SEQUENCING METHODS

• US 20150066385A1
• Filed: 08/27/2014
• Published: 03/05/2015
• Est. Priority Date: 08/30/2013
• Status: Active Grant

• Current Assignee: 10X Genomics Incorporated
• Original Assignee: 10x Technology Inc.
• Inventors: SCHNALL-LEVIN, Michael, JAROSZ, Mirna, SAXONOV, Serge, NESS, Kevin, HINDSON, Benjamin
• Granted Patent: US 10,395,758 B2
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 30/20 Sequence assembly

Abstract

The invention described herein solves challenges in providing a proficient, rapid and meaningful analysis of sequencing data. Methods and computer program products of the invention allow for a system to receive, analyze, and display sequencing data in real-time. The invention provides solutions to several difficulties encountered in assembling short sequencing-reads, and by doing so the invention improves the worth and significance of sequencing data.

Claims

1. A method of analyzing sequencing data associated with a sample, the method comprising:

a) receiving by a computer system a first sequencing read associated with a sequencing assay while the sequencing assay is in progress, wherein the computer system comprises a processor; and

b) comparing by the processor the first sequencing read with another sequence to provide a comparison before the sequencing assay is complete.

2. The method of claim 1, wherein the other sequence is a second sequencing read.

3. The method of claim 1, further comprising determining whether the first sequencing read and the other sequence share a common subsequence.

4. The method of claim 1, further comprising determining whether the first sequencing read and the other sequence correspond to a common biomolecule.

5. The method of claim 1, further comprising aligning the first sequencing read and the other sequence.

6. The method of claim 1, further comprising determining whether the first sequencing read and the other sequence share a common barcode.

7. The method of claim 1, wherein the other sequence is a reference sequence.

8. The method of claim 1, further comprising identifying a mutation in the sample based on the comparison.

9. The method of claim 1, further comprising identifying a single nucleotide polymorphism in the sample based on the comparison.

10. The method of claim 1, further comprising identifying a translocation in the sample based on the comparison.

11. The method of claim 1, further comprising determining a candidate sequence, wherein the candidate sequence incorporates a portion of the first sequencing read.

12. The method of claim 11, wherein determining the candidate sequence is performed at a rate, wherein the computer system receives a number of sequencing reads, wherein the rate increases as the number of sequencing reads increases.

13. The method of claim 1, further comprising determining to which haplotype in a pair of haplotypes the first sequencing read corresponds.

14. The method of claim 1, wherein the sample is associated with a plurality of distinct barcodes.

15. The method of claim 1, wherein the sequencing data is DNA sequencing data.

16. The method of claim 1, wherein the sequencing data is RNA sequencing data.

17. The method of claim 1, wherein the sequencing data is genomic sequencing data.

18. The method of claim 1, wherein the sequencing data is peptide sequencing data.

19. The method of claim 1, further comprising outputting a result of the comparing.

20. The method of claim 1, further comprising providing a therapeutic intervention to a subject based on a result of analyzing the sequencing data.

21. The method of claim 1, wherein the first sequencing read is a partial sequencing read.

22. The method of claim 1, wherein the first sequencing read is a complete sequencing read.

23. A computer program product comprising a computer-readable medium having computer-executable code encoded therein, the computer-executable code adapted to be executed to implement a method of analyzing sequencing data, the method comprising:

a) providing a sequencing data analysis system, wherein the sequencing data analysis system comprises;

i) a receiving module configured to receive sequencing data associated with a sequencing assay while the sequencing assay is in progress; and

ii) an alignment module configured to align sequencing data while the sequencing assay is in progress;

b) receiving by the receiving module a set of sequencing reads associated with the sequencing assay while the sequencing assay is in progress; and

c) performing an alignment by the alignment module of at least one received sequencing read with another sequence while the sequencing assay is in progress.

24. The computer program product of claim 23, wherein the sequencing data analysis system further comprises a database access module, wherein the method further comprises accessing a database to obtain the other sequence.

25. The computer program product of claim 23, wherein the sequencing data analysis system further comprises a reference sequence, wherein the other sequence aligned with the sequencing read is the reference sequence.

26. The computer program product of claim 23, wherein the sequencing data analysis system further comprises a barcode module, wherein the method further comprises identifying by the barcode module at least two sequencing reads in the set of sequencing reads that share a common barcode.

27. The computer program product of claim 23, wherein the sequencing data analysis system further comprises a candidate module, wherein the method further comprises building by the candidate module a candidate sequence based on the alignment.

28. The computer program product of claim 27, wherein the sequencing data analysis system further comprises a mutation module, wherein the method further comprises estimating by the mutation module a likelihood that the candidate sequence comprises a mutation.

29. The computer program product of claim 28, wherein the mutation is a single nucleotide polymorphism.

30. The computer program product of claim 28, wherein the mutation is a copy number variant.

31. The computer program product of claim 28, wherein the mutation is a translocation.

32. The computer program product of claim 23, wherein the sequencing data analysis system further comprises a haplotype module, wherein the method further comprises determining by the haplotype module to which haplotype in a pair of haplotypes one of sequencing reads of the set of sequencing reads corresponds.

33. The computer program product of claim 23, wherein the sequencing reads associated with the sequencing assay are received from an instrument conducting the sequencing assay.

34. The computer program product of claim 23, wherein the sequencing reads associated with the sequencing assay are received from a database.

35. The computer program product of claim 23, wherein the computer program product is in communication with a sequencing instrument.

36. The computer program product of claim 35, wherein the sequencing data analysis system further comprises a user information module, wherein the method further comprises obtaining by the user information module user information from the sequencing instrument.

37. The computer program product of claim 35, wherein the sequencing data analysis system further comprises a user information module, wherein the method further comprises obtaining by the user information module user information associated with a configuration of the sequencing instrument.

38. The computer program product of claim 23, wherein the computer program product is in communication with a plurality of sequencing instruments.

39. The computer program product of claim 23, wherein the sequencing data analysis system analyzes DNA sequencing data.

40. The computer program product of claim 23, wherein the sequencing data analysis system analyzes RNA sequencing data.

41. The computer program product of claim 23, wherein the sequencing data analysis system analyzes genomic sequencing data.

42. The computer program product of claim 23, wherein the sequencing data analysis system analyzes peptide sequencing data.

43. The computer program product of claim 23, wherein the sequencing data analysis system further comprises an output module, wherein the method further comprises outputting by the output module a result of the alignment.