Detecting prostate cancer
Provided herein is technology for prostate cancer screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of prostate cancer.
1. A method for characterizing a biological sample comprising:
measuring a methylation level of a CpG site for SERPINB9_3389, and FLOT1_1665 in a biological sample of a human individual through
treating genomic DNA in the biological sample with bisulfite;
amplifying the bisulfite-treated genomic DNA using primers specific for a CpG site for SERPINB9_3479 and primers specific for a CpG site for FLOT1_1665,
wherein the primers specific for SERPINB9_3389 are capable of binding an amplicon bound by SEQ ID Nos: 129 and 130 or SEQ ID Nos: 147 and 148, wherein the amplicon bound by SEQ ID Nos: 129 and 130 or SEQ ID Nos: 147 and 148 is at least a portion of a genetic region comprising chromosome 6 coordinates 2903389-2903479,
wherein the primers specific for FLOT1_1665 are capable of binding an amplicon bound by SEQ ID Nos: 150 and 151, wherein the amplicon bound by SEQ ID Nos: 150 and 151 is at least a portion of a genetic region comprising chromosome 6 coordinates 30711586-30711665; and
determining the methylation level of the bisulfite-treated genomic DNA amplified with the primers specific for SERPINB9_3389 and primers specific for FLOT1_1665 in the genes selected from SERPINB9_3389 and FLOT1_1665 by methylation-specific PCR, quantitative methylation-specific PCR, methylation-sensitive DNA restriction enzyme analysis, quantitative bisulfite pyrosequencing, or bisulfite genomic sequencing PCR.
2. The method of claim 1 , wherein the biological sample is a blood sample or a tissue sample.
3. The method of claim 2 , wherein the tissue is prostate tissue.
4. The method of claim 1 , wherein said CpG site is present in a coding region or a regulatory region.
5. The method of claim 1 , wherein said measuring the methylation level of the CpG site for SERPINB9_3389 and FLOT1_1665 comprises a determination selected from the group consisting of determining the methylation score of said CpG site and determining the methylation frequency of said CpG site.
6. A method for measuring the methylation level of one or more CpG sites in a gene selected from SERPINB9_3389, and FLOT1_1665 comprising:
a) extracting genomic DNA from a biological sample of a human individual suspected of having or having prostate cancer,
b) treating the extracted genomic DNA with bisulfite,
c) amplifying the bisulfite-treated genomic DNA with primers specific for a CpG site for SERPINB9_3389 and primers specific for a CpG site for FLOT1_1665,
wherein the primers specific for SERPINB9_3479 are capable of binding an amplicon bound by SEQ ID Nos: 129 and 130 or SEQ ID Nos: 147 and 148, wherein the amplicon bound by SEQ ID Nos: 129 and 130 or SEQ ID Nos: 147 and 148 is at least a portion of a genetic region comprising chromosome 6 coordinates 2903389-2903479,
wherein the primers specific for FLOT1_1665 are capable of binding an amplicon bound by SEQ ID Nos: 150 and 151, wherein the amplicon bound by SEQ ID Nos: 150 and 151 is at least a portion of a genetic region comprising chromosome 6 coordinates 30711586-30711665; and
d) measuring the methylation level of the bisulfite-treated genomic DNA amplified with the primers specific for SERPINB9_3389 and primers specific for FLOT1_1665 in the genes selected from SERPINB9_3389 and FLOT1_1665 by methylation-specific PCR, quantitative methylation-specific PCR, methylation sensitive DNA restriction enzyme analysis or bisulfite genomic sequencing PCR.
7. The method of claim 6 wherein the sample is a prostate tissue sample.