Methods for identifying risk of breast cancer and treatments thereof
First Claim
1. A method for identifying a subject at risk of breast cancer, which comprises detecting the presence or absence of one or more polymorphic variations associated with breast cancer in a nucleic acid sample from a subject, wherein the one or more polymorphic variations are detected in a nucleotide sequence selected from the group consisting of:
- (a) a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B;
(d) a fragment of a nucleotide sequence of (a), (b), or (c);
whereby the presence of the polymorphic variation is indicative of the subject being at risk of breast cancer.
1 Assignment
0 Petitions
Accused Products
Abstract
Provided herein are methods for identifying a risk of cancer in a subject and/or a subject at risk of cancer, reagents and kits for carrying out the methods, methods for identifying candidate therapeutics for treating cancer, and therapeutic methods for treating cancer in a subject. These embodiments are based upon an analysis of polymorphic variations in a KLF12 nucleic acid, which has a nucleotide sequence exemplified in SEQ ID NO: 1, 2 or 3.
14 Citations
57 Claims
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1. A method for identifying a subject at risk of breast cancer, which comprises detecting the presence or absence of one or more polymorphic variations associated with breast cancer in a nucleic acid sample from a subject, wherein the one or more polymorphic variations are detected in a nucleotide sequence selected from the group consisting of:
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(a) a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(d) a fragment of a nucleotide sequence of (a), (b), or (c);
whereby the presence of the polymorphic variation is indicative of the subject being at risk of breast cancer. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 13)
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11. A method for identifying a polymorphic variation associated with breast cancer proximal to an incident polymorphic variation associated with breast cancer, which comprises:
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identifying a polymorphic variation proximal to the incident polymorphic variation associated with breast cancer, wherein the polymorphic variation is detected in a nucleotide sequence selected from the group consisting of;
(a) a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising the polymorphic variation;
determining the presence or absence of an association of the proximal polymorphic variant with breast cancer. - View Dependent Claims (12, 14, 15, 16, 17)
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18. An isolated nucleic acid comprising a nucleotide sequence selected from the group consisting of:
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(a) a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(d) a fragment of a nucleotide sequence of (a), (b), or (c); and
(e) a nucleotide sequence complementary to the nucleotide sequences of (a), (b), (c), or (d);
wherein the nucleotide sequence comprises a nucleotide at a position in FIGS. 1A-1YYYY associated with breast cancer selected from the group consisting of a guanine at position 78265, a guanine at position 79169, a thymine at position 96429, a cytosine at position 96535, a thymine at position 117297, a cytosine at position 117617, a guanine at position 118870, and a cytosine at position 123880. - View Dependent Claims (19, 20, 21)
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22. A method for identifying a candidate molecule that modulates cell proliferation, which comprises:
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(a) introducing a test molecule to a system which comprises a nucleic acid comprising a nucleotide sequence selected from the group consisting of;
(i) a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(ii) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(iii) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(iv) a fragment of a nucleotide sequence of (i), (ii), or (iii);
or introducing a test molecule to a system which comprises a protein encoded by a nucleotide sequence of (i), (ii), (iii), or (iv); and
(b) determining the presence or absence of an interaction between the test molecule and the nucleic acid or protein, whereby the presence of an interaction between the test molecule and the nucleic acid or protein identifies the test molecule as a candidate molecule that modulates cell proliferation. - View Dependent Claims (23, 24, 25, 26, 27, 28)
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29. A method for identifying a candidate therapeutic for treating breast cancer, which comprises:
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(a) introducing a test molecule to a system which comprises a nucleic acid comprising a nucleotide sequence selected from the group consisting of;
(i) a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(ii) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(iii) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(iv) a fragment of a nucleotide sequence of (i), (ii), or (iii);
or introducing a test molecule to a system which comprises a protein encoded by a nucleotide sequence of (i), (ii), (iii), or (iv); and
(b) determining the presence or absence of an interaction between the test molecule and the nucleic acid or protein, whereby the presence of an interaction between the test molecule and the nucleic acid or protein identifies the test molecule as a candidate therapeutic for treating breast cancer.
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30. A method for treating breast cancer in a subject, which comprises contacting one or more cells of a subject in need thereof with a nucleic acid, wherein the nucleic acid comprises a nucleotide sequence selected from the group consisting of:
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(a) a nucleotide sequence FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(d) a fragment of a nucleotide sequence of (a), (b), or (c); and
(e) a nucleotide sequence complementary to the nucleotide sequences of (a), (b), (c), or (d);
whereby contacting the one or more cells of the subject with the nucleic acid treats breast cancer in the subject. - View Dependent Claims (31, 32, 33)
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34. A method for treating breast cancer in a subject, which comprises contacting one or more cells of a subject in need thereof with a protein, wherein the protein is encoded by a nucleotide sequence which comprises a polynucleotide sequence selected from the group consisting of:
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(a) a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(d) a fragment of a nucleotide sequence of (a), (b), or (c);
whereby contacting the one or more cells of the subject with the protein treats breast cancer in the subject.
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35. A method for treating breast cancer in a subject, which comprises:
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detecting the presence or absence of one or more polymorphic variations associated with breast cancer in a nucleic acid sample from a subject, wherein the one or more polymorphic variation are detected in a nucleotide sequence selected from the group consisting of;
(a) a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising the polymorphic variation; and
administering a breast cancer treatment to a subject in need thereof based upon the presence or absence of the one or more polymorphic variations in the nucleic acid sample. - View Dependent Claims (36, 37, 38, 39, 40, 41)
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42. A method for detecting or preventing breast cancer in a subject, which comprises:
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detecting the presence or absence of one or more polymorphic variations associated with breast cancer in a nucleic acid sample from a subject, wherein the polymorphic variation is detected in a nucleotide sequence selected from the group consisting of;
(a) a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising the polymorphic variation; and
administering a breast cancer preventative or detection procedure to a subject in need thereof based upon the presence or absence of the one or more polymorphic variations in the nucleic acid sample. - View Dependent Claims (43, 44, 45, 46, 47)
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48. A method of targeting information for preventing or treating breast cancer to a subject in need thereof, which comprises:
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detecting the presence or absence of one or more polymorphic variations associated with breast cancer in a nucleic acid sample from a subject, wherein the polymorphic variation is detected in a nucleotide sequence selected from the group consisting of;
(a) a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising the polymorphic variation; and
directing information for preventing or treating breast cancer to a subject in need thereof based upon the presence or absence of the one or more polymorphic variations in the nucleic acid sample. - View Dependent Claims (49, 50, 51)
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52. A composition comprising a breast cancer cell and an antibody that specifically binds to a protein, polypeptide or peptide encoded by a nucleotide sequence identical to or 90% or more identical to a nucleotide sequence in FIGS. 1A-1YYYY or
FIGS. 2A-2B .
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53. A composition comprising a breast cancer cell and a RNA, DNA, PNA or ribozyme molecule comprising a nucleotide sequence identical to or 90% or more identical to a portion of a nucleotide sequence in FIGS. 1A-1YYYY or
FIGS. 2A-2B .
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55. A method of selecting a subject that will respond to a treatment of breast cancer, which comprises:
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detecting the presence or absence of one or more polymorphic variations associated with breast cancer in a nucleic acid sample from a subject, wherein the polymorphic variation is detected in a nucleotide sequence selected from the group consisting of;
(a) the nucleotide sequence of FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(b) a nucleotide sequence which encodes a polypeptide consisting of an amino acid sequence encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to an amino acid sequence encoded by a nucleotide sequence in FIGS. 1A-1YYYY or FIGS. 2A-2B ; and
(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising the polymorphic variation; and
selecting a subject that will respond to the breast cancer treatment based upon the presence or absence of the one or more polymorphic variations in the nucleic acid sample. - View Dependent Claims (56, 57)
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Specification