Methods for measuring biomarkers in gastrointestinal cancer
AssigneeAgency for Science, Technology and Research
InventorsBoon Ooi Patrick TAN, Masafumi MURATANI, Aditi QAMRA
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Abstract
The present invention is directed to methods for determining the activity of a promoter. The present invention further describes a method for determining the susceptibility of a subject to cancer and biomarkers for detecting cancer in a subject.
Claims33
A method for determining the activity of at least one promoter in a cancerous biological sample relative to a non-cancerous biological sample, comprising:
- mapping isolated nucleic acid comprising at least one promoter sequence obtained from said cancerous biological sample against a reference nucleic acid obtained from said non-cancerous biological sample to obtain a read per kilo-base per million (RPKM) value or fragments per kilo-base per million (FPKM) value for said at least one promoter;
- and
- determining the differential activity of the at least one promoter sequence in the nucleic acid relative to the activity of the at least one promoter in the reference nucleic acid sequence using said RPKM or FPKM value.
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A biomarker for detecting cancer in a subject, the biomarker comprising at least one promoter having increased activity in a cancerous biological sample relative to a normal non-cancerous biological sample, wherein the promoter comprises an increase of SUZ12 binding sites relative to the total promoter population.
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A method for determining the presence of at least one promoter associated with cancer in a cancerous biological sample relative to a non-cancerous biological sample, comprising;
- mapping isolated nucleic acid comprising at least one promoter sequence obtained from said cancerous biological sample against a reference nucleic acid obtained from said non-cancerous biological sample;
- generating a matrix of sequencing tag counts for said at least one promoter based on said mapping;
- analysing said matrix of sequencing tag counts;
- and
- determining the differential enrichment of the at least one promoter in the nucleic acid relative to the at least one promoter in the reference nucleic acid using the analysis of said matrix of sequencing tag counts, wherein the differential enrichment of the at least one promoter in the cancerous biological sample obtained from the subject relative to that in the non-cancerous sample is indicative of the presence of a promoter associated with cancer in a subject.
A method for determining the activity of at least one promoter in a cancerous biological sample relative to a non-cancerous biological sample, comprising;
- mapping isolated nucleic acid comprising at least one promoter sequence obtained from said cancerous biological sample against a reference nucleic acid obtained from said non-cancerous biological sample;
- generating a matrix of sequencing tag counts for said at least one promoter based on said mapping;
- analysing said matrix of sequencing tag counts;
- and
- determining the differential activity of the at least one promoter in the nucleic acid relative to the at least one promoter in the reference nucleic acid using the analysis of said matrix of sequencing tag counts.
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Dependencies are inferred from the claim text.