Method, computer-accessible medium and system for base-calling and alignment

Patent metadata

Field	Value
Publication number	US-10964408-B2
Application number	US-201013266662-A
Country	US
Kind code	B2
Filing date	Apr 27, 2010
Priority date	Apr 27, 2009
Publication date	Mar 30, 2021
Grant date	Mar 30, 2021

Abstract

Exemplary methods, procedures, computer-accessible medium, and systems for base-calling, aligning and polymorphism detection and analysis using raw output from a sequencing platform can be provided. A set of raw outputs can be used to detect polymorphisms in an individual by obtaining a plurality of sequence read data from one or more technologies (e.g., using sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, Sanger sequencing, etc.). For example, provided herein are exemplary methods, procedures, computer-accessible medium and systems, which can include and/or be configured for obtaining raw output from a sequencing platform configured to be used for reading fragment(s) of genomes, obtaining reference sequences for the genomes obtained independently from the raw output, and generating a base-call interpretation and/or alignment using the raw output and the reference sequences. For example, a score function can be determined based on information associated with the sequencing platform that can be used to analyze polymorphisms based on the base-call interpretation and/or alignment.

First claim

What is claimed is:

1. A non-transitory computer-accessible medium having stored thereon computer executable instructions for assembling at least one genetic sequence which, when executed by a hardware processing arrangement, configure the hardware processing arrangement to:
(a) obtain a series of raw intensity outputs from a sequencing platform configured to (i) be used for reading a fragment of at least one genome and (ii) use a sequencing-by-ligation procedure, wherein each of the obtained raw intensity outputs comprises a plurality of randomly located short sequence reads, and wherein each of the randomly located short sequence reads has a read length of at least 48 base pairs (bps);
(b) obtain at least one reference sequence for the at least one genome, wherein the at least one reference sequence for the at least one genome is obtained independently from the series of first raw intensity outputs obtained from the sequencing platform;
(c) automatically generate a search tree comprising a plurality of nodes, wherein each of the plurality of nodes corresponds to a particular nucleotide base;
(d) automatically select a node of the plurality of nodes in the search tree;
(e) automatically expand the selected node by creating a plurality of child nodes, each of the plurality of child nodes corresponding to a particular further nucleotide base;
(f) automatically generate a score for one or more of the plurality of child nodes, wherein the score is a function of (i) at least one raw intensity output from the series of raw intensity outputs, (ii) the plurality of reference sequences, and (iii) the nucleotide base to which a particular one of the plurality of child nodes corresponds;
(g) automatically select one or more of the plurality of child nodes based on the score;
(h) automatically repeat procedures (e)-(g) for the selected child node;
(i) automatically generate a path through the plurality of nodes; and
(j) automatically assemble the at least one genetic sequence based on the path.

2. The computer-accessible medium of claim 1 , wherein the processing arrangement is further configured to:
automatically generate the score using a score function;
determine the score function based on information associated with a sequencing platform from which the series of raw intensity outputs are obtained; and
with the score function, analyze polymorphisms based on at least one of the raw intensity outputs or the reference sequences.

3. The computer-accessible medium of claim 1 , wherein the sequencing platform is further configured to utilize at least one of a Sanger chemistry procedure or a sequencing-by-synthesis procedure.

4. The computer-accessible medium of claim 1 , wherein the read length is at least 78 bps.

5. The computer-accessible medium of claim 1 , wherein each of the raw intensity outputs further comprises at least one error associated with at least one of the plurality of randomly located short sequence reads.

6. The computer-accessible medium of claim 5 , wherein the at least one error is related to at least one of an incorrect base-call, a missing base, one or more inserted bases, one or more deleted bases, or a homopolymeric compression.

7. The computer-accessible medium of claim 1 , wherein the at least one genome comprises a genome from at least one of (i) one or more diseased cells, (ii) one or more normal cells, (iii) at least one individual organism, (iv) at least one population, or (v) at least one ecological system.

8. The computer-accessible medium of claim 1 , wherein the at least one reference sequence is obtained from at least one of (i) a mathematical model, (ii) existing data, (iii) genomic single-molecules, or (iv) genomic materials that are at least one of amplified or otherwise modified.

9. The computer-accessible medium of claim 2 , wherein the analyzing procedure comprises a branch-and-bound process.

10. The computer-accessible medium of claim 1 , wherein the processing arrangement is further configured to generate the score based on an alignment between the raw intensity outputs and the at least one reference sequence.

11. The computer-accessible medium of claim 10 , wherein the alignment includes determining, with the processing arrangement, if any of the raw intensity outputs is contained are within the reference sequences.

12. A method for assembling at least one genetic sequence, comprising:
(a) obtaining a series of raw intensity outputs from a sequencing platform configured to (i) be used for reading a fragment of at least one genome and (ii) use a sequencing-by-ligation procedure, wherein each of the obtained raw intensity outputs comprises a plurality of randomly located short sequence reads, and wherein each of the randomly located short sequence reads has a read length of at least 48 base pairs (bps);
(b) obtaining at least one reference sequence for the at least one genome, wherein the at least one reference sequence for the at least one genome is obtained independently from the series of raw intensity outputs obtained from the sequencing platform;
(c) automatically generating a search tree comprising a plurality of nodes, wherein each of the plurality of nodes corresponds to a particular nucleotide base;
(d) automatically selecting a node of the plurality of nodes in the search tree;
(e) automatically expanding the selected node by creating a plurality of child nodes, each of the child nodes corresponding to a particular further nucleotide base;
(f) automatically generating a score for one or more of the child nodes, wherein the score is a function of (i) at least one raw intensity output from the series of raw intensity outputs, (ii) the plurality of reference sequences, and (iii) the nucleotide base to which a particular one of the plurality of child nodes corresponds;
(g) automatically selecting one or more of the plurality of child nodes based on the score;
(h) automatically repeating procedures (e)-(g) for the selected child node;
(i) automatically generating a path through the plurality of nodes; and
(j) using a computer hardware arrangement, automatically assembling the at least one genetic sequence based on the path.

13. The method of claim 12 , further comprising:
automatically generating the score using a score function;
automatically determining the score function based on information associated with a sequencing platform from which the series of raw intensity outputs are obtained; and
with the score function, automatically analyzing polymorphisms based on at least one of the raw intensity outputs or the reference sequences.

14. The method of claim 12 , wherein the sequencing platform is further configured to utilize at least one of a Sanger chemistry procedure or a sequencing-by-synthesis procedure.

15. The method of claim 12 , wherein the read length is at least 78 bps.

16. The method of claim 12 , wherein each of the raw intensity outputs further comprises at least one error associated with at least one of the plurality of randomly located short sequence reads.

17. The method of claim 16 , wherein the at least one error is related to at least one of an incorrect base-call, a missing base, one or more inserted bases, one or more deleted bases, or a homopolymeric compression.

18. The method of claim 12 , wherein the at least one genome comprises a genome from at least one of (i) one or more diseased cells, (ii) one or more normal cells, (iii) at least one individual organism, (iv) at least one population, or (v) at least one ecological system.

19. The method of cl

Assignees

• Mishra Bhubaneswar
• Narzisi Giuseppe
• Univ New York

Inventors

• Mishra Bhubaneswar
• Narzisi Giuseppe

Classifications

• G16B30/00 Primary

  ICT specially adapted for sequence analysis involving nucleotides or amino acids · CPC title

• G16B30/20

  Sequence assembly · CPC title

• G16B30/10

  Sequence alignment; Homology search · CPC title

• C12Q1/6869

  Methods for sequencing · CPC title