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US 2022/0033882 A1Published application
Methods of diagnosing and treating patients with pigmented skin lesions
AssigneeCastle Biosciences, Inc.
InventorsRobert Willis COOK, Derek MAETZOLD, Kyle R. COVINGTON, Olga ZOLOCHEVSKA
Life of this patent
Estimating the term…
Abstract
The present disclosure relates to methods for diagnosing a skin lesion as malignant or benign.
Claims30
A method for treating a patient with a skin lesion, the method comprising:
- (a) obtaining a diagnosis identifying the skin lesion as a malignant lesion, an intermediate risk lesion, or a benign lesion in a sample from the skin lesion of the patient, wherein the diagnosis was obtained by:
- (1) determining the expression level of at least 12 genes in a gene set;
- wherein the at least 12 genes in the gene set are selected from:
- ABLIM1, ANXA8L1, ATP6V0E2, BAP1, BCL2A1, BTG1, CLCA2, CST6, CSTA, CXCL14, DCT, DSP, DUSP4, GATA3, GJA1, GPR143, HAL, MGP, KLF5, KRT2, KRT17, NES, PPL, RPL37A, PTN, RPS16, S100A8, S100A9, SAP130, SFN, TP63, and WIPI1;
- (2) comparing the expression levels of the at least 12 genes in the gene set from the sample to the expression levels of the at least 12 genes in the gene set from a predictive training set to generate a probability score;
- (3) providing an indication as to whether the skin lesion is a malignant lesion, an intermediate risk lesion, or a benign lesion based on the probability score generated in step (2);
- and
- (4) identifying that the skin lesion is a malignant lesion based on the probability score;
- and
- (b) administering to the patient an aggressive treatment when the determination is made in the affirmative that the patient has a skin lesion that is a malignant lesion.
7 more elements
A method of treating a patient with a skin lesion, the method comprising administering an aggressive cancer treatment regimen to the patient,
- wherein the patient has a skin lesion identified as a malignant lesion as generated by comparing the expression levels of at least 12 genes wherein the at least 12 genes are selected from ABLIM1, ANXA8L1, ATP6V0E2, BAP1, BCL2A1, BTG1, CLCA2, CST6, CSTA, CXCL14, DCT, DSP, DUSP4, GATA3, GJA1, GPR143, HAL, MGP, KLF5, KRT2, KRT17, NES, PPL, RPL37A, PTN, RPS16, S100A8, S100A9, SAP130, SFN, TP63, and WIPI1, from the skin lesion with the expression levels of the same at least 12 genes are selected from ABLIM1, ANXA8L1, ATP6V0E2, BAP1, BCL2A1, BTG1, CLCA2, CST6, CSTA, CXCL14, DCT, DSP, DUSP4, GATA3, GJA1, GPR143, HAL, MGP, KLF5, KRT2, KRT17, NES, PPL, RPL37A, PTN, RPS16, S100A8, S100A9, SAP130, SFN, TP63, and WIPI1 from a predictive training set.
A kit comprising primer pairs suitable for the detection and quantification of nucleic acid expression of at least 12 genes, wherein the at least 12 genes are selected from:
- ABLIM1, ANXA8L1, ATP6V0E2, BAP1, BCL2A1, BTG1, CLCA2, CST6, CSTA, CXCL14, DCT, DSP, DUSP4, GATA3, GJA1, GPR143, HAL, MGP, KLF5, KRT2, KRT17, NES, PPL, RPL37A, PTN, RPS16, S100A8, S100A9, SAP130, SFN, TP63, and WIPI1.
A method for diagnosing a skin lesion from a patient as a malignant lesion, an intermediate risk lesion, or a benign lesion, the method comprising:
- (a) obtaining a sample from the skin lesion from the patient and isolating mRNA from the sample;
- (b) determining the expression level of at least 12 genes in a gene set;
- wherein the at least 12 genes in the gene set are selected from:
- ABLIM1, ANXA8L1, ATP6V0E2, BAP1, BCL2A1, BTG1, CLCA2, CST6, CSTA, CXCL14, DCT, DSP, DUSP4, GATA3, GJA1, GPR143, HAL, MGP, KLF5, KRT2, KRT17, NES, PPL, RPL37A, PTN, RPS16, S100A8, S100A9, SAP130, SFN, TP63, and WIPI1;
- (c) comparing the expression levels of the at least 12 genes in the gene set from the sample to the expression levels of the at least 12 genes in the gene set from a predictive training set to generate a probability score;
- and
- (d) providing an indication as to whether the skin lesion is a malignant lesion, an intermediate risk lesion, or a benign lesion, based on the probability score generated in step (c).
4 more elements
A method for diagnosing a skin lesion from a patient as a malignant lesion, an intermediate risk lesion, or a benign lesion, the method comprising:
- (a) obtaining a sample from skin lesion from the patient and isolating mRNA from the sample;
- (b) determining the expression level of at least 12 genes in a gene set;
- wherein the at least 12 genes in the gene set are:
- ABLIM1, ANXA8L1, ATP6V0E2, BAP1, BCL2A1, BTG1, CLCA2, CST6, CSTA, CXCL14, DCT, DSP, DUSP4, GATA3, GJA1, GPR143, HAL, MGP, KLF5, KRT2, KRT17, NES, PPL, RPL37A, PTN, RPS16, S100A8, S100A9, SAP130, SFN, TP63, and WIPI1;
- and
- (c) providing an indication as to whether the skin lesion is a malignant lesion, an intermediate risk lesion, or a benign lesion, based on the expression level of the at least 12 genes generated in step (b).
3 more elements
Dependencies are inferred from the claim text.