DNA Methylation and Mutational Analysis Methods for Bladder Cancer Surveillance
AssigneeGenomic Health, Inc.
InventorsMargarita LOPATIN, Athanasios TSIATIS, Christopher N. SILK, David P. MILLER, Michael R. CRAGER, Phillip FEBBO, Dejan KNEZEVIC
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Abstract
The present disclosure relates to methods of monitoring bladder cancer patients and analyzing patient samples for presence of methylated DNA and optionally particular gene mutations. In some embodiments, analysis results are correlated with clinical outcome measures such as risk of bladder cancer recurrence.
Claims10
1-73. (canceled)
A composition comprising a set of primers for PCR amplification of bisulfite modified DNA of at least four genes selected from MEIS1, NKPD1, ONECUT2, KLF2, OSR1, SOX1, EOMES, DDX25, and TMEM106A and from at least one reference gene.
A system for quantifying DNA methylation in a urine sediment sample from a bladder cancer patient, comprising (a) at least one cartridge with at least one well, the at least one well comprising primers for amplification of bisulfite modified DNA of at least four genes selected from MEIS1, NKPD1, ONECUT2, KLF2, OSR1, SOX1, EOMES, DDX25, and TMEM106A, and at least one reference gene, wherein the cartridge is configured for performance of methylation-specific quantitative PCR on the genes, and wherein the primers are optionally attached to the at least one well;
- (b) a detection device for detecting amplified DNA from each gene;
- and (c) computer software for quantifying the amount and/or concentration of methylated DNA from the genes, wherein the software optionally compares the amount and/or concentration of methylation for the patient to the amount and/or concentration of methylation for a reference set of bladder cancer patients.
A cartridge comprising at least one well comprising primers for amplification of bisulfite modified DNA of at least four genes selected from MEIS1, NKPD1, ONECUT2, KLF2, OSR1, SOX1, EOMES, DDX25, and TMEM106A, and at least one reference gene, wherein the cartridge is configured for performance of methylation-specific quantitative PCR on the genes, and wherein the primers are optionally attached to the at least one well.
Dependencies are inferred from the claim text.