# US 8,785,122 B2 · Methods of detecting mutations associated with ataxia-ocular apraxia 2 (AOA2)

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- Number: US 8,785,122 B2
- Document ID: US8785122B2
- Status: Granted
- Kind: B2
- Application number: 13/487,358
- Filed: 2012-06-04
- Published: 2012-09-20
- Granted: 2014-07-22
- Earliest claimed: 2006-01-27
- Assignees: Athena Diagnostics, Inc.
- Applicants: Corey D. Braastad; Narasimhan Nagan; Jeffrey G. Jones; William K. Seltzer; Susan Allen; Sat Dev Batish; Hui Zhu
- Inventors: Corey D. Braastad; Narasimhan Nagan; Jeffrey G. Jones; William K. Seltzer; Susan Allen; Sat Dev Batish; Hui Zhu
- Web page: https://patentgrep.com/patent/US8785122B2

## CPC

- C12Q 1/6883: for diseases caused by alterations of genetic material
- C12Q 2600/156: Polymorphic or mutational markers
- C12Q 2600/158: Expression markers
- 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

Methods of identifying polymorphisms associated with ataxia-ocular apraxia 2 (AOA2), are described. The polymorphisms associated with AOA2 include specific mutations in the senataxin (SETX) gene. Also described are methods of diagnosis of AOA2, as well as methods of assessing an individual for carrier status for AOA2.

## Claims

### Claim 1

A method of detecting a genetic polymorphism in a human individual, comprising:
detecting in a test sample from a human individual at least one mutation of interest in a senataxin (SETX) gene comprising SEQ ID NO:1, wherein the at least one mutation of interest results in a premature STOP codon causing truncation of the encoded SETX protein, wherein the one mutation of interest is a single base transition C→T at position 4234 of the SETX gene, and wherein the presence of the single base transition C→T at position 4234 indicates the presence of a genetic polymorphism associated with AOA2.

### Claim 2 (depends on 1)

The method of claim 1, wherein the test sample from the human individual comprises genomic DNA.

### Claim 3 (depends on 1)

The method of claim 1, wherein detecting the test sample comprises amplifying all or a fragment of the senataxin gene.

### Claim 4 (depends on 1)

The method of claim 1, wherein detecting the test sample comprises direct sequence analysis.

### Claim 5 (depends on 1)

The method of claim 1, wherein the at least one mutation of interest includes an additional mutation selected from the group consisting of:
a) a 2 base deletion of positions 6114-6115;
b) a 2 base insertion of AT between positions 2747-2748;
c) a 6 base deletion of positions 4873-4878 accompanied by an insertion of GG at the same location;
d) a single base insertion of G between positions 4891-4892;
e) a 2 base insertion of CA between positions 5301-5302;
f) a 4 base deletion of positions 5308-5311;
g) a 2 base deletion of positions 5591-5592;
h) a single base deletion of position 5958;
i) a single base insertion of A between positions 6422-6423;
j) a four base deletion of positions 6848-6851;
k) a single base insertion of T between positions 479-480;
l) a single base transition C→T at nucleotide 4816; and
m) a single base transition C→T at nucleotide 6292.

### Claim 6

A method of diagnosing ataxia-ocular apraxia 2 (AOA2) in a human individual, comprising:
detecting in a test sample from a human individual at least one mutation of interest in a first allele of a senataxin (SETX) gene comprising SEQ ID NO:1, wherein the at least one mutation of interest results in a premature STOP codon causing truncation of the encoded SETX protein,
wherein one mutation of interest is a single base transition C→T at position 4234 of the SETX gene
detecting at least one mutation of interest in the second allele of the SETX gene; and
diagnosing the human individual as having AOA2 when the single base transition C→T at position 4234 is detected and when the at least one mutation of interest is detected in the second allele of the SETX gene.

### Claim 7 (depends on 6)

The method of claim 6, wherein the second allele of the senataxin (SETX) gene comprises at least one mutation of interest selected from the group consisting of:
a) a 2 base deletion of nucleotides 6114-6115;
b) a 2 base insertion of AT between nucleotides 2747-2748;
c) a single base transition C→T at nucleotide 4234;
d) a single base transition C→T at nucleotide 4816;
e) a 6 base deletion of nucleotides 4873-4878 accompanied by an insertion of GG at the same location;
f) a single base insertion of G between nucleotides 4891-4892;
g) a 2 base insertion of CA between nucleotides 5301-5302;
h) a 4 base deletion of nucleotides 5308-5311;
i) a 2 base deletion of nucleotides 5591-5592;
j) a single base deletion of nucleotide 5958;
k) a single base insertion of A between nucleotides 6422-6423;
1) a single base transition C→T at nucleotide 6292;
m) a four base deletion of nucleotides 6848-6851; and
n) a single base insertion of T between nucleotides 479-480.

### Claim 8 (depends on 7)

The method of claim 7, wherein both the first and the second alleles of the senataxin gene comprise the same mutation or mutations.

### Claim 9 (depends on 6)

The method of claim 6, wherein the test sample from the human individual comprises genomic DNA.

### Claim 10 (depends on 6)

The method of claim 6, wherein detecting the test sample comprises amplifying all or a fragment of the senataxin gene.

### Claim 11 (depends on 6)

The method of claim 6, wherein detecting the test sample comprises direct sequence analysis.

### Claim 12 (depends on 6)

The method of claim 6, wherein the at least one mutation of interest includes an additional mutation selected from the group consisting of:
a) a 2 base deletion of positions 6114-6115;
b) a 2 base insertion of AT between positions 2747-2748;
c) a 6 base deletion of positions 4873-4878 accompanied by an insertion of GG at the same location;
d) a single base insertion of G between positions 4891-4892;
e) a 2 base insertion of CA between positions 5301-5302;
f) a 4 base deletion of positions 5308-5311;
g) a 2 base deletion of positions 5591-5592;
h) a single base deletion of position 5958;
i) a single base insertion of A between positions 6422-6423;
j) a four base deletion of positions 6848-6851; and
k) a single base insertion of T between positions 479-480.

### Claim 13

A method of assessing a human individual for carrier status for ataxia-ocular apraxia 2 (AOA2), comprising:
detecting in a test sample from a human individual at least one mutation of interest in a first allele of the senataxin (SETX) gene comprising SEQ ID NO: 1 of the individual, wherein the at least one mutation of interest comprises a single base transition C-T at position 4234;
detecting the absence of the at least one mutation of interest in the second allele of the SETX gene,
wherein the presence of the at least one mutation of interest in the first allele of the senataxin gene, and the absence of the at least one mutation of interest in the second allele of the senataxin gene, is indicative of carrier status for ataxia-ocular apraxia 2.

### Claim 14 (depends on 13)

The method of claim 13, wherein the test sample from the human individual comprises genomic DNA.

### Claim 15 (depends on 13)

The method of claim 13, wherein detecting the test sample comprises amplifying all or a fragment of the senataxin gene.

### Claim 16 (depends on 13)

The method of claim 13, wherein detecting the test sample comprises direct sequence analysis.

### Claim 17 (depends on 13)

The method of claim 13, wherein the at least one mutation of interest includes an additional mutation selected from the group consisting of:
a) a 2 base deletion of positions 6114-6115;
b) a 2 base insertion of AT between positions 2747-2748;
c) a 6 base deletion of positions 4873-4878 accompanied by an insertion of GG at the same location;
d) a single base insertion of G between positions 4891-4892;
e) a 2 base insertion of CA between positions 5301-5302;
f) a 4 base deletion of positions 5308-5311;
g) a 2 base deletion of positions 5591-5592;
h) a single base deletion of position 5958;
i) a single base insertion of A between positions 6422-6423;
j) a four base deletion of positions 6848-6851; and
k) a single base insertion of T between positions 479-480.