SYSTEM AND METHOD TO CORRECT OUT OF PHASE ERRORS IN DNA SEQUENCING DATA BY USE OF A RECURSIVE ALGORITHM

• US 20110213563A1
• Filed: 03/08/2011
• Published: 09/01/2011
• Est. Priority Date: 02/15/2007
• Status: Active Grant

• Current Assignee: 454 Life Sciences Corporation (Roche Holding AG)
• Original Assignee: 454 Life Sciences Corporation (Roche Holding AG)
• Inventors: Wong, Chiu Tai Andrew, Chen, Yi-Ju
• Granted Patent: US 8,364,417 B2
• Time in Patent Office: Days
• US Class Current: 702/20
• 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

An embodiment of a method for correcting an error associated with phasic synchrony of sequence data generated from a population of template molecules is described that comprises the steps of 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 that is 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 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) revising the carry forward value and the incomplete extension value using a noise value, wherein the noise value is derived from a plurality of observed values associated with the negative incorporation values;

(e) 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

(f) repeating steps (d)-(e) until convergence of the plurality of positive incorporation values and the plurality of negative incorporation values.

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:

the carry forward value and the incomplete extension value employed in step (c) are determined using a parameter estimation model.

5. 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.

6. The method of claim 5, wherein:

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

7. The method of claim 6, wherein:

the threshold value is 0.2.

8. The method of claim 5, wherein:

the threshold value is defined by using a reference sequence to predict a plurality of positions where no nucleotide species is present.

9. The method of claim 1, wherein:

the noise value is the average of the observed values associated with negative incorporation values from a number of nucleotide species introduced.

10. The method of claim 9, wherein:

the number of nucleotide species introduced comprises the first 48 nucleotide species introduced.

11. The method of claim 1, wherein:

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

12. A method for recursively correcting an error associated with phasic synchrony of 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) revising the carry forward value and the incomplete extension value using a noise value, wherein the noise value is derived from a plurality of observed values associated with the negative incorporation values;

(e) 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

(f) repeating steps (d)-(e) until convergence of the carry forward value and the incomplete extension value.

13. A system for recursively correcting an error associated with phasic synchrony of 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. revising the carry forward value and the incomplete extension value using a noise value, wherein the noise value is derived from a plurality of observed values associated with the negative incorporation values;

iv. 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

v. repeating steps iii-iv until convergence of the carry forward value and the incomplete extension value.

14. The system of claim 13, wherein:

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

15. The system of claim 14, wherein:

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

16. The system of claim 13, wherein:

the carry forward value and the incomplete extension value employed in step (ii) are determined using a parameter estimation model.

17. The system of claim 13, 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.

18. The system of claim 17, wherein:

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

19. The system of claim 18, wherein:

the threshold value is 0.2.

20. The system of claim 17, wherein:

the computer defines the threshold value using a reference sequence to predict a plurality of positions where no nucleotide species is present.

21. The system of claim 13, wherein:

the noise value is the average of the observed values associated with negative incorporation values from a number of nucleotide species introduced by the sequencing instrument.

22. The system of claim 21, wherein:

the number of nucleotide species introduced comprises the first 48 nucleotide species introduced.

23. The system of claim 13, wherein:

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