Biologic Ingredient Dosage Form BLA Number Approval Date Patent No. Assignee Estimated Patent Expiration Status Orphan Source
Schering INTRON A interferon alfa-2b VIAL 103132 001 1986-06-04   Start Trial Illumina, Inc. (San Diego, CA) 2037-11-04 RX search
Schering INTRON A interferon alfa-2b VIAL 103132 002 1986-06-04   Start Trial Illumina, Inc. (San Diego, CA) 2037-11-04 RX search
Schering INTRON A interferon alfa-2b VIAL 103132 003 1986-06-04   Start Trial Illumina, Inc. (San Diego, CA) 2037-11-04 RX search
>Applicant >Tradename >Biologic Ingredient >Dosage Form >BLA >Number >Approval Date >Patent No. >Assignee >Estimated Patent Expiration >Status >Orphan >Source

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