Analysis methods

• US 10,370,710 B2
• Filed: 11/20/2017
• Issued: 08/06/2019
• Est. Priority Date: 10/17/2011
• Status: Active Grant

• Current Assignee: Invitae Corporation
• Original Assignee: Good Start Genetics, Inc. (Invitae Corporation)
• Inventors: Porreca, Gregory, Umbarger, Mark, Kennedy, Caleb
• Primary Examiner(s): Zhang, Kaijiang
• Application Number:
  US15/818,165
• Publication Number:
  US 20180298440A1
• Time in Patent Office: 624 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2563/185 Nucleic acid dedicated to use as a hidden marker/bar code, e.g. inclusion of nucleic acids to mark art objects or animals

Abstract

The invention generally relates to methods for analyzing nucleic acids to identify novel mutations associated with diseases. In certain embodiments, methods of the invention involve obtaining nucleic acid from a subject having a disease, identifying at least one mutation in the nucleic acid, and comparing the mutation to a database of mutations known to be associated with the disease, wherein mutations that do not match to the database are identified as novel mutations.

Claims

1. A method for identifying a novel mutation associated with a disease, the method comprising:

obtaining nucleic acid from a subject having a disease;

determining that the nucleic acid comprises a variant comprising an insertion or deletion;

comparing the variant to a database of variants known to be associated with the disease, wherein a variant that does not match to the database is identified as a novel variant;

determining a lower boundary and an upper boundary of an equivalent insertion/deletion region (EIR) of the novel variant;

determining that part of the EIR falls within a functional region.

2. The method according to claim 1, wherein determining that the nucleic acid comprises a variant comprising an insertion or deletion comprises:

sequencing the nucleic acid; and

comparing the sequence of the nucleic acid to a reference sequence.

3. The method according to claim 2, wherein sequencing is sequencing-by-synthesis.

4. The method according to claim 3, wherein sequencing-by-synthesis is single molecule sequencing-by-synthesis.

5. The method according to claim 2, wherein the reference sequence is a consensus human sequence or a sequence from a non-diseased sample.

6. The method according to claim 1, wherein prior to determining that the nucleic acid comprises a variant comprising an insertion or deletion, the method further comprises attaching a barcode sequence to the nucleic acid.

7. The method according to claim 1, wherein the disease is cystic fibrosis.

8. The method according to claim 7, wherein the subject is Hispanic.

9. The method according to claim 1, further comprising determining that the novel variant is causative of the disease by annotating the variant with functional information.

10. A method for determining if a mutation is causative of a disease, the method comprising:

conducting an assay to obtain a nucleic acid sequence from a subject having a disease;

determining a presence of at least one novel variant comprising an insertion or deletion in the sequence;

annotating the variant with appropriate functional information;

identifying a lower and upper boundary of an equivalent insertion/deletion region (EIR) of the novel variant; and

determining that part of the EIR falls within a functional region.