Methods for DNA sequencing and analysis using multiple tiers of aliquots

• US 9,637,784 B2
• Filed: 08/20/2013
• Issued: 05/02/2017
• Est. Priority Date: 06/15/2005
• Status: Active Grant

• Current Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Original Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Inventors: Drmanac, Radoje
• Primary Examiner(s): WOOLWINE, SAMUEL C
• Application Number:
  US13/971,801
• Publication Number:
  US 20140018246A1
• Time in Patent Office: 1,351 Days
• Field of Search: None
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C07K 1/047 Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/682 Signal amplification
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2521/307 Single strand endonuclease
• CPC Class Codes: C12Q 2525/151 repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2525/313 Branched oligonucleotides
• CPC Class Codes: C12Q 2531/125 Rolling circle
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2563/179 the label being a nucleic acid
• CPC Class Codes: C12Q 2565/513 characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: C12Q 2565/514 characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• CPC Class Codes: G01N 15/1404 Handling flow, e.g. hydrodynamic focusing
• CPC Class Codes: G01N 15/1434 Optical arrangements
• CPC Class Codes: Y10S 977/778 within specified host or matrix material, e.g. nanocomposite films
• CPC Class Codes: Y10S 977/789 in array format
• CPC Class Codes: Y10S 977/792 : Nucleic acid array, e.g. human genome array
• CPC Class Codes: Y10S 977/88 : with arrangement, process, or apparatus for testing
• CPC Class Codes: Y10S 977/882 : Assembling of separate components, e.g. by attaching

Abstract

The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered. In one aspect, this process is carried out in a hierarchical fashion until the one or more target polynucleotides are characterized, e.g. by their nucleic acid sequences, or by an ordering of sequence segments, or by an ordering of single nucleotide polymorphisms (SNPs), or the like.

Claims

1. A method of processing genomic DNA, comprising:

preparing a first tier of aliquots, at least some of which contain one or more polynucleotides that include a nucleotide sequence from a portion of a genome tagged with an oligonucleotide such that polynucleotides present in different aliquots have different tag sequences, and polynucleotides present in the same aliquot of the first tier have the same tag sequence;

preparing a second tier of aliquots;

at least some of which contain one or more of the polynucleotides from the first tier of aliquots; and

producing multiple fragments from the polynucleotides in the second tier of aliquots, wherein the fragments include a nucleotide sequence from a portion of the genome.

2. The method of claim 1, comprising amplifying the polynucleotides in the first tier of aliquots.

3. The method of claim 1, comprising combining a plurality of polynucleotides from a plurality of aliquots together into one or more mixtures.

4. The method of claim 1, comprising obtaining sequence information from each of a plurality of the tagged polynucleotides, wherein such sequence information includes the nucleotide sequence of a portion of the fragment and the nucleotide sequence of the respective oligonucleotide.

5. The method of claim 4, wherein the step of obtaining the sequence information comprises:

arraying the tagged fragments on a surface such that a majority of the fragments are optically resolvable;

optionally amplifying the tagged fragments before or after the arraying; and

obtaining sequence reads from the tagged fragments on the surface.

6. The method of claim 4, further comprising characterizing the genome using said sequence information.

7. The method of claim 1, wherein any given portion of the target polynucleotide(s) is represented by a single non-overlapping fragment in sixty percent or more of the mixtures containing such portion.

8. The method of claim 1, wherein at least ninety percent of the aliquots containing a mixture of fragments contain only non-overlapping fragments.

9. The method of claim 1, wherein the number of aliquots is selected so that the probability of overlapping fragments is less than 0.1%.

10. A method of processing genomic DNA, comprising:

preparing a first tier of aliquots, at least some of which contain one or more polynucleotides that include a nucleotide sequence from a portion of a genome;

preparing a second tier of aliquots;

at least some of which contain one or more of the polynucleotides from the first tier of aliquots;

producing multiple fragments from the polynucleotides in the second tier of aliquots, wherein the fragments include a nucleotide sequence from a portion of the genome;

obtaining sequence reads from each of a plurality of the fragments from the second tier of aliquots; and

then

characterizing the genome by a process that comprises grouping sequence reads from portions of the genome represented in the same aliquot in the first tier, and grouping sequence reads from portions of the genome represented in the same aliquot in the second tier.

11. The method of claim 10, wherein the polynucleotides in the first tier of aliquots are tagged with a first oligonucleotide such that polynucleotides present in different aliquots of the first tier have different tag sequences, and polynucleotides present in the same aliquot of the first tier have the same tag sequence.

12. The method of claim 11, wherein at least some of the sequence reads include the sequence of the first oligonucleotide, and the characterizing comprises grouping sequence reads having the same first oligonucleotide tag sequence.

13. The method of claim 10, wherein the polynucleotides in the second tier of aliquot are tagged with a second oligonucleotide such that the polynucleotides present in different aliquots of the second tier have different tag sequences, and the polynucleotides present in the same aliquot of the second tier have the same tag sequence.

14. The method of claim 13, wherein at least some of the sequence reads include the sequence of the second oligonucleotide, and the characterizing comprises grouping sequence reads having the same second oligonucleotide tag sequence.

15. The method of claim 10, wherein the step of obtaining the sequence information comprises:

arraying the tagged fragments on a surface such that a majority of the fragments are optically resolvable;

optionally amplifying the tagged fragments before or after the arraying; and

obtaining sequence reads from the tagged fragments on the surface.

16. The method of claim 10, wherein the number of aliquots in the first tier or the second tier is 96, 384, or 1536.

17. A method of processing a target polynucleotide, comprising:

preparing a first tier of aliquots, at least some of which contain one or more polynucleotides that include a nucleotide sequence from a portion of a target polynucleotide tagged with an oligonucleotide such that polynucleotides present in different aliquots have different tag sequences, and polynucleotides present in the same aliquot of the first tier have the same tag sequence;

preparing a second tier of aliquots;

at least some of which contain one or more of the polynucleotides from the first tier of aliquots; and

producing multiple fragments from the polynucleotides in the second tier of aliquots, wherein the fragments include a nucleotide sequence from a portion of the target polynucleotide.

18. A method of processing a target polynucleotide, comprising:

preparing a first tier of aliquots, at least some of which contain one or more polynucleotides that include a nucleotide sequence from a portion of a target polynucleotide;

preparing a second tier of aliquots;

at least some of which contain one or more of the polynucleotides from the first tier of aliquots;

producing multiple fragments from the polynucleotides in the second tier of aliquots, wherein the fragments include a nucleotide sequence from a portion of the target polynucleotide;

obtaining sequence reads from each of a plurality of the fragments from the second tier of aliquots; and

then

characterizing the target polynucleotide by a process that comprises grouping sequence reads from portions of the target polynucleotide represented in the same aliquot in the first tier, and grouping sequence reads from portions of the target polynucleotide represented in the same aliquot in the second tier.

19. The method of claim 18, wherein the target polynucleotide comprises a mammalian genome.

20. The method of claim 18, wherein the target polynucleotide has been prepared by a process that comprises reverse transcribing mRNA molecules obtained from a biological sample.