# US 10,370,710 B2 · Analysis methods

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- Number: US 10,370,710 B2
- Document ID: US10370710B2
- Status: Granted
- Kind: B2
- Application number: 15/818,165
- Filed: 2017-11-20
- Published: 2018-10-18
- Granted: 2019-08-06
- Earliest claimed: 2011-10-17
- Applicants: Good Start Genetics, Inc.
- Inventors: Gregory Porreca; Mark Umbarger; Caleb Kennedy
- Web page: https://patentgrep.com/patent/US10370710B2

## CPC

- C12Q 1/6874: involving nucleic acid arrays, e.g. sequencing by hybridisation
- C12Q 1/6869: Methods for sequencing
- C12Q 1/6883: for diseases caused by alterations of genetic material
- 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
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES

## 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

### Claim 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.

### Claim 2 (depends on 1)

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.

### Claim 3 (depends on 2)

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

### Claim 4 (depends on 3)

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

### Claim 5 (depends on 2)

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

### Claim 6 (depends on 1)

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.

### Claim 7 (depends on 1)

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

### Claim 8 (depends on 7)

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

### Claim 9 (depends on 1)

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.

### Claim 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.