Methods, systems, computer readable media, and kits for sample identification

• US 10,704,164 B2
• Filed: 08/30/2012
• Issued: 07/07/2020
• Est. Priority Date: 08/31/2011
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Hubbell, Earl
• Primary Examiner(s): Woitach, Joseph
• Application Number:
  US13/599,876
• Publication Number:
  US 20130053256A1
• Time in Patent Office: 2,868 Days
• Field of Search: None
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00466 in a slurry
• CPC Class Codes: B01J 2219/00547 Bar codes
• CPC Class Codes: B01J 2219/00572 Chemical means
• CPC Class Codes: B01J 2219/00653 the compounds being bound to electrodes embedded in or on the solid supports
• CPC Class Codes: C40B 20/04 Identifying library members by means of a tag, label, or other readable or detectable entity associated with the library members, e.g. decoding processes
• CPC Class Codes: C40B 50/16 involving encoding steps
• CPC Class Codes: C40B 70/00 Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

A method for sequencing a polynucleotide sample having a barcode sequence, includes: introducing a series of nucleotides to the polynucleotide sample according to a predetermined flow ordering; obtaining a series of signals resulting from the introducing of nucleotides to the polynucleotide sample; and resolving the series of signals over the barcode sequence to render a flowspace string, wherein the flowspace string is a codeword of an error-tolerant code capable of distinguishing the barcode sequence from other barcode sequences in the presence of one or more errors.

Claims

1. A method for sequencing a polynucleotide, the method comprising:

introducing, into a polynucleotide, a barcode sequence to create a polynucleotide sample, wherein the barcode sequence is a series of nucleotide bases determined by a predetermined flowspace vector corresponding to a predetermined order of nucleotide flows used for sequencing, wherein the predetermined flowspace vector is a string of characters with each character representing an expected number of nucleotide incorporations resulting from a nucleotide flow of the predetermined order of nucleotide flows;

inserting the created polynucleotide sample into a flow chamber of a sequencing instrument comprising the flow chamber, a sensor in the flow chamber, and a fluidics controller configured to control the flow of nucleotides into the flow chamber;

exposing the created polynucleotide sample in the flow chamber to the series of nucleotides in a presence of a polymerase and a primer by individually flowing the series of nucleotides into the flow chamber according to the predetermined order of nucleotide flows using the fluidics controller, wherein incorporation of nucleotides of the series of nucleotides into the created polynucleotide sample produces a synthesized polynucleotide complementary to the polynucleotide sample;

obtaining, using the sensor, a series of signals resulting from the exposing of the created polynucleotide sample to the series of nucleotides, the series of signals indicating one or more nucleotide incorporations or one or more nucleotide non-incorporations for each nucleotide flow;

outputting the series of signals as data to a computing unit in communication with the sensor, the computing unit comprising a processor and a memory configured to receive and store the data;

resolving, using the processor, the series of signals to generate a rendered flowspace string of characters, wherein each character represents a number of nucleotide incorporations resulting from a respective nucleotide flow of the predetermined order of nucleotide flows;

comparing, using the processor, the rendered flowspace string of characters to predetermined flowspace strings of characters corresponding to a set of barcode sequences comprising the introduced barcode sequence, wherein the predetermined flowspace strings of characters are codewords of an error-tolerant code, the error-tolerant code is an error-correcting code configured to correct one or more errors present in the rendered flowspace string of characters based on differences between the rendered flowspace string and the predetermined flowspace strings of characters; and

identifying, by the processor, the polynucleotide of the polynucleotide sample based on the comparison.

2. The method of claim 1, wherein the error-correcting code is a ternary code using a three character alphabet.

3. The method of claim 2, wherein a first character of the alphabet represents a 0-mer signal, a second character in the alphabet represents a 1-mer signal, and a third character in the alphabet represents a 2-mer signal.

4. The method of claim 2, wherein the ternary code is a ternary Hamming code.

5. The method of claim 2, wherein the ternary code is a ternary Golay code.

6. The method of claim 1, wherein the rendered flowspace string of characters has a length of 15 or fewer characters.

7. The method of claim 1, wherein the error-correcting code is capable of correcting up to two errors in the rendered flowspace string of characters.

8. The method of claim 1, wherein the error-correcting code is capable of correcting three or more errors in the rendered flowspace string of characters.

9. The method of claim 1, wherein the barcode sequence has a length in a range of 5-15 bases.

10. The method of claim 1, further comprising determining whether the rendered flowspace string of characters contains an error based on the differences between the rendered flowspace string of characters and the predetermined flowspace strings of characters.

11. The method of claim 10, further comprising correcting the rendered flowspace string of characters if the rendered flowspace string of characters is determined to contain an error.

12. The method of claim 11, further comprising translating the rendered flowspace string of characters into a base sequence.

13. The method of claim 1, further comprising:

decoding the rendered flowspace string of characters to one of the codewords of the error-correcting code; and

translating the codeword into a base sequence.

14. The method of claim 1, further comprising providing multiple different polynucleotide samples for multiplex sequencing by the exposing to the series of nucleotides, each different polynucleotide sample comprising a different barcode sequence from the set of barcode sequences.

15. The method of claim 14, wherein any two codewords of the error-correcting code have a minimal Hamming distance of 3.

16. The method of claim 14, wherein any two codewords of the error-correcting code have a minimal Hamming distance of 5.

17. The method of claim 1, wherein obtaining the series of signals further comprises at least one of:

(i) detecting hydrogen ions released by the incorporation of nucleotides into the polynucleotide sample, wherein an amplitude of the signals is related to an amount of hydrogen ions detected, and (ii) detecting inorganic pyrophosphate released by incorporation of nucleotides into the polynucleotide sample, wherein an amplitude of the signals is related to an amount of inorganic pyrophosphate detected.

19. The method of claim 1, wherein the sequencing instrument comprises the computing unit.

18. A system comprising:

a sequencing instrument comprising;

a flow chamber configured to receive a polynucleotide sample, a polymerase, and a primer, the polynucleotide sample comprising a polynucleotide incorporating a barcode sequence, wherein the barcode sequence is a series of nucleotide bases determined by a predetermined flowspace vector corresponding to a predetermined order of nucleotide flows used for sequencing, wherein the predetermined flowspace vector is a string of characters with each character representing an expected number of nucleotide incorporations resulting from a nucleotide flow of the predetermined order of nucleotide flows;

a fluidics controller configured to flow nucleotides into the flow chamber to expose the polynucleotide sample to a series of nucleotides by individually flowing the series of nucleotides according to the predetermined order of nucleotide flows, and

a sensor configured to obtain a series of signals resulting from the exposing of the polynucleotide sample to the series of nucleotides, and output the series of signals as data, the series of signals indicating one or more nucleotide incorporations or one or more nucleotide non-incorporations for each nucleotide flow; and

a computing unit in communication with the sensor, the computing unit comprising a processor and a memory configured to receive and store the data, the processor configured to;

resolve the series of signals to generate a rendered flowspace string of characters, wherein each character represents a number of nucleotide incorporations resulting from a respective nucleotide flow of the predetermined order of nucleotide flows;

compare the rendered flowspace string of characters to predetermined flowspace strings of characters corresponding to a set of barcode sequences comprising the incorporated barcode sequence, wherein the predetermined flowspace strings of characters are codewords of an error-tolerant code, the error-tolerant code is an error-correcting code configured to correct one or more errors present in the rendered flowspace string of characters based on differences between the rendered flowspace string of characters and the predetermined flowspace strings of characters; and

identify the polynucleotide of the polynucleotide sample based on the comparison.

20. The system of claim 18, wherein the sequencing instrument comprises the computing unit.