Characterizing methylated dna, rna, and proteins in the detection of lung neoplasia
AssigneesExact Sciences Development Company, LLC, Mayo Foundation for Medical Education and Research
InventorsHatim Allawi, Graham P. Lidgard, Maria Giakoumopoulos, David A. Ahlquist, William R. Taylor, Douglas Mahoney
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Abstract
Provided herein is technology relating to detecting neoplasia and particularly, but not exclusively, to methods, compositions, and related uses for detecting neoplasms such as lung cancer.
Claims46
A method of characterizing a sample, comprising:
- a) measuring an amount of at least one methylation marker gene in DNA from the sample, wherein the at least one methylation marker gene comprises at least one of IFFO1 and HOPX;
- b) measuring the amount of at least one reference marker in the DNA;
- and
- c) calculating a value for the amount of the at least one methylation marker measured in the DNA as a percentage of the amount of the reference marker measured in the DNA, wherein the value indicates the amount of the at least one methylation marker gene measured in the sample.
A method of characterizing at least one sample from a subject, comprising
- a) measuring an amount of at least one methylation marker gene in DNA from a sample obtained from a subject, the method comprising:
- i) measuring an amount of at least one reference marker in the DNA;
- and
- iii) calculating a value for the amount of the at least one methylation marker gene measured in the DNA as a percentage of the amount of the reference marker measured in the DNA, wherein the value indicates the amount of the at least one methylation marker gene measured in the sample;
- and one or more of
- b) measuring an amount of at least one RNA marker in a sample obtained from the subject;
- and
- c) assaying for the presence or absence of at least one protein marker in a sample obtained from the subject.
A kit, comprising:
- a) at least one marker oligonucleotide, wherein at least a portion of said oligonucleotide specifically hybridizes to a methylation marker selected from the group consisting of IFFO1 and HOPX, and
- b) at least one reference oligonucleotide, wherein at least a portion of said reference oligonucleotide specifically hybridizes to a reference nucleic acid.
A composition comprising a reaction mixture comprising at least one complex comprising a methylation marker DNA and a marker oligonucleotide specifically hybridized to the methylation marker DNA, wherein the methylation marker DNA is selected from IFFO1 and HOPX, and an additional complex comprising an additional methylation marker DNA and an additional marker oligonucleotide specifically hybridized to the additional methylation marker DNA, wherein the additional methylation marker DNA is selected from said the group consisting of BARX1, LOC100129726, SPOCK2, TSC22D4, MAX.chr8.124, RASSF1, ZNF671, ST8SIA1, NKX6_2, FAM59B, DIDO1, MAX_Chr1.110, AGRN, SOBP, MAX_chr10.226, ZMIZ1, MAX_chr8.145, MAX_chr10.225, PRDM14, ANGPT1, MAX.chr16.50, PTGDR_9, ANKRD13B, DOCK2, MAX_chr19.163, ZNFJ32, MAX chr19.372, HOXA9, TRH, SP9, DMRTA2, ARHGEF4, CYP26C1, ZNF781, PTGDR, GRIN2D, MATK, BCAT1, PRKCB_28, ST8SIA_22, FLJ45983, DLX4, SHOX2, EMX1, HOXB2, MAX.chr12.526, BCL2L11, OPLAH, PARP15, KLHDC7B, SLC12a, BHLHE23, CAPN2, FGF14, FLJ34208, B3GALT6, BIN2_Z, DNMT3A, FERMT3, NFIX, SIPR4, SKI, SUCLG2, TBX15, ZDHHC1, and ZNF32.
Dependencies are inferred from the claim text.