Sequencing method and apparatus

• US 20030186276A1
• Filed: 03/25/2003
• Published: 10/02/2003
• Est. Priority Date: 07/05/2000
• Status: Active Grant

• Current Assignee: GE Healthcare UK Limited (Danaher Corporation)
• Original Assignee: Amersham Biosciences UK Ltd (GE Healthcare Technologies, Inc.)
• Inventors: Odedra, Raj
• Granted Patent: US 7,133,782 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/20 Sequence assembly

Abstract

In a method of identifying an unknown nucleotide sequence using base addition, a sequence of bases is obtained from a template, a base in the sequence is identified as an unknown base, an “unknown” indicator is included in the sequence, and an output sequence is generated containing the unknown base indicator. The sequence of bases is obtained from the template by evaluation of a reporter and assigning the bases in accordance therewith. A determination is made as to whether the reporter is from a preceding cycle of base determination, and if the reporter is from a preceding cycle of base determination, the base assignation is discarded.

Claims

1. A method of identifying an unknown nucleotide sequence using base addition, comprising the steps of:

obtaining a sequence of bases from a template;

identifying a base in the sequence as an unknown base and including an ‘

unknown’

indicator in the sequence; and

providing an output sequence containing the unknown base indicator.

2. A method according to claim 1, further comprising counting the number of consecutive unknown bases, and providing an indication when the number of consecutive unknown bases exceeds a predetermined threshold value.

3. A method according to claim 2, wherein when the threshold is exceeded, the preceding base is marked as misincorporated.

4. A method according to claim 1, further comprising the step of sequence alignment between the output sequence and a reference sequence.

5. A method according to claim 2, further comprising the step of sequence alignment between the output sequence and a reference sequence.

6. A method according to claim 1, wherein the sequence is determined by evaluation of a reporter, and further comprising the step of determining whether the reporter is from a preceding cycle of base determination.

11. A computer program comprising program code means for performing all the steps of any one of claims 1 to 7, when said program is run on a computer.

7. A method of identifying an unknown nucleotide sequence, comprising the steps of:

obtaining a sequence of bases from a template by evaluation of a reporter and assigning the bases in accordance therewith;

determining whether the reporter is from a preceding cycle of base determination;

if the reporter is from a preceding cycle of base determination, discarding the base assignation; and

providing an output sequence.

8. Apparatus for identifying an unknown nucleotide sequence using base addition, comprising:

means for obtaining a sequence of bases from a template;

means for identifying a base in the sequence as an unknown base and including an ‘

unknown’

indicator in the sequence; and

means for providing an output sequence containing the unknown base indicator.

9. Apparatus for identifying an unknown nucleotide sequence using base addition, comprising:

means for obtaining a sequence of bases from a template by evaluation of a reporter and assigning the bases in accordance therewith;

means for determining whether the reporter is from a preceding cycle of base determination, and if the reporter is from a preceding cycle of base determination, for discarding the base assignation; and

means for providing an output sequence.

10. A computer program product for identifying an unknown nucleotide sequence using base extension which, when loaded into a computer, will control the computer to perform the following steps:

obtain a sequence of bases from a template;

identify a base in the sequence as an unknown base and include an ‘

unknown’

indicator in the sequence; and

provide an output sequence containing the unknown base indicator.