System and method to correct out of phase errors in DNA sequencing data by use of a recursive algorithm

• US 9,317,654 B2
• Filed: 12/18/2012
• Issued: 04/19/2016
• Est. Priority Date: 02/16/2006
• Status: Expired due to Fees

• Current Assignee: 454 Life Sciences Corporation (Roche Holding AG)
• Original Assignee: 454 Life Sciences Corporation (Roche Holding AG)
• Inventors: Chen, Yi-Ju, Andrew Wong, Chiu Tai
• Primary Examiner(s): Brusca, John S
• Application Number:
  US13/718,852
• Publication Number:
  US 20130131995A1
• Time in Patent Office: 1,218 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2535/113 Cycle sequencing
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• CPC Class Codes: C12Q 2565/301 Pyrophosphate (PPi)
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

Provided herein are methods for correcting an error associated with phasic synchrony of sequence data generated from a population of template molecules by detecting signals generated in response to nucleotide species introduced during a sequencing reaction; generating an observed value for the signal detected from each of the nucleotide species; defining positive incorporation values and negative incorporation values from the observed values using a carry forward value and an incomplete extension value; revising the carry forward value and the incomplete extension value using a noise value derived from observed values associated with the negative incorporation values; re-defining the positive incorporation values and the negative incorporation values using the revised carry forward value and the revised incomplete extension value; and repeating the steps of revising and re-defining until convergence of the positive incorporation values and the negative incorporation values.

Claims

1. A method for recursively correcting an error associated with phasic synchrony of nucleic acid sequence data generated from a population of substantially identical copies of a template molecule, comprising:

(a) detecting a plurality of signals generated in response to a plurality of nucleotide species introduced during a sequencing reaction;

(b) generating an observed value for the signal detected from each of the nucleotide species;

(c) defining a plurality of positive incorporation values and a plurality of negative incorporation values from the observed values using a carry forward value and an incomplete extension value;

(d) simultaneously calculating a carry forward perturbation increment and an incomplete extension perturbation increment;

(e) revising the carry forward value and the incomplete extension value using the carry forward perturbation increment and the incomplete extension perturbation increment;

(f) re-defining the plurality of positive incorporation values and the plurality of negative incorporation values using the revised carry forward value and the revised incomplete extension value; and

(g) repeating steps (d)-(f) until convergence of the plurality of positive incorporation values and the plurality of negative incorporation values, thereby generating a corrected nucleic acid sequence read.

2. The method of claim 1, wherein:

the positive incorporation value and the negative incorporation value are integers.

3. The method of claim 2, wherein:

the positive incorporation value is a 1 and the negative incorporation value is a 0.

4. The method of claim 1, wherein:

prior to step (c) the positive incorporation values and the negative incorporation values are assigned using a threshold value, wherein the positive incorporation value is assigned when the observed value is above the threshold value and the negative incorporation value is assigned when the observed value is below the threshold value.

5. The method of claim 4, wherein:

the threshold value comprises a value in the range between 0 and 1.

6. The method of claim 5, wherein:

the threshold value is 0.2.

7. The method of claim 1, wherein:

the positive incorporation values and the negative incorporation values are defined by using a reference sequence to predict a plurality of positions where no nucleotide species is present.

8. The method of claim 1, wherein:

a plurality of the sequencing reactions are executed in parallel, wherein steps (a)-(g) are executed for each of the sequencing reactions.

9. A method for recursively correcting an error associated with phasic synchrony of nucleic acid sequence data generated from a population of substantially identical copies of a template molecule, comprising the steps of:

(a) detecting a plurality of signals generated in response to a plurality of nucleotide species introduced during a sequencing reaction;

(b) generating an observed value for the signal detected from each of the nucleotide species;

(c) defining a plurality of positive incorporation values and a plurality of negative incorporation values from the observed values using a carry forward value and an incomplete extension value;

(d) simultaneously calculating a carry forward perturbation increment and an incomplete extension perturbation increment;

(e) revising the carry forward value and the incomplete extension value using the carry forward perturbation increment and the incomplete extension perturbation increment;

(f) re-defining the plurality of positive incorporation values and the plurality of negative incorporation values using the revised carry forward value and the revised incomplete extension value; and

(g) repeating steps (d)-(f) until convergence of the carry forward value and the incomplete extension value, thereby generating a corrected nucleic acid sequence read.

10. A system for recursively correcting an error associated with phasic synchrony of nucleic acid sequence data generated from a population of substantially identical copies of a template molecule, comprising:

(a) a sequencing instrument that detects a plurality of signals generated in response to a plurality of nucleotide species introduced during a sequencing reaction;

(b) a computer comprising executable code stored thereon which performs a method comprising the steps of;

i. generating an observed value for the signal detected from each of the nucleotide species;

ii. defining a plurality of positive incorporation values and a plurality of negative incorporation values from the observed values using a carry forward value and an incomplete extension value;

iii. simultaneously calculating a carry forward perturbation increment and an incomplete extension perturbation increment;

iv. revising the carry forward value and the incomplete extension value using the carry forward perturbation increment and the incomplete extension perturbation increment;

v. re-defining the plurality of positive incorporation values and the plurality of negative incorporation values using the revised carry forward value and the revised incomplete extension value; and

vi. repeating steps iii-v until convergence of the carry forward value and the incomplete extension value, thereby generating a corrected nucleic acid sequence read.

11. The system of claim 10, wherein:

the positive incorporation value and the negative incorporation value are integers.

12. The system of claim 11, wherein:

the positive incorporation value is a 1 and the negative incorporation value is a 0.

13. The system of claim 10, wherein:

prior to step (ii) the computer assigns the positive incorporation values and the negative incorporation values using a threshold value, wherein the positive incorporation value is assigned when the observed value is above the threshold value and the negative incorporation value is assigned when the observed value is below the threshold value.

14. The system of claim 13, wherein:

the threshold value comprises a value in the range between 0 and 1.

15. The system of claim 14, wherein:

the threshold value is 0.2.

16. The system of claim 10, wherein:

the computer defines the positive incorporation values and the negative incorporation vales using a reference sequence to predict a plurality of positions where no nucleotide species is present.

17. The system of claim 10, wherein:

the sequencing system executes a plurality of the sequencing reactions in parallel, wherein the computer executes steps (i)-(vi) for each of the sequencing reactions.