Methods and systems for processing polynucleotides

• US 10,323,279 B2
• Filed: 08/01/2018
• Issued: 06/18/2019
• Est. Priority Date: 08/14/2012
• Status: Active Grant

• Current Assignee: 10X Genomics Incorporated
• Original Assignee: 10X Genomics Incorporated
• Inventors: Hindson, Christopher, Schnall-Levin, Michael, Price, Andrew, Hardenbol, Paul, Li, Yuan
• Primary Examiner(s): Thomas, David C
• Application Number:
  US16/052,486
• Publication Number:
  US 20180371540A1
• Time in Patent Office: 321 Days
• 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 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• 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 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2563/149 Particles, e.g. beads
• CPC Class Codes: C12Q 2563/159 Microreactors, e.g. emulsion PCR or sequencing, droplet PCR, microcapsules, i.e. non-liquid containers with a range of different permeability's for different reaction components
• CPC Class Codes: C12Q 2563/179 the label being a nucleic acid
• 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: C12Q 2565/519 characterised by the capture moiety being a single stranded oligonucleotide

Abstract

This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.

Claims

1. A method for polynucleotide barcoding, comprising:

(a) providing a first set of partitions comprising (i) a first set of nucleic acid barcode molecules comprising barcode sequences and (ii) a plurality of polynucleotides and attaching said first set of nucleic acid barcode molecules to said plurality of polynucleotides to generate a first set of barcoded polynucleotides;

(b) pooling contents of said first set of partitions;

(c) partitioning (i) a second set of nucleic acid barcode molecules comprising barcode sequences and (ii) at least a portion of said contents from (b) into a second set of partitions different than said first set of partitions; and

(d) in said second set of partitions, attaching said second set of nucleic acid barcode molecules to said first set of barcoded polynucleotides to generate a second set of barcoded polynucleotides.

2. The method of claim 1, wherein a subset of barcoded polynucleotides of said first set of barcoded polynucleotides have identical barcode sequences.

3. The method of claim 1, wherein at least a subset of barcoded polynucleotides of said second set of barcoded polynucleotides have different barcode sequences.

4. The method of claim 1, wherein said plurality of polynucleotides is attached to beads.

5. The method of claim 1, wherein said plurality of polynucleotides is a plurality of cellular polynucleotides.

6. The method of claim 1, wherein said first set of partitions are a first set of wells and said second set of partitions are a second set of wells.

7. The method of claim 1, wherein said first set of partitions are a first set of droplets and said second set of partitions are a second set of droplets.

8. The method of claim 1, wherein said first set of nucleic acid barcode molecules are attached to said plurality of polynucleotides by a nucleic acid reaction or (ii) said second set of nucleic acid barcode molecules are attached to said first set of barcoded polynucleotides by a nucleic acid reaction.

9. The method of claim 1, wherein (i) said first set of nucleic acid barcode molecules are attached to said plurality of polynucleotides by a nucleic acid primer extension reaction or (ii) said second set of nucleic acid barcode molecules are attached to said first set of barcoded polynucleotides by a nucleic acid primer extension reaction.

10. The method of claim 1, wherein (i) said first set of nucleic acid barcode molecules are attached to said plurality of polynucleotides by a nucleic acid amplification reaction or (ii) said second set of nucleic acid barcode molecules are attached to said first set of barcoded polynucleotides by a nucleic acid amplification reaction.

11. The method of claim 1, wherein (i) said first set of nucleic acid barcode molecules are attached to said plurality of polynucleotides by ligation or (ii) said second set of nucleic acid barcode molecules are attached to said first set of barcoded polynucleotides by ligation.

12. The method of claim 1, wherein said first set of barcoded polynucleotides or said second set of barcoded polynucleotides are coupled to a plurality of beads.

13. The method of claim 12, wherein said first set of barcoded polynucleotides or said second set of barcoded polynucleotides are releasable from said plurality of beads.

14. The method of claim 12, wherein said plurality of beads is a plurality of gel beads.

15. The method of claim 14, wherein each gel bead of said plurality of gel beads is dissolvable or disruptable.

16. The method of claim 1, wherein each nucleic acid barcode molecule of said first set of nucleic acid barcode molecules or said second set of nucleic acid barcode molecules further comprises a primer sequence.

17. The method of claim 16, wherein said primer sequence is a targeted primer sequence or a random primer sequence.

18. The method of claim 1, wherein each nucleic acid barcode molecule of said first set of nucleic acid barcode molecules or said second set of nucleic acid barcode molecules further comprises a random N-mer.

19. The method of claim 1, wherein said barcode sequences of said first set of nucleic acid barcode molecules or said barcode sequences of said second set of nucleic acid barcode molecules are greater than 4 nucleic acid bases in length.

20. The method of claim 1, wherein said barcode sequences of said first set of nucleic acid barcode molecules or said barcode sequences of said second set of nucleic acid barcode molecules are 4 to 20 nucleic acid bases in length.

21. The method of claim 1, wherein each barcoded polynucleotide of said second set of barcoded polynucleotides comprises a barcode sequence that is at least 15 nucleic acid bases in length.

22. The method of claim 1, wherein said second set of barcoded polynucleotides comprises at least 100,000 different barcode sequences.

23. The method of claim 1, wherein said second set of barcoded polynucleotides comprises at least 1,000,000 different barcode sequences.

24. The method of claim 1, wherein said second set of barcoded polynucleotides comprises at least 10,000,000 different barcode sequences.

25. The method of claim 1, further comprising:

(e) pooling contents of said second set of partitions;

(f) partitioning (i) a third set of nucleic acid barcode molecules comprising barcode sequences and (ii) at least a portion of said contents from (e) into a third set of partitions different than said first set of partitions and said second set of partitions; and

(g) in said third set of partitions, attaching said third set of nucleic acid barcode molecules to said second set of barcoded polynucleotides to generate a third set of barcoded polynucleotides.

26. The method of claim 25, further comprising:

(h) pooling contents of said third set of partitions;

(i) partitioning (i) a fourth set of nucleic acid barcode molecules comprising barcode sequences and (ii) at least a portion of said contents from (h) into a fourth set of partitions different than said first set of partitions, said second set of partitions, and said third set of partitions; and

(j) in said fourth set of partitions, attaching said fourth set of nucleic acid barcode molecules comprising barcode sequences to said third set of barcoded polynucleotides to provide a fourth set of barcoded polynucleotides.

27. The method of claim 26, wherein said first set of nucleic acid barcode molecules are attached to said plurality of polynucleotides by a nucleic acid primer extension reaction, wherein said second set of nucleic acid barcode molecules are attached to said first set of barcoded polynucleotides by ligation, wherein said third set of nucleic acid barcode molecules are attached to said second set of barcoded polynucleotides by ligation, and wherein said fourth set of nucleic acid barcode molecules are attached to said third set of barcoded polynucleotides by a nucleic acid amplification reaction.

28. The method of claim 1, wherein said first set of barcoded polynucleotides and said second set of barcoded polynucleotides are coupled to a plurality of beads.