EPIGENETIC MARKERS AND RELATED METHODS AND MEANS FOR THE DETECTION AND MANAGEMENT OF OVARIAN CANCER
First Claim
1. A method of determining the presence or absence of, or response to therapy against, an ovarian cancer in a woman, said method comprising the steps:
- providing a biological sample from said woman, said sample comprising cell-free DNA of said woman; and
determining, in at least one molecule of said cell-free DNA, the methylation status at one or more CpGs located within one or more of the nucleotide sequences independently selected from the group consisting of;
SEQ ID NOs;
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 and 31, or a nucleotide sequence present within about 2,000 bp 5′
or 3′
thereof, or an allelic variant and/or complementary sequence of said nucleotide sequence(s),wherein, the presence in at least one of said cell-free DNA molecules of one or more;
(i) methylated CpGs associated with one or more of said nucleotide sequences independently selected from;
SEQ ID NOs;
1, 2, 3, 4, 10, 12, 14, 15, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29 and 30; and
/or (ii) un-methylated CpGs associated with one or more of said nucleotide sequences independently selected from;
SEQ ID NOs;
5, 6, 7, 8, 9, 11, 13, 16, 17, 22 and 31, indicates the presence of, or a reduced response to therapy against, an ovarian cancer in said woman.
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Accused Products
Abstract
The present invention relates to methods of determining the presence or absence of an ovarian cancer in a woman, as well as to related methods to determine the response to therapy against ovarian cancer in a woman. Such methods are based on the detection—from cell-free DNA of said woman—of one or more methylated (or un-methylated) CpGs being associated with differentially methylated regions (DMRs) of the present invention;such as methylation (or un-methylation) at one or more or all of certain CpGs being associated with such DMRs. Accordingly, such methods have diagnostic, prognostic and/or predictive utility for detectingor managing ovarian cancer in women. The present invention further relates to nucleic acids comprising certain sequences that may be detected during the method, or nucleic acids (such as probes and/or primers) that are usefulto detect such sequences, as wells as compositions, kits, computer program products and other aspects that are useful for or related to the practice or application of such methods.
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Citations
67 Claims
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1. A method of determining the presence or absence of, or response to therapy against, an ovarian cancer in a woman, said method comprising the steps:
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providing a biological sample from said woman, said sample comprising cell-free DNA of said woman; and determining, in at least one molecule of said cell-free DNA, the methylation status at one or more CpGs located within one or more of the nucleotide sequences independently selected from the group consisting of;
SEQ ID NOs;
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 and 31, or a nucleotide sequence present within about 2,000 bp 5′
or 3′
thereof, or an allelic variant and/or complementary sequence of said nucleotide sequence(s),wherein, the presence in at least one of said cell-free DNA molecules of one or more;
(i) methylated CpGs associated with one or more of said nucleotide sequences independently selected from;
SEQ ID NOs;
1, 2, 3, 4, 10, 12, 14, 15, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29 and 30; and
/or (ii) un-methylated CpGs associated with one or more of said nucleotide sequences independently selected from;
SEQ ID NOs;
5, 6, 7, 8, 9, 11, 13, 16, 17, 22 and 31, indicates the presence of, or a reduced response to therapy against, an ovarian cancer in said woman. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60, 61, 62, 63, 64, 65, 66)
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48. A nucleic acid comprising at least 10 (preferable at least about 15, such as at least 50, for any SEQ ID other than SEQ ID NO:
- 58) contiguous bases comprised in a sequence selected from the group consisting of;
SEQ ID NOs 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 and 62, wherein said nucleic acid sequence includes one or more of the bases identified by “
Y”
therein is a U or T and, preferably, where one or more of the bases identified by “
Y”
therein is a C, or an allelic variant and/or complementary sequence of said nucleotide sequence. - View Dependent Claims (49, 50, 51, 52, 53, 56, 57, 67)
- 58) contiguous bases comprised in a sequence selected from the group consisting of;
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54. A nucleic acid primer pair for amplifying a nucleic acid sequence consisting of at least 10 (preferable at least about 15, such as at least 50, for any SEQ ID other than SEQ ID NO:
- 89) contiguous bases comprised in a sequence) selected from the group consisting of;
SEQ ID NOs;
SEQ ID NOs 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92 and 93, or a nucleotide sequence present within about 2,000 bp 5′
or 3′
thereof, or an allelic variant and/or complementary sequence said nucleotide sequence(s), preferably wherein at least one primer of said pair includes a sequence corresponding to at least one bisulphite-converted CpG present in said nucleotide sequence(s). - View Dependent Claims (55)
- 89) contiguous bases comprised in a sequence) selected from the group consisting of;
Specification