METHODS AND COMPOSITIONS FOR DETECTING CANCER BASED ON MIRNA EXPRESSION PROFILES
The disclosure in some aspects provides methods of determining the likelihood that a subject has lung cancer based on the expression of informative miRNAs. In other aspects, the disclosure provides methods for determining a treatment course for a subject based on the expression of informative-miRNAs. The disclosure also provides computer implemented methods for processing genomic information relating to miRNA expression. Related compositions and kits are provided in other aspects of the disclosure.
1 . 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 expression levels in the biological sample of at least two miRNAs selected from Table 6; and
using the expression levels to assist in determining the likelihood that the subject has lung cancer.
2 . The method of claim 1 , wherein the step of determining comprises transforming the expression levels into a lung cancer risk-score that is indicative of the likelihood that the subject has lung cancer.
3 . The method of claim 2 , wherein the lung cancer risk-score is the combination of weighted expression levels.
4 . The method of claim 3 , wherein the lung cancer risk-score is the sum of weighted expression levels.
5 . The method of claim 3 , wherein the expression levels are weighted by their relative contribution to predicting increased likelihood of having lung cancer
6 - 11 . (canceled)
12 . The method of claim 1 further comprising creating a report summarizing the results of the gene expression analysis.
13 . The method of claim 1 further comprising creating a report that indicates the lung cancer risk-score.
14 . The method of claim 1 , wherein the biological sample is obtained from the respiratory epithelium of the subject.
15 . The method of claim 14 , wherein the respiratory epithelium is of the mouth, nose, pharynx, trachea, bronchi, bronchioles, or alveoli.
16 . The method of claim 1 , wherein the biological sample is obtained using bronchial brushings, broncho-alveolar lavage, or a bronchial biopsy.
17 - 18 . (canceled)
19 . The method of claim 1 , wherein the at least two miRNAs are selected from the group consisting of: hsa-miR-210; hsa-miR-378; hsa-miR-221*; hsa-miR-320b; hsa-miR-1226*; hsa-miR-744; hsa-miR-320a; hsa-miR-1243; hsa-miR-345; and hsa-miR-200b.
20 . The method of claim 1 , wherein the at least two miRNAs are selected from the group consisting of: hsa-miR-210; hsa-miR-378; hsa-miR-221*; hsa-miR-320b; and hsa-miR-1226*.
21 . The method of claim 1 , wherein the at least two miRNAs are selected from the group consisting of: hsa-miR-210; hsa-miR-378; and hsa-miR-221*.
22 . The method of claim 1 , wherein the gene expression analysis comprises determining the expression levels in the RNA sample of at least five miRNAs selected from Table 6.
23 . (canceled)
24 . The method of claim 1 , 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.
25 - 26 . (canceled)
27 . The method of claim 1 , wherein the lung cancer is a adenocarcinoma, squamous cell carcinoma, small cell cancer or non-small cell cancer.
28 . A computer implemented method for processing genomic information, the method comprising:
obtaining data representing expression levels in a biological sample of at least two miRNAs selected from Table 6, 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.
29 . The computer implemented method of claim 28 , wherein the step of determining comprises calculating a risk-score indicative of the likelihood that the subject has lung cancer.
30 . The computer implemented method of claim 29 , wherein computing the risk-score involves determining the combination of weighted expression levels, wherein the expression levels are weighted by their relative contribution to predicting increased likelihood of having lung cancer.
31 - 32 . (canceled)
33 . The computer implemented method of claim 28 , wherein the at least two miRNAs are selected from the group consisting of: hsa-miR-210; hsa-miR-378; hsa-miR-221*; hsa-miR-320b; hsa-miR-1226*; hsa-miR-744; hsa-miR-320a; hsa-miR-1243; hsa-miR-345; and hsa-miR-200b.
34 - 56 . (canceled)