METHODS FOR IDENTIFYING RISK OF BREAST CANCER AND TREATMENTS THEREOF

• US 20090258344A1
• Filed: 05/27/2004
• Published: 10/15/2009
• Est. Priority Date: 05/27/2004
• Status: Abandoned Application

• Current Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Denissenko, Mikhail F., Rosette, Caridad, Reneland, Rikard, Braun, Andreas, Hoyal-Wrightson, Carolyn R., Roth, Richard B., Nelson, Matthew Roberts, Kammerer, Stefan M.
• Application Number:
  US11/570,427
• Publication Number:
  US 20090258344A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/172 Haplotypes

Abstract

Provided herein are methods for identifying risk of breast cancer in a subject and/or a subject at risk of breast cancer, reagents and kits for carrying out the methods, methods for identifying candidate therapeutics for treating breast cancer, and therapeutic methods for treating breast cancer in a subject. These embodiments are based upon an analysis of polymorphic variations in nucleotide sequences within the human genome.

Claims

1-85. -85. (canceled)

86. 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 nucleotide sequence set forth in SEQ ID NO:

1, a substantially identical sequence thereof or complement of the foregoing, in a sample from a subject, whereby the presence of a polymorphic variant associated with breast cancer is indicative of the subject being at risk of breast cancer.

87. The method of claim 86, wherein the one or more polymorphic variations are selected from the group consisting of rs3811728, rs3811729, rs602646, rs488277, rs1629673, rs670232, rs575326, rs575386, rs684846, rs471365, rs496251, rs831246, rs831247, rs512071, rs1502761, rs681516, rs683302, rs619424, rs620722, rs529055, rs664010, rs678454, rs2653845, rs472795, rs507079, rs534333, rs535298, rs536213, rs831245, rs639690, rs684174, rs571761, rs1983421, rs4630966, rs2314415, rs6788196, rs2103062, rs9827084, rs9864865, rs6804951, rs6770548, rs1403452, rs7609994, rs9838250, rs9863404, rs903950, rs6787284, rs2017340, rs2001449, rs1317288, rs7635891, rs10704581, rs11371910, rs10937118, rs7642053, rs3821522, rs2029926, rs1390831, rs7643890, rs11925606, rs9826325, rs6800429, rs6803368, rs1353566, rs2272115, rs2272116, rs3732603, rs940055, rs2314730, rs2030578, rs2049280, rs3732602, rs2293203, rs7639705, and position 13507 of SEQ ID NO:

1.

88. The method of claim 86, which further comprises obtaining the nucleic acid sample from the subject.

89. The method of claim 86, wherein a polymorphic variation is detected at one or more positions in a region spanning positions 14647 to 48849 in SEQ ID NO:

1.

90. The method of claim 86, wherein a polymorphic variation is rs4630966.

91. The method of claim 86, wherein a polymorphic variation is rs9827084.

92. The method of claim 86, wherein a polymorphic variation is rs9864865.

93. The method of claim 86, wherein a polymorphic variation is rs6804951.

94. The method of claim 86, wherein a polymorphic variation is rs6770548, rs1403452 and rs2001449.

95. The method of claim 86, wherein one or more polymorphic variations are detected at one or more positions in linkage disequilibrium with a polymorphic variation at one or more positions selected from the group consisting of rs3811728, rs3811729, rs602646, rs488277, rs1629673, rs670232, rs575326, rs575386, rs684846, rs471365, rs496251, rs831246, rs831247, rs512071, rs1502761, rs681516, rs683302, rs619424, rs620722, rs529055, rs664010, rs678454, rs2653845, rs472795, rs507079, rs534333, rs535298, rs536213, rs831245, rs639690, rs684174, rs571761, rs1983421, rs4630966, rs2314415, rs6788196, rs2103062, rs9827084, rs9864865, rs6804951, rs6770548, rs1403452, rs7609994, rs9838250, rs9863404, rs903950, rs6787284, rs2017340, rs2001449, rs1317288, rs7635891, rs10704581, rs11371910, rs10937118, rs7642053, rs3821522, rs2029926, rs1390831, rs7643890, rs11925606, rs9826325, rs6800429, rs6803368, rs1353566, rs2272115, rs2272116, rs3732603, rs940055, rs2314730, rs2030578, rs2049280, rs3732602, rs2293203, rs7639705, and position 13507 of SEQ ID NO:

1.

96. The method of claim 86, wherein detecting the presence or absence of the one or more polymorphic variations comprises:

hybridizing an oligonucleotide to the nucleic acid sample, wherein the oligonucleotide is complementary to a nucleotide sequence in the nucleic acid and hybridizes to a region adjacent to the polymorphic variation;

extending the oligonucleotide in the presence of one or more nucleotides, yielding extension products; and

detecting the presence or absence of a polymorphic variation in the extension products.

97. The method of claim 86, wherein the subject is a human.

98. A method of genotyping a nucleic acid which comprises determining the nucleotide corresponding to position 13507 of SEQ ID NO:

1 in the nucleic acid.

99. An isolated nucleic acid which comprises a cytosine at position 13507 of SEQ ID NO:

1, or a cytosine at a position corresponding to position 13507 of SEQ ID NO;

1 in a substantially identical nucleic acid.

100. An oligonucleotide comprising a nucleotide sequence complementary to a portion of the nucleotide sequence of claim 99, wherein the 3′

end of the oligonucleotide is adjacent to a polymorphic variation.

101. A microarray comprising an isolated nucleic acid of claim 99 linked to a solid support.

102. An isolated polypeptide encoded by the isolated nucleic acid sequence of claim 99.

103. A method of targeting information for preventing or treating breast cancer to a subject in need thereof, which comprises detecting the presence or absence of one or more polymorphic variations associated with breast cancer in SEQ ID NO:

1, a substantially identical nucleotide sequence thereof or complement of the foregoing in a nucleic acid sample from a subject, 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.

104. The method of claim 103, wherein the polymorphic variation is detected in a nucleotide sequence selected from the group consisting of:

(a) a nucleotide sequence in SEQ ID NO;

1, 2 or 3;

(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in SEQ ID NO;

1, 2 or 3;

(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 SEQ ID NO;

1, 2 or 3;

(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising the polymorphic variation.

105. The method of claim 103, wherein the one or more polymorphic variations are detected at one or more positions corresponding to a position selected from the group consisting of rs3811728, rs3811729, rs602646, rs488277, rs1629673, rs670232, rs575326, rs575386, rs684846, rs471365, rs496251, rs831246, rs831247, rs512071, rs1502761, rs681516, rs683302, rs619424, rs620722, rs529055, rs664010, rs678454, rs2653845, rs472795, rs507079, rs534333, rs535298, rs536213, rs831245, rs639690, rs684174, rs571761, rs1983421, rs4630966, rs2314415, rs6788196, rs2103062, rs9827084, rs9864865, rs6804951, rs6770548, rs1403452, rs7609994, rs9838250, rs9863404, rs903950, rs6787284, rs2017340, rs2001449, rs1317288, rs7635891, rs10704581, rs11371910, rs10937118, rs7642053, rs3821522, rs2029926, rs1390831, rs7643890, rs11925606, rs9826325, rs6800429, rs6803368, rs1353566, rs2272115, rs2272116, rs3732603, rs940055, rs2314730, rs2030578, rs2049280, rs3732602, rs2293203, rs7639705, and position 13507 of SEQ ID NO:

1.

106. The method of claim 103, wherein the information comprises a description of a breast cancer detection procedure, a chemotherapeutic treatment, a surgical treatment, a radiation treatment, a preventative treatment of breast cancer, and combinations of the foregoing.