Methods for obtaining a sequence

• US 9,725,765 B2
• Filed: 09/10/2012
• Issued: 08/08/2017
• Est. Priority Date: 09/09/2011
• Status: Expired due to Fees

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Inventors: Pushkarev, Dmitry, Quake, Stephen R., Kertesz, Michael, Voskoboynik, Ayelet
• Primary Examiner(s): Zhang, Kaijiang
• Application Number:
  US13/608,770
• Publication Number:
  US 20130157870A1
• Time in Patent Office: 1,793 Days
• Field of Search: None
• 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 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2527/146 Concentration of target or template
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: Y02A 50/30 Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Abstract

The invention generally relates to methods for obtaining a sequence, such as a consensus sequence or a haplotype sequence. In certain embodiments, methods of the invention involve determining an amount of amplifiable nucleic acid present in a sample, partitioning the nucleic acid based upon results of the determining step such that each partitioned portion includes, on average, a subset of unique sequences, sequencing the nucleic acid to obtain sequence reads, and assembling a consensus sequence from the reads.

Claims

1. A method for analyzing a plurality of target polynucleotides, the method comprising:

(a) providing a sample comprising a plurality of target polynucleotide fragments, wherein each target polynucleotide fragment has a length of 5 kb to 40 kb;

(b) performing a size selection on the plurality of target polynucleotide fragments to select 5-7 kb fragments;

(c) ligating amplification adaptors at each end of at least a portion of the 5-7 kb fragments to produce a library of amplifiable fragments, wherein the adaptors serve as primer binding sites;

(d) quantitating via qPCR to establish a number of amplifiable fragments in the library of amplifiable fragments;

(e) determining a dilution factor based on the number of amplifiable fragments in the library of amplifiable fragments;

(f) diluting and partitioning the library into a plurality of partitions based on the dilution factor such that each partition comprises, on average, a unique subset of 500 or more of the amplifiable fragments;

(g) amplifying via polymerase chain reaction the partitioned amplifiable fragments;

(h) subjecting the partitions to polynucleotide fragmentation thereby generating a set of smaller fragments; and

(i) obtaining partial or complete sequence information from at least a subset of the smaller fragments.

3. The method of claim 1, wherein the adaptors coupled to each end of the 5-7 kb fragments comprise a first adaptor and a second adaptor, and the first adaptor is not the same as the second adaptor.

4. The method of claim 1, wherein the smaller fragments within a partition are labeled with one or more partition specific barcodes.

5. The method of claim 4, wherein the barcodes are nucleic acid sequences.

6. The method of claim 4, wherein the barcodes are greater than 3 nucleotides long.

7. The method of claim 4, wherein the barcodes are greater than 5 nucleotides long.

8. The method of claim 4, wherein the one or more partition specific barcodes comprise 2 barcodes that are each greater than 2 nucleotides long.

9. The method of claim 8, wherein all two partition specific barcodes comprise at least two differences in the nucleic acid sequence.

10. The method as in one of claims 1-2 wherein the sequence information comprises sequence reads obtained by sequencing.

11. The method as in one of claims 1-2, wherein the sequence information has an average accuracy of greater than 99%.

12. The method as in one of claims 1-2, wherein the sequence information has an average accuracy of greater than 95%.

13. The method as in one of claims 1-2, wherein the sequence information has an average accuracy of greater than 90%.

14. The method as in one of claims 1-2, wherein the sequence information has an average accuracy of greater than 80%.

15. The method of claim 10, wherein the sequence reads have an accuracy of greater than 99.98%.

16. The method of claim 10, wherein the sequence information spans more than 50 bp.

17. The method of claim 10, wherein the sequence information spans more than 100 bp.

18. The method of claim 10, wherein the sequence information spans more than 200 bp.

19. The method as in one of claims 1-2, wherein all sequence information is obtained in less than 1 month.

20. The method as in one of claims 1-2 wherein all sequence information is obtained in less than 2 weeks.

21. The method as in one of claims 1-2, wherein all sequence information is obtained in less than 1 week.

22. The method as in one of claims 1-2, wherein all sequence information is obtained in less than 1 day.

23. The method as in one of claims 1-2, wherein all sequence information is obtained in less than 3 hours.

24. The method as in one of claims 1-2, wherein all sequence information is obtained in less than 1 hour.

25. The method as in one of claims 1-2, wherein all sequence information is obtained in less than 30 minutes.

26. The method as in one of claims 1-2, wherein all sequence information is obtained in less than 10 minutes.

27. The method as in one of claims 1-2, wherein all sequence information is obtained in less than 5 minutes.

28. The method as in one of claims 1-2, wherein at least one target polynucleotide fragment within the sample is flagged if one or more of its sequence segments are substantially similar to one or more sequence segments of a second target polynucleotide fragment partitioned into the same partition.

29. The method as in one of claims 1-2, further comprising a sequence coverage of greater than 20 fold.

30. The method as in one of claims 1-2, further comprising an average sequence coverage of less than 500 fold.

31. The method of claim 10, wherein the sequencing comprises sequencing by synthesis.

32. The method of claim 10, wherein the sequencing comprises ion semiconductor sequencing.

33. The method of claim 10, wherein the sequencing comprises single molecule real time sequencing.

34. The method of claim 10, wherein the sequencing comprises nanopore sequencing.

35. The method of claim 10, wherein the sequencing comprises sequencing by electron microscopy.

36. The method as in one of claims 1-2, wherein the plurality of target polynucleotide fragments originates from genomic DNA.

37. The method of claim 36, wherein the genomic DNA originates from a polyploid genome.

38. The method as in one of claims 1-2, wherein at least one of the target polynucleotide fragments comprises a portion of a major histocompatibility complex gene.

39. The method as in one of claims 1-2, wherein at least one of the target polynucleotide fragments originates from fetal DNA.

40. The method of claim 10, wherein the sequencing comprises obtaining paired end reads.

41. The method as in one of claims 1-2, further comprising utilizing computing resources that are delivered over a network to improve detection of sequence variants and detection average accuracy.

42. The method as in one of claims 1-2, wherein the plurality of target polynucleotide fragments originate from a single molecule, and wherein the related sequence information links two or more positions on the single molecule.

43. The method of claim 42, wherein the two or more positions on the single molecule are separated by more than 5000 bp.

44. The method of claim 42, wherein the two or more positions on the single molecule are separated by more than 10000 bp.

45. The method as in one of claims 1-2, wherein the one or more target polynucleotide fragments comprise a first target polynucleotide and a second polynucleotide and the related sequence information to the first target polynucleotide and the related sequence information to the second target polynucleotide are linked.

46. The method as in one of claims 1-2, further comprising detecting a genomic structural variation.

47. The method as in one of claims 1-2, wherein the one or more target polynucleotide fragments originate from one or more tissue samples, wherein relating sequence information comprises detecting a plurality of sequence variants in the one or more tissue samples, and wherein the plurality of sequence variants from one or more tissue sample are compared.

48. The method as in one of claims 1-2, further comprising providing a diagnosis based on the related sequence information.

49. The method of claim 48, wherein the diagnosis is directed to a disease selected from the group consisting of allergic rhinitis, allergic conjunctivitis, allergic asthma, atopic eczema, atopic dermatitis, food allergy, severe combined immunodeficiency (SCID), hypereosinophilic syndrome, chronic granulomatous disease, leukocyte adhesion deficiency I and II, hyper IgE syndrome, Chediak Higashi, neutrophilias, neutropenias, aplasias, Agammaglobulinemia, hyper-IgM syndromes, DiGeorge/Velocardial-facial syndromes and Interferon gamma-TH1 pathway defects, rheumatoid arthritis, diabetes, systemic lupus erythematosus, Graves'"'"' disease, Graves ophthalmopathy, Crohn'"'"'s disease, multiple sclerosis, psoriasis, systemic sclerosis, goiter and struma lymphomatosa (Hashimoto'"'"'s thyroiditis, lymphadenoid goiter), alopecia aerata, autoimmune myocarditis, lichen sclerosis, autoimmune uveitis, Addison'"'"'s disease, atrophic gastritis, myasthenia gravis, idiopathic thrombocytopenic purpura, hemolytic anemia, primary biliary cirrhosis, Wegener'"'"'s granulomatosis, polyarteritis nodosa, and inflammatory bowel disease, allograft rejection and tissue destructive from allergic reactions to infectious microorganisms or to environmental antigens, hemangiomatosis in newborns, secondary progressive multiple sclerosis, chronic progressive myelodegenerative disease, neurofibromatosis, ganglioneuromatosis, keloid formation, Paget'"'"'s Disease of the bone, fibrocystic disease (e.g., of the breast or uterus), sarcoidosis, Peronies and Duputren'"'"'s fibrosis, cirrhosis, atherosclerosis and vascular restenosis, hematologic malignancies and solid tumors, 21 hydroxylase deficiency, cystic fibrosis, Fragile X Syndrome, Turner Syndrome, Duchenne Muscular Dystrophy, Down Syndrome or other trisomies, heart disease, single gene diseases, HLA typing, phenylketonuria, sickle cell anemia, Tay-Sachs Disease, thalassemia, Klinefelter Syndrome, Huntington Disease, autoimmune diseases, lipidosis, obesity defects, hemophilia, inborn errors of metabolism, and diabetes.

50. The method as in one of claims 1-2, wherein the one or more target polynucleotide fragments comprise at least a first target polynucleotide adjacent to a first known nucleotide sequence at at least one end and a second target polynucleotide adjacent to a second known nucleotide sequence at at least one end, wherein the first known nucleotide sequence is not the same as the second known nucleotide sequence.

51. The method of claim 50, wherein the first target polynucleotide further comprises a third known nucleotide sequence at at least one end, wherein the second target polynucleotide further comprises a fourth known nucleotide sequence at at least one end, wherein the third known nucleotide sequence is dependent on the first known nucleotide sequence and wherein the fourth known nucleotide sequence is dependent on the second known nucleotide sequence.

52. The method of claim 51, wherein relating sequence information from the plurality of fragments into the first target polynucleotide comprises linking the first and the third known nucleotide sequences.

53. The method of claim 52, wherein the first and third known nucleotide sequences are different from the second and fourth known nucleotide sequences.

54. The method as in one of claims 1-2, further comprising identifying the presence of a pathogen in the at least one sample.

55. The method of claim 54, wherein the pathogen is selected from the group consisting of a bacterial agent, a virus, a parasite, and a fungus.

56. The method of claim 55, wherein the bacterial agent is selected from the group consisting of Escherichia coli, Salmonella, Shigella, Klebsiella Pseudomonas, Listeria monocytogenes, Mycobacterium tuberculosis, Mycobacterium aviumintracellulare, Yersinia, Francisella, Pasteurella, Brucella, Clostridia, Bordetella pertussis, Bacteroides, Staphylococcus aureus, Streptococcus pneumonia, B-Hemolytic strep., Corynebacteria, Legionella, Mycoplasma, Ureaplasma, Chlamydia, Neisseria gonorrhea, Neisseria meningitides, Hemophilus influenza, Enterococcus faecalis, Proteus vulgaris, Proteus mirabilis, Helicobacter pylori, Treponema palladium, Borrelia burgdorferi, Borrelia recurrentis, Rickettsial pathogens, Nocardia, and Acitnomycetes.

57. The method of claim 55, wherein the fungus is selected from the group consisting of Cryptococcus neoformans, Blastomyces dermatitidis, Histoplasma capsulatum, Coccidioides immitis, Paracoccidioides brasiliensis, Candida albicans, Aspergillus fumigautus, Phycomycetes (Rhizopus), Sporothrix schenckii, Chromomycosis, and Maduromycosis.

58. The method of claim 55, wherein the virus is selected from the group consisting of human immunodeficiency virus, human T-cell lymphocytotrophic virus, hepatitis viruses (e.g., Hepatitis B Virus and Hepatitis C Virus), Epstein-Barr Virus, cytomegalovirus, human papillomaviruses, orthomyxo viruses, paramyxo viruses, adenoviruses, corona viruses, rhabdo viruses, polio viruses, toga viruses, bunya viruses, arena viruses, rubella viruses, and reo viruses.

59. The method of claim 55, wherein the parasite is selected from the group consisting of Plasmodium falciparum, Plasmodium malaria, Plasmodium vivax, Plasmodium ovale, Onchoverva volvulus, Leishmania, Trypanosoma spp., Schistosoma spp., Entamoeba histolytica, Cryptosporidum, Giardia spp., Trichimonas spp., Balatidium coli, Wuchereria bancrofti, Toxoplasma spp., Enterobius vermicularis, Ascaris lumbricoides, Trichuris trichiura, Dracunculus medinesis, trematodes, Diphyllobothrium latum, Taenia spp., Pneumocystis carinii, and Necator americanis.

60. The method of claim 54, wherein the pathogen comprises a drug resistant pathogen.

61. The method of claim 60, wherein the drug resistant pathogen is selected from the group consisting of vancomycin-resistant Enterococcus faecium, methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, multi-drug resistant Mycobacterium tuberculosis, and AZT-resistant human immunodeficiency virus.

62. The method of claim 1, wherein the quantitating via qPCR and the amplifying via polymerase chain reaction both use the primer binding sites provided by the adaptors on the amplifiable fragments.

2. A method for analyzing a plurality of target polynucleotides, the method comprising:

(a) providing at least one sample comprising a plurality of target polynucleotide fragments, wherein each target polynucleotide fragment has of a length of 5 kb to 40 kb;

(b) performing a size selection on the plurality of target polynucleotide fragments to select 5-7 kb fragments;

(c) ligating amplification adaptors to each end of at least a portion of the 5-7 kb fragments to produce a library of amplifiable fragments, wherein the adaptor serves as a primer binding site;

(d) quantitating via qPCR to establish a number of amplifiable fragments in the library of amplifiable fragments;

(e) determining a dilution factor based on the number of amplifiable fragments in the library of amplifiable fragments;

(f) diluting and partitioning the library based on the dilution factor into a plurality of partitions such that each partition comprises, on average, a unique subset of 500 or more of the amplifiable fragments;

(g) amplifying via a polymerase chain reaction the partitioned amplifiable fragments;

(h) subjecting the partitions to polynucleotide fragmentation thereby generating a set of smaller fragments;

(i) coupling a partition specific barcode to at least a subset of the smaller fragments; and

(j) obtaining partial or complete sequence information from at least a subset of the smaller fragments coupled with the partition specific barcodes.

63. The method of claim 2, wherein the quantitating via qPCR and the amplifying via polymerase chain reaction both use the primer binding sites provided by the adaptors on the amplifiable fragments.