Detection of lung neoplasia by amplification of rna sequences

Abstract

Provided herein is technology for lung neoplasia screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of lung cancer.

1 . A method of screening for a lung neoplasm in a sample obtained from a subject, the method comprising:
 a) assaying a sample from a subject for an amount of at least one RNA marker selected from the group consisting of GAGE12D, FAM83A, LRG1, XAGE-1 d, MAGEA4, SFTPB, AKAP4, and CYP24A1 in a sample obtained from a subject;   b) assaying said sample for an amount of reference marker in said sample;   c) comparing the amount of said at least one RNA marker to the amount of reference marker in said sample to determine a level of expression for said at least one marker gene in said sample; and   d) generating a record reporting the expression for said at least one marker gene in said sample.   
     
     
         2 . The method of  claim 1 , wherein said assaying comprises obtaining a sample comprising RNA from a subject and treating the RNA with a reverse transcriptase to form a cDNA copy of at least a portion of said RNA. 
     
     
         3 . The method of  claim 1 , wherein said at least one RNA marker is at least two of said markers. 
     
     
         4 . The method of  claim 1 , wherein said at least one RNA marker comprises the group consisting of GAGE, FAM83A, LRG1 and MAGEA4. 
     
     
         5 . The method of  claim 1 , wherein said at least one RNA marker comprises the group consisting of GAGE, FAM83A, LRG1, CYP24A1, XAGE1D and MAGEA4. 
     
     
         6 . The method of  claim 1 , wherein said reference marker is an RNA selected from the group consisting of CASC3 mRNA, β-actin mRNA, U1 snRNA and U6 snRNA. 
     
     
         7 . The method of  claim 1 , wherein the assaying comprises using polymerase chain reaction, nucleic acid sequencing, mass spectrometry, mass-based separation, a flap endonuclease assay, and/or target capture. 
     
     
         8 - 9 . (canceled) 
     
     
         10 . The method of  claim 1 , wherein assaying the expression of the RNA marker comprises detecting an increased or decreased expression of the RNA marker relative to a normal expression of the marker. 
     
     
         11 . The method of  claim 1  wherein the sample is a tissue sample, a blood sample, a serum sample, or a sputum sample. 
     
     
         12 - 13 . (canceled) 
     
     
         14 . A kit, comprising:
 a) at least one oligonucleotide, wherein at least a portion of said oligonucleotide specifically hybridizes to a marker selected from the group consisting of GAGE12D, FAM83A, LRG1, XAGE-1 d, MAGEA4, SFTPB, AKAP4, and CYP24A1, and   b) at least one additional oligonucleotide, wherein at least a portion of said additional oligonucleotide specifically hybridizes to a reference nucleic acid.   
     
     
         15 . The kit of  claim 14 , wherein said kit comprises at least two additional oligonucleotides. 
     
     
         16 . The kit of  claim 14 , wherein said kit further comprises one or more components selected from the group consisting of reverse transcriptase, flap endonuclease, DNA polymerase, and a FRET cassette. 
     
     
         17 - 18 . (canceled) 
     
     
         19 . The kit of  claim 16 , wherein said kit comprises at least 4 oligonucleotides, wherein each of the markers in the group consisting of GAGE, FAM83A, LRG1, and MAGEA4 specifically hybridizes to at least one of said 4 oligonucleotides. 
     
     
         20 . (canceled) 
     
     
         21 . The kit of  claim 16 , wherein said oligonucleotide is selected from one or more of a capture oligonucleotide, a pair of nucleic acid primers, a nucleic acid probe, and an invasive oligonucleotide. 
     
     
         22 . The kit of  claim 14 , wherein said reference marker is an RNA selected from the group consisting of CASC3, β-actin, U1 RNA and U6 RNA. 
     
     
         23 . A composition comprising a reaction mixture comprising a complex of at least one RNA marker selected from the group consisting of GAGE12D, FAM83A, LRG1, XAGE-1 d, MAGEA4, SFTPB, AKAP4, and CYP24A1 and an oligonucleotide that specifically hybridizes to said RNA marker. 
     
     
         24 . The composition of  claim 23 , further comprising a complex of at least one reference marker and an oligonucleotide that specifically hybridizes to said reference marker. 
     
     
         25 - 26 . (canceled) 
     
     
         27 . The composition of  claim 24 , wherein said reference marker is an RNA selected from the group consisting of CASC3, β-actin, U1 RNA and U6 RNA. 
     
     
         28 . The composition of  claim 23 , wherein said oligonucleotide is selected from one or more of a capture oligonucleotide, a pair of nucleic acid primers, a nucleic acid probe, and an invasive oligonucleotide. 
     
     
         29 . The composition of  claim 23 , further comprising one or more components selected from the group consisting of reverse transcriptase, flap endonuclease, thermostable DNA polymerase, and a FRET cassette. 
     
     
         30 . The composition of  claim 23 , wherein said composition comprises a nucleic acid probe oligonucleotide comprising a reporter molecule. 
     
     
         31 - 33 . (canceled)