# US 2014/0154684 A1 · Diagnosis of melanoma and solar lentigo by nucleic acid analysis

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- Number: US 2014/0154684 A1
- Document ID: US20140154684A1
- Status: Published application
- Kind: A1
- Application number: 14/172,784
- Filed: 2014-02-04
- Published: 2014-06-05
- Earliest claimed: 2008-05-14
- Assignees: DermTech International
- Applicants: DermTech International
- Inventors: Sherman H. Chang
- Web page: https://patentgrep.com/patent/US20140154684A1

## CPC

- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- C12Q 1/68: involving nucleic acids
- G16B 35/00: ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
- G16C 20/60: In silico combinatorial chemistry
- C12Q 2600/112: Disease subtyping, staging or classification
- C12Q 2600/158: Expression markers
- C12Q 2600/16: Primer sets for multiplex assays
- C12Q 2600/178: miRNA, siRNA or ncRNA
- 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
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16C: COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE

## Abstract

The present invention provides methods for diagnosing melanoma and/or solar lentigo in a subject by analyzing nucleic acid molecules obtained from the subject. The present invention also provides methods for distinguishing melanoma from solar lentigo and/or dysplastic nevi and/or normal pigmented skin. The methods include analyzing expression or mutations in epidermal samples, of one or more skin markers. The methods can include the use of a microarray to analyze gene or protein profiles from a sample

## Claims

### Claim 1

A method of distinguishing melanoma from dysplastic nevi or normal pigmented skin in a human subject comprising:
(a) obtaining a sample of a skin lesion from a human subject;
(b) analyzing expression of a nucleic acid molecule encoding a protein selected from among:
endothelin receptor type B; Hypothetical protein MGC40222; tetratricopeptide repeat domain 3; staufen, RNA binding protein (Drosophila); actinin, alpha 4; KIAA1212; glycoprotein M6B; v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog; c-Maf-inducing protein; adaptor-related protein complex 2, mu 1 subunit; syntaxin 5A; chemokine-like factor superfamily 4; UDP-Gal: betaGlcNAc beta 1,4-galactosyl-transferase, polypeptide 5; fibrosin 1; ortholog of mouse neighbor of Punc E11; myosin, heavy polypeptide 14; preferentially expressed antigen in melanoma; jumonji domain containing 3; BCL2-related protein A1; formin binding protein 1, and combinations thereof, in the sample; and
(c) characterizing the skin lesion as being melanoma, dysplastic nevi, or normal pigmented skin, thereby distinguishing melanoma from dysplastic nevi or normal pigmented skin in a human subject.

### Claim 2 (depends on 1)

The method of claim 1, wherein the nucleic acid molecule is RNA.

### Claim 3 (depends on 1)

The method of claim 1, further comprising amplifying the nucleic acid molecule prior to analyzing.

### Claim 4 (depends on 1)

The method of claim 1, wherein the nucleic acid molecule or an amplification product thereof, is applied to a microarray.

### Claim 5 (depends on 4)

The method of claim 4, wherein an expression profile is detected using the microarray.

### Claim 6 (depends on 1)

The method of claim 1, wherein the sample is obtained by applying an adhesive tape to a target area of skin in a manner sufficient to isolate the sample adhering to the adhesive tape.

### Claim 7 (depends on 1)

The method of claim 1, wherein the sample is obtained from a biopsy taken at the site of the skin lesion.

### Claim 8 (depends on 6)

The method of claim 6, wherein the tape comprises a rubber adhesive on a polyurethane film.

### Claim 9 (depends on 6)

The method of claim 6, wherein about one to ten adhesive tapes or one to ten applications of a tape are applied and removed from the skin.

### Claim 10 (depends on 6)

The method of claim 6, wherein about one to eight adhesive tapes or one to eight applications of a tape are applied and removed from the skin.

### Claim 11 (depends on 6)

The method of claim 6, wherein about one to five adhesive tapes or one to five applications of a tape are applied and removed from the skin.

### Claim 12 (depends on 6)

The method of claim 6, wherein the method further comprises taking a biopsy of the target area of the skin.

### Claim 13 (depends on 1)

The method of claim 1, wherein the analyzing is performed in situ.

### Claim 14 (depends on 1)

The method of claim 1, further comprising determining a treatment regimen.

### Claim 15

A method for diagnosing melanoma in a subject, comprising:
(a) providing a gene expression profile of a target area suspected of being melanoma on the skin of the subject, wherein the target area of the skin simultaneously expresses a plurality of genes at the protein level that are markers for melanoma; and
(b) analyzing the subject's gene expression profile to a reference gene expression profile obtained from a corresponding normal skin sample, wherein the reference gene expression profile comprises an expression value of a target gene that encodes a protein selected from the group consisting of:
endothelin receptor type B; Hypothetical protein MGC40222; tetratricopeptide repeat domain 3; staufen, RNA binding protein (Drosophila); actinin, alpha 4; KIAA1212; glycoprotein M6B; v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog; c-Maf-inducing protein; adaptor-related protein complex 2, mu 1 subunit; syntaxin 5A; chemokine-like factor superfamily 4; UDP-Gal: betaGlcNAc beta 1,4-galactosyl-transferase, polypeptide 5; fibrosin 1; ortholog of mouse neighbor of Punc E11; myosin, heavy polypeptide 14; preferentially expressed antigen in melanoma; jumonji domain containing 3; BCL2-related protein A1; formin binding protein 1; or any combination thereof.

### Claim 16 (depends on 15)

The method of claim 15, wherein the reference gene expression profile further comprises an expression value of an additional target gene listed in Tables 1-7.

### Claim 17 (depends on 15)

The method of claim 15, wherein the reference gene expression profile is contained with a database.

### Claim 18 (depends on 15)

The method of claim 15, wherein the analyzing step is carried out using a computer.

### Claim 19

A kit for characterizing a skin lesion in a subject comprising a skin sample collection device and one or more probes or primers that selectively bind to a nucleic acid molecule encoding a protein selected from among:
endothelin receptor type B; Hypothetical protein MGC40222; tetratricopeptide repeat domain 3; staufen, RNA binding protein (Drosophila); actinin, alpha 4; KIAA1212; glycoprotein M6B; v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog; c-Maf-inducing protein; adaptor-related protein complex 2, mu 1 subunit; syntaxin 5A; chemokine-like factor superfamily 4; UDP-Gal: betaGlcNAc beta 1,4-galactosyl-transferase, polypeptide 5; fibrosin 1; ortholog of mouse neighbor of Punc E11; myosin, heavy polypeptide 14; preferentially expressed antigen in melanoma; jumonji domain containing 3; BCL2-related protein A1; and formin binding protein 1.

### Claim 20 (depends on 19)

The kit of claim 19, wherein the skin sample collection device is an adhesive tape.