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US 12,612,664 B2Granted
Detection and analysis of methylated DNA
AssigneesExact Sciences Corporation, 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 for lung neoplasia screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of lung cancer.
Claims15
A composition comprising a reaction mixture comprising:
- i) nucleic acid from a human sample;
- ii) for each of at least three methylation marker genes selected from the group consisting of SHOX2, HOXA9, ZNF781, BARX1, and EMX1, a pair of primers that specifically hybridize to and are extendible by a DNA polymerase from a region within a methylation marker gene in a target DNA when the target DNA is present in the nucleic acid from the human sample, wherein the target DNA comprises a differentially methylated region of the methylation marker gene that is differently methylated between DNA from a human subject having a lung neoplasm and DNA from a human subject who does not have a lung neoplasm;
- iii) amplicon DNA amplified from at least one target DNA by extension of a pair of primers of ii) and comprising a differentially methylated region of the methylation marker gene;
- iv) a pair of B3GALT6 primers that specifically hybridize to and are extendible by a DNA polymerase from a region within a B3GALT6 DNA;
- v) B3GALT6 amplicon DNA amplified from the B3GALT6 DNA by extension of a pair of primers of iv);
- and
- vi) one or more of a FRET cassette, a FEN-1 endonuclease, and a thermostable DNA polymerase.
4 more elements
A composition comprising a reaction mixture comprising:
- i) nucleic acid from a human sample comprising DNA treated with a methylation-sensitive restriction enzyme or with a reagent that selectively modifies unmethylated cytosine nucleotides in DNA;
- ii) for each of at least three methylation marker genes selected from the group consisting of SHOX2, HOXA9, ZNF781, BARX1, and EMX1, a pair of primers that specifically hybridize to and are extendible by a DNA polymerase from a region within the methylation marker gene in a target DNA when the target DNA is present in the nucleic acid from the human sample, wherein the target DNA comprises a differentially methylated region of the methylation marker gene that is differently methylated between DNA from a human subject having a lung neoplasm and DNA from a human subject who does not have a lung neoplasm;
- iii) amplicon DNA amplified from at least one target DNA by extension of a pair of primers of ii) and comprising a differentially methylated region of the methylation marker gene;
- iv) a pair of B3GALT6 primers that specifically hybridize to and are extendible by a DNA polymerase from a region within a B3GALT6 DNA;
- and
- v) B3GALT6 amplicon DNA amplified from the B3GALT6 DNA by extension of a pair of primers of iv).
3 more elements
Dependencies are inferred from the claim text.