Sequence assembly

• US 8,738,300 B2
• Filed: 06/12/2012
• Issued: 05/27/2014
• Est. Priority Date: 04/04/2012
• Status: Active Grant

• Current Assignee: Invitae Corporation
• Original Assignee: Good Start Genetics, Inc. (Invitae Corporation)
• Inventors: Porreca, Gregory, Kennedy, Caleb J.
• Primary Examiner(s): Brusca, John S
• Application Number:
  US13/494,616
• Publication Number:
  US 20130268206A1
• Time in Patent Office: 714 Days
• Field of Search: None
• US Class Current: 702/20
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 30/20 Sequence assembly

Abstract

The invention relates to assembly of sequence reads. The invention provides a method for identifying a mutation in a nucleic acid involving sequencing nucleic acid to generate a plurality of sequence reads. Reads are assembled to form a contig, which is aligned to a reference. Individual reads are aligned to the contig. Mutations are identified based on the alignments to the reference and to the contig.

Claims

1. A system for identifying a mutation in a nucleic acid, the system comprising:

a computing device including a tangible, non-transitory memory coupled to a processor configured to execute computer program instructions to cause the processor to;

receive a plurality of sequence reads;

create a contig based on the reads;

align the contig to a reference sequence;

align the individual reads back to the contig; and

identify a mutation based on the alignments to the contig and the reference sequence.

2. The system of claim 1, wherein the computing device is further configured to divide the reads into subsets.

3. The system of claim 1, wherein the computing device is further configured to determine a position of the mutation in the nucleic acid.

4. The system of claim 1, wherein the mutation is selected from the group consisting of:

a single nucleotide polymorphism (SNP), an insertion, a deletion, a substitution, a translocation, and a copy number variation.

5. The system of claim 1, wherein the computing device is configured to identify a plurality of mutations.

6. The system of claim 5, wherein a first mutation is within about 100 nucleotides of a second mutation.

7. The system according to claim 6, wherein the first mutation is a substitution and the second mutation is a deletion.

8. The system of claim 1 wherein the mutation is a deletion at an end of a sequence read.

9. The system of claim 1, wherein the mutation is associated with a disease.