Methods, compositions and kits for the detection and monitoring of breast cancer

A method for identifying a subset of polynucleotides showing complementary tissue-specific expression profiles in a tissue of interest, said method comprising the steps of:

• (a) performing a first expression analysis selected from the group consisting of DNA microarray and quantitative PCR to identify a first polynucleotide that is at least two-fold over-expressed in a first tissue sample of interest obtained from a first patient but not over-expressed in a second tissue sample of interest as compared to a control tissue;
• and
• (b) performing a second expression analysis selected from the group consisting of DNA microarray and quantitative PCR to identify a second polynucleotide that is at least two-fold over-expressed in a second tissue sample of interest obtained from a second patient but not over-expressed in a first tissue sample of interest as compared to said control tissue;
• wherein the first tissue sample and said second tissue sample are of the same tissue type, and wherein over-expression of said first polynucleotide in only said first tissue samples of interest and over-expression of said second polynucleotide in only said second tissue sample of interest indicates complementary tissue-specific expression of said first polynucleotide and said second polynucleotide.

A method for determining the presence of a cancer cell in a patient, said method comprising the steps of:

• (a) obtaining a biological sample from said patient;
• (b) contacting said biological sample with a first oligonucleotide that hybridizes to a first polynucleotide said first polynucleotide selected from the group consisting of polynucleotides depicted in SEQ ID NO:73, SEQ ID NO:74 and SEQ ID NO:76;
• (c) contacting said biological sample with a second oligonucleotide that hybridizes to a second polynucleotide selected from the group consisting of SEQ ID NO:
• 1, 3, 5-7, 11, 13, 15, 17, 19-24, 30, 32, and 75;
• (d) detecting in said sample an amount of a polynucleotide that hybridizes to at least one of said oligonucleotides;
• and
• (e) comparing the amount of the polynucleotide that hybridizes to said oligonucleotide to a predetermined cut-off value, and therefrom determining the presence or absence of a cancer in the patient.

A method for determining the presence or absence of a cancer in a patient, said method comprising the steps of:

• (a) obtaining a biological sample from said patient;
• (b) contacting said biological sample with a first oligonucleotide that hybridizes to a first polynucleotide selected from the group consisting of polynucleotides depicted in SEQ ID NO:73, SEQ ID NO:74 and SEQ ID NO:76;
• (c) contacting said biological sample with a second oligonucleotide that hybridizes to a second polynucleotide as depicted in SEQ ID NO:75;
• (d) contacting said biological sample with a third oligonucleotide that hybridizes to a third polynucleotide selected from the group consisting of polynucleotides depicted in SEQ ID NO:5, SEQ ID NO:6 and SEQ ID NO:7;
• (e) contacting said biological sample with a fourth oligonucleotide that hybridizes to a fourth polynucleotide selected from the group consisting of polynucleotides depicted in SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23 and SEQ ID NO:24;
• (f) detecting in said biological sample an amount of a polynucleotide that hybridizes to at least one of said oligonucleotides;
• and
• (g) comparing the amount of polynucleotide that hybridizes to the oligonucleotide to a predetermined cut-off value, and therefrom determining the presence or absence of a cancer in the patient.

A method for determining the presence or absence of a cancer in a patient, said method comprising the steps of:

• (a) obtaining a biological sample from said patient;
• (b) contacting said biological sample with an oligonucleotide that hybridizes to a tissue-specific polynucleotide;
• (c) detecting in the sample a level of a polynucleotide that hybridizes to the oligonucleotide;
• and
• (d) comparing the level of polynucleotide that hybridizes to the oligonucleotide with a predetermined cut-off value, and therefrom determining the presence or absence of a cancer in the patient.

A method for monitoring the progression of a cancer in a patient, said method comprising the steps of:

• (a) obtaining a first biological sample from said patient;
• (b) contacting said biological sample with an oligonucleotide that hybridizes to a polynucleotide that encodes a breast tumor protein;
• (c) detecting in the sample an amount of said polynucleotide that hybridizes to said oligonucleotide;
• (d) repeating steps (b) and (c) using a second biological sample obtained from said patient at a subsequent point in time;
• and
• (e) comparing the amount of polynucleotide detected in step (d) with the amount detected in step (c) and therefrom monitoring the progression of the cancer in the patient.

A method for detecting the presence of a cancer cell in a patient, said method comprising the steps of:

• (a) obtaining a biological sample from said patient;
• (b) contacting said biological sample with a first oligonucleotide that hybridizes to a first polynucleotide selected from the group consisting of mammaglobin and lipophilin B;
• (c) contacting said biological sample with a second oligonucleotide that hybridizes to a second polynucleotide sequence selected from the group consisting of GABAπ (B899P), B726P, B511S, B533S, B305D and B311D;
• (d) detecting in said biological sample an amount of a polynucleotide that hybridizes to at least one of the oligonucleotides;
• and
• (e) comparing the amount of polynucleotide that hybridizes to the oligonucleotide to a predetermined cut-off value, and therefrom determining the presence or absence of a cancer in the patient.

A method for determining the presence of a cancer cell in a patient, said method comprising the steps of:

• (a) obtaining a biological sample from said patient;
• (b) contacting said biological sample with a first oligonucleotide that hybridizes to a first polynucleotide selected from the group consisting of a polynucleotide depicted in SEQ ID NO:73 and SEQ ID NO:74 or complement thereof;
• (c) contacting said biological sample with a second oligonucleotide that hybridizes to a second polynucleotide depicted in SEQ ID NO:75 or complement thereof;
• (d) contacting said biological sample with a third oligonucleotide that hybridizes to a third polynucleotide selected from the group consisting of a polynucleotide depicted in SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:6 and SEQ ID NO:7 or complement thereof;
• (e) contacting said biological sample with a fourth oligonucleotide that hybridizes to a fourth polynucleotide selected from the group consisting of a polynucleotide depicted in SEQ ID NO:
• 11 or complement thereof;
• (f) contacting said biological sample with a fifth oligonucleotide that hybridizes to a fifth polynucleotide selected from the group consisting of a polynucleotide depicted in SEQ ID NO:13, 15 and 17 or complement thereof;
• (g) contacting said biological sample with a sixth oligonucleotide that hybridizes to a sixth polynucleotide selected from the group consisting of a polynucleotide depicted in SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23 and SEQ ID NO:24 or complement thereof;
• (h) contacting said biological sample with a seventh oligonucleotide that hybridizes to a seventh polynucleotide depicted in SEQ ID NO:30 or complement thereof;
• (i) contacting said biological sample with an eighth oligonucleotide that hybridizes to an eighth polynucleotide depicted in SEQ ID NO:32 or complement thereof;
• (j) contacting said biological sample with a ninth oligonucleotide that hybridizes to a polynucleotide depicted in SEQ ID NO:76 or complement thereof;
• (k) detecting in said biological sample a hybridized oligonucleotide of any one of steps (b) through (j) and comparing the amount of polynucleotide that hybridizes to the oligonucleotide to a predetermined cut-off value,
• wherein the presence of a hybridized oligonucleotide in any one of steps (b) through (j) in excess of the pre-determined cut-off value indicates the presence of a cancer cell in the biological sample of said patient.

A method for determining the presence of a cancer cell in a patient, said method comprising the steps of:

• (a) obtaining a biological sample from said patient;
• (b) contacting said biological sample with a first oligonucleotide and a second oligonucleotide;
• i. wherein said first oligonucleotide and said second oligonucleotide hybridize to a first polynucleotide and a second polynucleotide, respectively;
• ii. wherein said first polynucleotide and said second polynucleotide are selected from the group consisting of polynucleotides deptided in SEQ ID NO:73, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:1, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:30, SEQ ID NO:32, and SEQ ID NO:76;
• and
• iii. wherein said first polynucleotide is unrelated in nucleotide sequence to said second polynucleotide;
• (c) detecting in said biological sample said hybridized first oligonucleotide and said hybridized second hybridized oligonucleotide;
• and
• (d) comparing the amount of said hybridized first oligonucleotide and said hybridized second hybridized oligonucleotide to a predetermined cut-off value;
• wherein an amount of said hybridized first oligonucleotide or said hybridized second oligonucleotide in excess of the pre-determined cut-off value indicates the presence of a cancer cell in the biological sample of said patient.

A method for determining the presence or absence of a cancer cell in a patient, said method comprising the steps of:

• (a) obtaining a biological sample from said patient;
• (b) contacting said biological sample with a first oligonucleotide and a second oligonucleotide;
• i. wherein said first oligonucleotide and said second oligonucleotide hybridize to a first polynucleotide and a second polynucleotide, respectively;
• ii. wherein said first polynucleotide and said second polynucleotide are both tissue-specific polynucleotides of the cancer cell to be detected;
• and
• iii. wherein said first polynucleotide is unrelated in nucleotide sequence to said second polynucleotide;
• (c) detecting in said biological sample said first hybridized oligonucleotide and said second hybridized oligonucleotide;
• and
• (d) comparing the amount of polynucleotide that hybridizes to the oligonucleotide to a predetermined cut-off value, wherein the presence of a hybridized first oligonucleotide or a hybridized second oligonucleotide in excess of the pre-determined cut-off value indicates the presence of a cancer cell in the biological sample of said patient.

A method for detecting the presence of a cancer cell in a patient, said method comprising the steps of:

• (a) obtaining a biological sample from said patient;
• (b) contacting said biological sample with a first oligonucleotide pair said first pair comprising a first oligonucleotide and a second oligonucleotide wherein said first oligonucleotide and said second oligonucleotide hybridize to a first polynucleotide and the complement thereof, respectively;
• (c) contacting said biological sample with a second oligonucleotide pair said second pair comprising a third oligonucleotide and a fourth oligonucleotide wherein said third and said fourth oligonucleotide hybridize to a second polynucleotide and the complement thereof, respectively, and wherein said first polynucleotide is unrelated in nucleotide sequence to said second polynucleotide;
• (d) amplifying said first polynucleotide and said second polynucleotide;
• and
• (e) detecting said amplified first polynucleotide and said amplified second polynucleotide;
• wherein the presence of said amplified first polynucleotide or said amplified second polynucleotide indicates the presence of a cancer cell in said patient.

A composition for detecting a cancer cell in a biological sample of a patient, said composition comprising:

• (a) a first oligonucleotide;
• and
• (b) a second oligonucleotide;
• wherein said first oligonucleotide and said second oligonucleotide hybridize to a first polynucleotide and to a second polynucleotide, respectively;
• wherein said first polynucleotide is unrelated in nucleotide sequence from said second polynucleotide;
• and
• wherein said first polynucleotide and said second polynucleotide are tissue-specific polynucleotides of the cancer cell to be detected.

A composition for detecting a cancer cell in a biological sample of a patient, said composition comprising:

• (a) a first oligonucleotide pair;
• and
• (b) a second oligonucleotide pair;
• wherein said first oligonucleotide pair and said second oligonucleotide pair hybridize to a first polynucleotide (or complement thereof) and to a second polynucleotide (or complement thereof), respectively;
• wherein said first polynucleotide is unrelated in nucleotide sequence from said second polynucleotide;
• and wherein said first polynucleotide and said second polynucleotide are tissue-specific polynucleotides of the cancer cell to be detected.