Diagnosis of melanoma and solar lentigo by nucleic acid analysis

• US 9,057,109 B2
• Filed: 03/06/2014
• Issued: 06/16/2015
• Est. Priority Date: 05/14/2008
• Status: Active Grant

• Current Assignee: DermTech International
• Original Assignee: DermTech International
• Inventors: Chang, Sherman H.
• Primary Examiner(s): MARSCHEL, ARDIN H
• Application Number:
  US14/199,900
• Publication Number:
  US 20140256584A1
• Time in Patent Office: 467 Days
• Field of Search: 435/6.1
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: C12Q 2600/178 miRNA, siRNA or ncRNA
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry

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

1. A method of detecting melanoma in a human subject comprising:

(a) obtaining a sample of a skin lesion suspected of comprising melanoma from a human subject, wherein the skin lesion sample comprises or is suspected of comprising a nucleic acid molecule expressed from C6orf218;

(b) detecting the presence of a nucleic acid molecule expressed from C6orf218 in the skin lesion sample, whereby the presence of a nucleic acid molecule expressed from C6orf218 in the skin lesion sample in an amount that is greater than the presence of C6orf218 in a non-melanoma sample is indicative of melanoma in the skin lesion sample, wherein detecting the presence of a nucleic acid molecule expressed from C6orf218 is by application of a detectably labeled probe that hybridizes to a nucleic acid molecule expressed from C6orf218; and

(c) characterizing the skin lesion as having melanoma or not having melanoma.

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

3. The method of claim 1, further comprising amplifying the nucleic acid molecule.

4. The method of claim 1, wherein the nucleic acid molecule or an amplification product thereof, is quantified using quantitative real-time PCR.

5. The method of claim 1, further comprising amplifying the nucleic acid molecule and quantifying the amplification product using quantitative real-time PCR.

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

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

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

9. 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.

10. 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.

11. 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.

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

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

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

15. A method for diagnosing melanoma in a subject, comprising:

(a) obtaining a sample of a skin lesion suspected of comprising melanoma from a subject, wherein the skin lesion sample comprises or is suspected of comprising a nucleic acid molecule expressed from C6orf218;

(b) detecting the presence of a nucleic acid molecule expressed from C6orf218 in the skin lesion sample, wherein detecting the presence of a nucleic acid molecule expressed from C6orf218 is by application of a detectably labeled probe that hybridizes to a nucleic acid molecule expressed from C6orf218; and

(c) comparing the presence of a nucleic acid molecule expressed from C6orf218 in the skin lesion sample to the presence of C6orf218 in a non-melanoma sample, whereby the increased presence of a nucleic acid molecule expressed from C6orf218 in the skin lesion sample as compared to the non-melanoma sample is indicative of melanoma, thereby diagnosing the skin lesion as having melanoma.

16. The method of claim 15, further comprising determining a treatment regimen.

17. The method of claim 15, wherein the presence of a nucleic acid molecule expressed from C6orf218 in the non-melanoma skin sample is contained with a database.

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