US2009317816A1PendingUtilityA1

Methods for identifying risk of breast cancer and treatments thereof

54
Assignee: SEQUENOM INCPriority: Nov 25, 2002Filed: Mar 9, 2009Published: Dec 24, 2009
Est. expiryNov 25, 2022(expired)· nominal 20-yr term from priority
Inventors:Richard RothMatthew NelsonStefan M. KammererAndreas BraunRikard Reneland
G01N 33/57515C12Q 2600/136C12Q 2600/172C12Q 2600/106C12Q 2600/156C12Q 1/6886G01N 2800/52
54
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Claims

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

exact text as granted — not AI-modified
1 . (canceled) 
     
     
         2 . A method for determining whether a human subject is at an increased risk or decreased risk of breast cancer, which comprises:
 (a) detecting in a nucleic acid of the human subject the presence of a polymorphic variant selected from the group consisting of an adenine corresponding to position 11963 of SEQ ID NO: 1, a guanine corresponding to position 36340 of SEQ ID NO: 1, an adenine corresponding to position 36992 of SEQ ID NO: 1, a guanine corresponding to position 37868 of SEQ ID NO: 1, a cytosine corresponding to position 41213 of SEQ ID NO: 1, a guanine corresponding to position 41419 of SEQ ID NO: 1, a cytosine corresponding to position 42407 of SEQ ID NO: 1, a cytosine corresponding to position 44247 of SEQ ID NO: 1, a guanine corresponding to position 44677 of SEQ ID NO: 1, a thymine corresponding to position 45256 of SEQ ID NO: 1, a cytosine corresponding to position 51102 of SEQ ID NO: 1 and a guanine corresponding to position 72360 of SEQ ID NO: 1, and a complement of the foregoing; or   (b) detecting in a nucleic acid of the human subject the presence of a polymorphic variant selected from the group consisting of a guanine corresponding to position 11963 of SEQ ID NO: 1, an adenine corresponding to position 36340 of SEQ ID NO: 1, a guanine corresponding to position 36992 of SEQ ID NO: 1, an adenine corresponding to position 37868 of SEQ ID NO: 1, a thymine corresponding to position 41213 of SEQ ID NO: 1, a cytosine corresponding to position 41419 of SEQ ID NO: 1, a guanine corresponding to position 42407 of SEQ ID NO: 1, a thymine corresponding to position 44247 of SEQ ID NO: 1, an adenine corresponding to position 44677 of SEQ ID NO: 1, a cytosine corresponding to position 45256 of SEQ ID NO: 1, a thymine corresponding to position 51102 of SEQ ID NO: 1 and an adenine corresponding to position 72360 of SEQ ID NO: 1, and a complement of the foregoing;   whereby it is determined that the subject is at an increased risk of breast cancer based on the presence of one or more of the polymorphic variants of (a), and whereby it is determined that the subject is at a decreased risk of breast cancer based on the presence of one or more of the polymorphic variations of (b).   
     
     
         3 . The method of  claim 2 , which further comprises obtaining the nucleic acid sample from the subject. 
     
     
         4 . The method of  claim 2 , wherein detecting the presence of the one or more polymorphic variants comprises:
 hybridizing an oligonucleotide to the nucleic acid from the subject, wherein the oligonucleotide is complementary to a nucleotide sequence in the nucleic acid and hybridizes to a region adjacent to the polymorphic variant;   extending the oligonucleotide in the presence of one or more nucleotides, yielding extension products; and   detecting the presence a polymorphic variant in the extension products.   
     
     
         5 . The method of  claim 2 , wherein the polymorphic variant detected is an adenine corresponding to position 11963 of SEQ ID NO: 1, or a complement thereof. 
     
     
         6 . The method of  claim 2 , wherein the polymorphic variant detected is a guanine corresponding to position 36340 of SEQ ID NO: 1, or a complement thereof. 
     
     
         7 . The method of  claim 2 , wherein the polymorphic variant detected is an adenine corresponding to position 36992 of SEQ ID NO: 1, or a complement thereof. 
     
     
         8 . The method of  claim 2 , wherein the polymorphic variant detected is a guanine corresponding to position 37868 of SEQ ID NO: 1, or a complement thereof. 
     
     
         9 . The method of  claim 2 , wherein the polymorphic variant detected is a cytosine corresponding to position 41213 of SEQ ID NO: 1, or a complement thereof. 
     
     
         10 . The method of  claim 2 , wherein the polymorphic variant detected is a guanine corresponding to position 41419 of SEQ ID NO: 1, or a complement thereof. 
     
     
         11 . The method of  claim 2 , wherein the polymorphic variant detected is a cytosine corresponding to position 42407 of SEQ ID NO: 1, or a complement thereof. 
     
     
         12 . The method of  claim 2 , wherein the polymorphic variant detected is a thymine corresponding to position 44247 of SEQ ID NO: 1, or a complement thereof. 
     
     
         13 . The method of  claim 2 , wherein the polymorphic variant detected is a guanine corresponding to position 44677 of SEQ ID NO: 1, or a complement thereof. 
     
     
         14 . The method of  claim 2 , wherein the polymorphic variant detected is a thymine corresponding to position 45256 of SEQ ID NO: 1, or a complement thereof. 
     
     
         15 . The method of  claim 2 , wherein the polymorphic variant detected is a cytosine corresponding to position 51102 of SEQ ID NO: 1, or a complement thereof. 
     
     
         16 . The method of  claim 2 , wherein the polymorphic variant detected is a guanine corresponding to position 72360 of SEQ ID NO: 1, or a complement thereof. 
     
     
         17 . The method of  claim 2 , wherein the polymorphic variant detected is an adenine corresponding to position 7573 of SEQ ID NO: 2, or a complement thereof. 
     
     
         18 . The method of  claim 2 , wherein the polymorphic variant detected is a guanine corresponding to position 11963 of SEQ ID NO: 1, or a complement thereof. 
     
     
         19 . The method of  claim 2 , wherein the polymorphic variant detected is an adenine corresponding to position 36340 of SEQ ID NO: 1, or a complement thereof. 
     
     
         20 . The method of  claim 2 , wherein the polymorphic variant detected is a guanine corresponding to position 36992 of SEQ ID NO: 1, or a complement thereof. 
     
     
         21 . The method of  claim 2 , wherein the polymorphic variant detected is an adenine corresponding to position 37868 of SEQ ID NO: 1, or a complement thereof. 
     
     
         22 . The method of  claim 2 , wherein the polymorphic variant detected is a thymine corresponding to position 41213 of SEQ ID NO: 1, or a complement thereof. 
     
     
         23 . The method of  claim 2 , wherein the polymorphic variant detected is a cytosine corresponding to position 41419 of SEQ ID NO: 1, or a complement thereof. 
     
     
         24 . The method of  claim 2 , wherein the polymorphic variant detected is a guanine corresponding to position 42407 of SEQ ID NO: 1, or a complement thereof. 
     
     
         25 . The method of  claim 2 , wherein the polymorphic variant detected is a thymine corresponding to position 44247 of SEQ ID NO: 1, or a complement thereof. 
     
     
         26 . The method of  claim 2 , wherein the polymorphic variant detected is an adenine corresponding to position 44677 of SEQ ID NO: 1, or a complement thereof. 
     
     
         27 . The method of  claim 2 , wherein the polymorphic variant detected is a cytosine corresponding to position 45256 of SEQ ID NO: 1, or a complement thereof. 
     
     
         28 . The method of  claim 2 , wherein the polymorphic variant detected is a thymine corresponding to position 51102 of SEQ ID NO: 1, or a complement thereof. 
     
     
         29 . The method of  claim 2 , wherein the polymorphic variant detected is an adenine corresponding to position 72360 of SEQ ID NO: 1, or a complement thereof. 
     
     
         30 . The method of  claim 2 , wherein the human subject is Caucasian. 
     
     
         31 . A method for determining whether a breast cancer detection procedure is administered to a human subject, which comprises:
 (a) detecting in a nucleic acid of the human subject the presence of a polymorphic variant selected from the group consisting of an adenine corresponding to position 11963 of SEQ ID NO: 1, a guanine corresponding to position 36340 of SEQ ID NO: 1, an adenine corresponding to position 36992 of SEQ ID NO: 1, a guanine corresponding to position 37868 of SEQ ID NO: 1, a cytosine corresponding to position 41213 of SEQ ID NO: 1, a guanine corresponding to position 41419 of SEQ ID NO: 1, a cytosine corresponding to position 42407 of SEQ ID NO: 1, a cytosine corresponding to position 44247 of SEQ ID NO: 1, a guanine corresponding to position 44677 of SEQ ID NO: 1, a thymine corresponding to position 45256 of SEQ ID NO: 1, a cytosine corresponding to position 51102 of SEQ ID NO: 1 and a guanine corresponding to position 72360 of SEQ ID NO: 1, and a complement of the foregoing; or   (b) detecting in a nucleic acid of the human subject the presence of a polymorphic variant selected from the group consisting of a guanine corresponding to position 11963 of SEQ ID NO: 1, an adenine corresponding to position 36340 of SEQ ID NO: 1, a guanine corresponding to position 36992 of SEQ ID NO: 1, an adenine corresponding to position 37868 of SEQ ID NO: 1, a thymine corresponding to position 41213 of SEQ ID NO: 1, a cytosine corresponding to position 41419 of SEQ ID NO: 1, a guanine corresponding to position 42407 of SEQ ID NO: 1, a thymine corresponding to position 44247 of SEQ ID NO: 1, an adenine corresponding to position 44677 of SEQ ID NO: 1, a cytosine corresponding to position 45256 of SEQ ID NO: 1, a thymine corresponding to position 51102 of SEQ ID NO: 1 and an adenine corresponding to position 72360 of SEQ ID NO: 1, and a complement of the foregoing; and   (c) administering a breast cancer detection procedure to a human subject determined to have an increased risk of breast cancer based on the presence of the one or more polymorphic variants of (a), or not administering a breast cancer detection procedure to a human subject determined to have a decreased risk of breast cancer based on the presence of the one or more polymorphic variants of (b).   
     
     
         32 . The method of  claim 31 , which further comprises obtaining the nucleic acid sample from the subject. 
     
     
         33 . The method of  claim 31 , wherein detecting the presence of the one or more polymorphic variants comprises:
 hybridizing an oligonucleotide to the nucleic acid from the subject, wherein the oligonucleotide is complementary to a nucleotide sequence in the nucleic acid and hybridizes to a region adjacent to the polymorphic variant;   extending the oligonucleotide in the presence of one or more nucleotides, yielding extension products; and   detecting the presence a polymorphic variant in the extension products.   
     
     
         34 . The method of  claim 31 , wherein the breast cancer detection procedure is selected from the group consisting of a mammography, an early mammography program, a frequent mammography program, a biopsy procedure, a breast biopsy and biopsy from another tissue, a breast ultrasound and optionally ultrasound analysis of another tissue, breast magnetic resonance imaging (MRI) and optionally MRI analysis of another tissue, electrical impedance (T-scan) analysis of breast and optionally of another tissue, ductal lavage, nuclear medicine analysis, scintimammography, BRCA1 and/or BRCA2 sequence analysis results, thermal imaging of the breast and optionally of another tissue, and a combination of the foregoing. 
     
     
         35 . The method of  claim 31 , wherein the polymorphic variant detected is an adenine corresponding to position 11963 of SEQ ID NO: 1, or a complement thereof. 
     
     
         36 . The method of  claim 31 , wherein the polymorphic variant detected is a guanine corresponding to position 36340 of SEQ ID NO: 1, or a complement thereof. 
     
     
         37 . The method of  claim 31 , wherein the polymorphic variant detected is an adenine corresponding to position 36992 of SEQ ID NO: 1, or a complement thereof. 
     
     
         38 . The method of  claim 31 , wherein the polymorphic variant detected is a guanine corresponding to position 37868 of SEQ ID NO: 1, or a complement thereof. 
     
     
         39 . The method of  claim 31 , wherein the polymorphic variant detected is a cytosine corresponding to position 41213 of SEQ ID NO: 1, or a complement thereof. 
     
     
         40 . The method of  claim 31 , wherein the polymorphic variant detected is a guanine corresponding to position 41419 of SEQ ID NO: 1, or a complement thereof. 
     
     
         41 . The method of  claim 31 , wherein the polymorphic variant detected is a cytosine corresponding to position 42407 of SEQ ID NO: 1, or a complement thereof. 
     
     
         42 . The method of  claim 31 , wherein the polymorphic variant detected is a thymine corresponding to position 44247 of SEQ ID NO: 1, or a complement thereof. 
     
     
         43 . The method of  claim 31 , wherein the polymorphic variant detected is a guanine corresponding to position 44677 of SEQ ID NO: 1, or a complement thereof. 
     
     
         44 . The method of  claim 31 , wherein the polymorphic variant detected is a thymine corresponding to position 45256 of SEQ ID NO: 1, or a complement thereof. 
     
     
         45 . The method of  claim 31 , wherein the polymorphic variant detected is a cytosine corresponding to position 51102 of SEQ ID NO: 1, or a complement thereof. 
     
     
         46 . The method of  claim 31 , wherein the polymorphic variant detected is a guanine corresponding to position 72360 of SEQ ID NO: 1, or a complement thereof. 
     
     
         47 . The method of  claim 31 , wherein the polymorphic variant detected is an adenine corresponding to position 7573 of SEQ ID NO: 2, or a complement thereof. 
     
     
         48 . The method of  claim 31 , wherein the polymorphic variant detected is a guanine corresponding to position 11963 of SEQ ID NO: 1, or a complement thereof. 
     
     
         49 . The method of  claim 31 , wherein the polymorphic variant detected is an adenine corresponding to position 36340 of SEQ ID NO: 1, or a complement thereof. 
     
     
         50 . The method of  claim 31 , wherein the polymorphic variant detected is a guanine corresponding to position 36992 of SEQ ID NO: 1, or a complement thereof. 
     
     
         51 . The method of  claim 31 , wherein the polymorphic variant detected is an adenine corresponding to position 37868 of SEQ ID NO: 1, or a complement thereof. 
     
     
         52 . The method of  claim 31 , wherein the polymorphic variant detected is a thymine corresponding to position 41213 of SEQ ID NO: 1, or a complement thereof. 
     
     
         53 . The method of  claim 31 , wherein the polymorphic variant detected is a cytosine corresponding to position 41419 of SEQ ID NO: 1, or a complement thereof. 
     
     
         54 . The method of  claim 31 , wherein the polymorphic variant detected is a guanine corresponding to position 42407 of SEQ ID NO: 1, or a complement thereof. 
     
     
         55 . The method of  claim 31 , wherein the polymorphic variant detected is a thymine corresponding to position 44247 of SEQ ID NO: 1, or a complement thereof. 
     
     
         56 . The method of  claim 31 , wherein the polymorphic variant detected is an adenine corresponding to position 44677 of SEQ ID NO: 1, or a complement thereof. 
     
     
         57 . The method of  claim 31 , wherein the polymorphic variant detected is a cytosine corresponding to position 45256 of SEQ ID NO: 1, or a complement thereof. 
     
     
         58 . The method of  claim 31 , wherein the polymorphic variant detected is a thymine corresponding to position 51102 of SEQ ID NO: 1, or a complement thereof. 
     
     
         59 . The method of  claim 31 , wherein the polymorphic variant detected is an adenine corresponding to position 72360 of SEQ ID NO: 1, or a complement thereof. 
     
     
         60 . The method of  claim 31 , wherein the human subject is Caucasian.

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