DETECTION AND PROGNOSIS OF LUNG CANCER
First Claim
1. A method for identifying lung cancer or its precursor, or predisposition to lung cancer, comprising:
- detecting in a test sample containing lung cells or nucleic acids from lung cells, epigenetic modification of at least one gene selected from the group consisting of DPYSL4, SULF2, JAM3, APC2, BMP7, ACSL6, ALS2CL, ARTS-1, BEX1, BNIP3, CBR3, CD248, CD44, CHD5, DLK1, DSC2, EDNRB, EPB41L3, EPHB6, ERBB3, FBLN2, FBN2, FOXL2, GNAS, GSTP1, HS3ST2, HPN, IGFBP7, IRF7, LOX, LY6D, LY6K, MACF1, MCAM, NCBP1, NEFH, NID2, PCDHB15, PCDHGA12, PFKP, PGRMC1, PHACTR3, PHKA2, POMC, PRKCA, PSEN1, RASSF1A, RASSF2, RBP1, RRAD, SFRP1, SGK, SOD3, SOX17, TIMP3, TJP2, TRPV2, UCHL1, WDR69, ZFP42, ZNF442, and ZNF655; and
identifying the test sample as containing cells that are neoplastic, precursor to neoplastic, or predisposed to neoplasia, or as containing nucleic acids from cells that are neoplastic, precursor to neoplastic, or predisposed to neoplasia.
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Abstract
Methods and tools are provided for detecting and predicting lung cancer. The methods and tools are based on epigenetic modification due to methylation of genes in lung cancer or pre-lung cancer. The tools can be assembled into kits or can be used seperately. Genes found to be epigentically silenced in association with lung cancer include ACSL6, ALS2CL, APC2, ART-S1, BEX1, BMP7, BNIP3, CBR3, CD248, CD44, CHD5, DLK1, DPYSL4, DSC2, EDNRB, EPB41L3, EPHB6, ERBB3, FBLN2, FBN2, FOXL2, GNAS, GSTP1, HS3ST2, HPN, IGFBP7, IRF7, JAM3, LOX, LY6D, LY6K, MACF1, MCAM, NCBP1, NEFH, NID2, PCDHB15, PCDHGA12, PFKP, PGRMC1, PHACTR3, PHKA2, POMC, PRKCA, PSEN1, RASSF1A, RASSF2, RBP1, RRAD, SFRP1, SGK, SOD3, SOX17, SULF2, TIMP3, TJP2, TRPV2, UCHL1, WDR69, ZFP42, ZNF442, and ZNF655.
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Citations
53 Claims
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1. A method for identifying lung cancer or its precursor, or predisposition to lung cancer, comprising:
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detecting in a test sample containing lung cells or nucleic acids from lung cells, epigenetic modification of at least one gene selected from the group consisting of DPYSL4, SULF2, JAM3, APC2, BMP7, ACSL6, ALS2CL, ARTS-1, BEX1, BNIP3, CBR3, CD248, CD44, CHD5, DLK1, DSC2, EDNRB, EPB41L3, EPHB6, ERBB3, FBLN2, FBN2, FOXL2, GNAS, GSTP1, HS3ST2, HPN, IGFBP7, IRF7, LOX, LY6D, LY6K, MACF1, MCAM, NCBP1, NEFH, NID2, PCDHB15, PCDHGA12, PFKP, PGRMC1, PHACTR3, PHKA2, POMC, PRKCA, PSEN1, RASSF1A, RASSF2, RBP1, RRAD, SFRP1, SGK, SOD3, SOX17, TIMP3, TJP2, TRPV2, UCHL1, WDR69, ZFP42, ZNF442, and ZNF655; and identifying the test sample as containing cells that are neoplastic, precursor to neoplastic, or predisposed to neoplasia, or as containing nucleic acids from cells that are neoplastic, precursor to neoplastic, or predisposed to neoplasia. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 51, 52, 53)
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33. A kit for assessing lung cancer or its precursor, or predisposition to lung cancer in a test sample containing lung cells or nucleic acids from lung cells, said kit comprising in a package:
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a reagent that (a) modifies methylated cytosine residues but not non-methylated cytosine residues, or that (b) modifies non-methylated cytosine residues but not methylated cytosine residues; and at least one pair of oligonucleotide primers that specifically hybridizes under amplification conditions to a region of a gene selected from the group consisting of DPYSL4, SULF2, JAM3, APC2, BMP7, ACSL6, ALS2CL, ARTS-1, BEX1, BNIP3, CBR3, CD248, CD44, CHD5, DLK1, DSC2, EDNRB, EPB41L3, EPHB6, ERBB3, FBLN2, FBN2, FOXL2, GNAS, GSTP1, HS3ST2, HPN, IGFBP7, IRF7, LOX, LY6D, LY6K, MACF1, MCAM, NCBP1, NEFH, NID2, PCDHB15, PCDHGA12, PFKP, PGRMC1, PHACTR3, PHKA2, POMC, PRKCA, PSEN1, RASSF1A, RASSF2, RBP1, RRAD, SFRP1, SGK, SOD3, SOX17, TIMP3, TJP2, TRPV2, UCHL1, WDR69, ZFP42, ZNF442, and ZNF655;
wherein the region is within about 3 kb of said gene'"'"'s transcription start site. - View Dependent Claims (34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50)
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36. A kit for assessing lung cancer or its precursor, or predisposition to lung cancer in a test sample containing lung cells or nucleic acids from lung cells, said kit comprising in a package:
at least two pairs of oligonucleotide primers that specifically hybridize under amplification conditions to a region of a gene selected from the group consisting of DPYSL4, SULF2, JAM3, APC2, BMP7, ACSL6, ALS2CL, ARTS-1, BEX1, BNIP3, CBR3, CD248, CD44, CHD5, DLK1, DSC2, EDNRB, EPB41L3, EPHB6, ERBB3, FBLN2, FBN2, FOXL2, GNAS, GSTP1, HS3ST2, HPN, IGFBP7, IRF7, LOX, LY6D, LY6K, MACF1, MCAM, NCBP1, NEFH, NID2, PCDHB15, PCDHGA12, PFKP, PGRMC1, PHACTR3, PHKA2, POMC, PRKCA, PSEN1, RASSF1A, RASSF2, RBP1, RRAD, SFRP1, SGK, SOD3, SOX17, TIMP3, TJP2, TRPV2, UCHL1, WDR69, ZFP42, ZNF442, and ZNF655;
wherein the region is within about 3 kb of said gene'"'"'s transcription start site.- View Dependent Claims (37, 38)
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47. An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of SEQ ID NO:
- 1-449.
Specification