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US 12,584,179 B2Granted
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.
Claims19
A method of characterizing a urine sediment sample obtained from a subject, comprising:
- bisulfite converting DNA from the sample;
- and
- performing methylation-specific quantitative PCR on the bisulfite converted DNA to determine the amount and/or the concentration of methylated DNA in the sample from a set of genes consisting of at least four genes selected from MEIS1, NKPD1, ONECUT2, KLF2, OSR1, SOX1, EOMES, DDX25, TMEM106A, EPHX3, IRX5, NID2, VIM, and ITPKB, wherein the set of genes comprises one or both of NKPD1 and KLF2, and from a set of one or more reference genes, wherein the reference gene(s) have a methylation level that is not significantly different in a subject with bladder cancer compared to a subject without bladder cancer.
A method of characterizing a urine sediment sample obtained from a subject, comprising:
- bisulfite converting DNA from the sample;
- and
- performing methylation-specific quantitative PCR on the bisulfite converted DNA to determine the amount and/or the concentration of methylated DNA in the sample from a set of genes consisting of three or four genes, wherein the set of three or four genes comprises one or both of NKPD1 and KLF2;
- and from a set of one or more reference genes wherein the reference gene(s) have a methylation level that is not significantly different in a subject with bladder cancer compared to a subject without bladder cancer.
1 more element
Dependencies are inferred from the claim text.