# US 11,441,194 B2 · Methods and probe combinations for detecting melanoma

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- Number: US 11,441,194 B2
- Document ID: US11441194B2
- Status: Granted
- Kind: B2
- Application number: 17/146,366
- Filed: 2021-01-11
- Published: 2021-08-05
- Granted: 2022-09-13
- Earliest claimed: 2005-09-02
- Assignees: Abbott Molecular Inc.; The Regents of the University of California
- Applicants: Abbott Molecular Inc.; The Regents of the University of California
- Inventors: Boris Bastian; Larry E. Morrison; Susan Jewell
- Web page: https://patentgrep.com/patent/US11441194B2

## CPC

- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- C12Q 1/6841: In situ hybridisation
- C12Q 2537/143: Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
- C12Q 2600/112: Disease subtyping, staging or classification
- 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

The present invention is based on the discovery of methods and combinations of probes to chromosomal regions that are gained or lost or imbalanced in melanoma that provide highly specific and sensitive assays for the detection of melanoma cells.

## Claims

### Claim 1

A hybridization method comprising:
a) contacting a sample of a skin lesion from a human subject with a combination consisting of four detectably labeled in situ hybridization probes, the four detectably labeled in situ hybridization probes consisting of a probe that selectively hybridizes to a target sequence within chromosome subregion 6p25, a probe that selectively hybridizes to a target sequence within chromosome subregion 6q23, a chromosome 6 enumerator probe that comprises a repetitive DNA sequence and selectively hybridizes to the centromeric or peri-centromeric region of chromosome 6, and an additional probe,
wherein the additional probe is selected from the group consisting of a chromosome 10 enumerator probe that comprises a repetitive DNA sequence and selectively hybridizes to the centromeric or peri-centromeric region of chromosome 10, a probe that selectively hybridizes to a target sequence within chromosome subregion 7q34, a probe that selectively hybridizes to a target sequence within chromosome subregion 11q13, a probe that selectively hybridizes to a target sequence within chromosome subregion 17q25, and a probe that selectively hybridizes to a target sequence within chromosome subregion 20q13; and
wherein the target sequence for each probe is from 70,000 nucleotides to 800,000 nucleotides, and each probe hybridizes along the entire length of its target sequence;
b) incubating each probe of the combination with the skin lesion sample under in situ hybridization conditions in which each probe selectively hybridizes to its target sequence to form a stable hybridization complex, wherein each probe hybridizes to a lesser extent to, or not at all to non-target sequences, as compared to target sequences; and
c) detecting hybridization of the combination of probes to determine copy number at any chromosome subregion to which the probes selectively hybridize,
wherein the hybridization method employs no additional in situ hybridization probes beyond those in the combination.

### Claim 2 (depends on 1)

The method of claim 1, wherein the skin lesion sample is a formalin-fixed, paraffin-embedded sample.

### Claim 3 (depends on 1)

The method of claim 1, wherein the detectable label is a fluorescent label.

### Claim 4 (depends on 1)

The method of claim 1, wherein the additional probe is said chromosome 10 enumerator probe that comprises a repetitive DNA sequence and selectively hybridizes to the centromeric or peri-centromeric region of chromosome 10.

### Claim 5 (depends on 1)

The method of claim 1, wherein the additional probe is said probe that selectively hybridizes to a target sequence within chromosome subregion 7q34.

### Claim 6 (depends on 1)

The method of claim 1, wherein the additional probe is said probe that selectively hybridizes to said target sequence within chromosome subregion 11q13.

### Claim 7 (depends on 1)

The method of claim 1, wherein the additional probe is said probe that selectively hybridizes to said target sequence within chromosome subregion 17q25.

### Claim 8 (depends on 1)

The method of claim 1, wherein the additional probe is said probe that selectively hybridizes to a target sequence within chromosome subregion 20q13.

### Claim 9 (depends on 1)

The method of claim 1, wherein the target sequence for each probe is at least 100,000 nucleotides.