Methods for evaluating lung cancer status
AssigneeAllegro Diagnostics Corp.
InventorDuncan H. Whitney
Life of this patent
Estimating the term…
Abstract
The invention in some aspects provides methods of determining the likelihood that a subject has lung cancer based on the expression of informative-genes. In other aspects, the invention provides methods for determining an appropriate diagnostic intervention plan for a subject based on the expression of informative-genes. Related compositions and kits are provided in other aspects of the invention.
Claims58
A method of determining the likelihood that a subject has lung cancer, the method comprising:
- subjecting a biological sample obtained from a subject to a gene expression analysis, wherein the gene expression analysis comprises determining mRNA expression levels in the biological sample of at least 1-10 genes selected from Tables 4, 7-8, and 9-11;
- and
- determining the likelihood that the subject has lung cancer by determining a statistical significance on the mRNA expression levels.
A method for determining a treatment course for a subject, the method comprising:
- subjecting a biological sample obtained from the subject to a gene expression analysis, wherein the gene expression analysis comprises determining mRNA expression levels in the biological sample of at least 1-10 genes selected from Tables 4, 7-8, and 9-11;
- determining a treatment course for the subject based on the expression levels.
The method of any preceding claim further comprising creating a report summarizing the results of the gene expression analysis.
The method of any preceding claim, wherein the biological sample is obtained from the respiratory epithelium of the subject.
The method of any preceding claim, wherein the biological sample is obtained using bronchial brushings, broncho-alveolar lavage, or a bronchial biopsy.
The method of any preceding claim, wherein the subject exhibits one or more symptoms of lung cancer and/or has a lesion that is observable by computer-aided tomography or chest X-ray.
The method of any preceding claim, wherein the genes are selected from the group consisting of:
- BST1, APT12A, DEFB1, C3, TNFAIP2, SOD2, EPHX3, LST1, HCK, CA12, IRAK2, FMNL1, SERPING1, G0S2, and LCP2.
The method of any preceding claim, wherein the genes are selected from the group consisting of:
- TMTC2, SCHIP1, NMUR2, SORBS2, NPAS2, AKAP12, CSDA, SH3BGRL2, CD9, C9orf102, GRIK2, CAPN9, C19orf2, PRSS23, CA12, NCL, FUT8, PAWR, MTERFD3, RMND5A, OXR1, ALG1L, DAAM1, SLC26A2, AGPS, HDGFRP3, PLCB4, PAM, FOXJ3, TSPAN5, EDEM3, DEFB1, SLC17A5, ZBTB34, MYO1E, MIA3, and ZNF12.
The method of any preceding claim, wherein the genes are selected from the group consisting of:
- EPHX3, HLA-DQB2, BST1, ATP12A, HLA-DQB2, C3, CD82, INSR, PTPN7, FMNL1, IKBKE, RAC2, NINJ1, HLA-DPB1, MDK, ACSS2, HCK, GPRC5B, IRAK2, PLEK, COTL1, CYTH4, TNFAIP2, SCNN1B, LCP2, SOD2, HLA-DMB, CMTM1, SERPING1, CIITA, LILRA5, REC8, CORO1A, LST1, P2RY13, NCF4, G0S2, and TMC6.
The method of any preceding claim wherein the expression levels are determined using a quantitative reverse transcription polymerase chain reaction, a bead-based nucleic acid detection assay or a oligonucleotide array assay.
A method of determining the likelihood that a subject has lung cancer, the method comprising:
- subjecting a biological sample obtained from a subject to a gene expression analysis, wherein the gene expression analysis comprises determining an mRNA expression level in the biological sample of at least 1 to 10 genes selected from Tables 4, 7-8, and 9-11;
- and
- determining the likelihood that the subject has lung cancer based at least in part on the expression levels.
A method of determining the likelihood that a subject has lung cancer, the method comprising:
- subjecting a biological sample obtained from the respiratory epithelium of a subject to a gene expression analysis, wherein the gene expression analysis comprises determining an mRNA expression level in the biological sample of at least 1-10 genes selected from Tables 4, 7-8, and 9-11;
- and
- determining the likelihood that the subject has lung cancer based at least in part on the expression level.
The method of any preceding claim, wherein the lung cancer is a adenocarcinoma, squamous cell carcinoma, small cell cancer or non-small cell cancer.
The method of any preceding claim, wherein the expression level of each of the 15 genes in Table 4 is determined.
The method of any preceding claim, wherein the expression levels of at least 2 genes are evaluated.
The method of any preceding claim, wherein the expression levels of at least 3 genes are evaluated.
The method of any preceding claim, wherein the expression levels of at least 4 genes are evaluated.
The method of any preceding claim, wherein the expression levels of at least 5 genes are evaluated.
A computer implemented method for processing genomic information, the method comprising:
- obtaining data representing expression levels in a biological sample of at least 1-10 mRNAs selected from Tables 4, 7-8, and 9-11, wherein the biological sample was obtained of a subject;
- and
- using the expression levels to assist in determining the likelihood that the subject has lung cancer.
A composition consisting essentially of at least 1-10 nucleic acid probes, wherein each of the at least 1-10 nucleic acids probes specifically hybridizes with an mRNA expressed from a different gene selected from the genes of Tables 4, 7-8, and 9-11.
A composition comprising up to 5, up to 10, up to 25, up to 50, up to 100, or up to 200 nucleic acid probes, wherein each of at least 1-10 of the nucleic acid probes specifically hybridizes with an mRNA expressed from a different gene selected from the genes of Tables 4, 7-8, and 9-11.
A method of processing an RNA sample, the method comprising
- (a) obtaining an RNA sample;
- (b) determining the expression level of a first mRNA in the RNA sample;
- and
- (c) determining the expression level of a second mRNA in the RNA sample, wherein the expression level of the first mRNA and the second mRNA are determined in biochemically separate assays, and wherein the first mRNA and second mRNA are expressed from genes selected from Tables 4, 7-8, and 9-11.
Dependencies are inferred from the claim text.