Methods of assigning treatment to breast cancer patients

• US 7,171,311 B2
• Filed: 01/15/2003
• Issued: 01/30/2007
• Est. Priority Date: 06/18/2001
• Status: Expired due to Term

• Current Assignee: Rosetta Inpharmatics LLC (Merck & Co., Inc.), Netherlands Vaccine Institute
• Original Assignee: Rosetta Inpharmatics LLC (Merck & Co., Inc.), Netherlands Vaccine Institute
• Inventors: Linsley, Peter S., He, Yudong, Van't Veer, Laura Johanna, Van de Vijver, Marc J., Roberts, Christopher J., Mao, Mao, Bernards, Rene, Dai, Hongyue, Hart, A. A. M.
• Primary Examiner(s): Brusca; John S.
• Assistant Examiner(s): Zhou; Shobo (Joe)
• Application Number:
  US10/342,887
• Publication Number:
  US 20040058340A1
• Time in Patent Office: 1,476 Days
• Field of Search: None
• US Class Current: 702/19
• 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 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/158 Expression markers

Abstract

The present invention relates to genetic markers whose expression is correlated with breast cancer. Specifically, the invention provides sets of markers whose expression patterns can be used to differentiate clinical conditions associated with breast cancer, such as the presence or absence of the estrogen receptor ESR1, and BRCA1 and sporadic tumors, and to provide information on the likelihood of tumor distant metastases within five years of initial diagnosis. The invention relates to methods of using these markers to distinguish these conditions. The invention also provides methods of classifying and treating patients based on prognosis. The invention also relates to kits containing ready-to-use microarrays and computer software for data analysis using the diagnostic, prognostic and statistical methods disclosed herein.

Claims

1. A method of assigning treatment to a breast cancer patient, wherein said breast cancer patient is a human breast cancer patient, comprising:

(a) classifying said breast cancer patient as having a prognosis selected from the group consisting of a first prognosis, a second prognosis, and a third prognosis on the basis of a first expression profile comprising the nucleic acid levels of expression of at least five genes listed in Table 5 in a clinically relevant cell sample from said breast cancer patient by a method comprising

(a1) determining the similarity between said first expression profile and a first good prognosis expression profile comprising the nucleic acid levels of expression of said at least five genes to obtain a patient similarity value, wherein said nucleic acid levels of expression in said first good prognosis expression profile represent the nucleic acid levels of expression of said genes in patients having no distant metastases within five years of initial diagnosis; and

(a2) classifying said breast cancer patient as having said first prognosis if said patient similarity value exceeds a second similarity threshold value, said second prognosis if said patient similarity value exceeds a first similarity threshold value but does not exceed said second similarity threshold value, and said third prognosis if said patient similarity value does not exceed said first similarity threshold value, wherein said second similarity threshold indicates greater similarity to said first good prognosis expression profile than does said first similarity threshold; and

(b) assigning said breast cancer patient a treatment without adjuvant chemotherapy if the breast cancer patient is lymph node negative and is classified as having said first prognosis or said second prognosis, or assigning said breast cancer patient a treatment with adjuvant chemotherapy if said breast cancer patient (b1) is lymph node positive and is classified as having said first prognosis, said second prognosis, or said third prognosis, or (b2) is lymph node negative and is classified as having said third prognosis.

2. The method of claim 1, further comprising determining prior to step (a1) said nucleic acid levels of expression of said at least five genes in said clinically relevant cell sample.

3. The method of claim 1, wherein said patient similarity value is a correlation coefficient between said first expression profile and said good prognosis expression profile, and wherein said determining in step (a1) is carried out by a method comprising determining said correlation coefficient.

4. The method of claim 1, wherein said at least five genes are at least 10 genes listed in Table 5.

5. The method of claim 1, wherein said at least five genes are at least 20 genes listed in Table 5.

6. The method of claim 1, wherein said at least five genes are at least 30 genes listed in Table 5.

7. The method of claim 1, wherein said at least five genes are at least 40 genes listed in Table 5.

8. The method of claim 1, wherein said at least five genes are at least 50 genes listed in Table 5.

9. The method of claim 1, wherein said at least five genes are all genes listed in Table 6.

10. The method of claim 1, wherein said first threshold similarity value and said second threshold similarity value are selected by a method comprising:

(i) rank ordering in descending order a plurality of breast cancer tumor samples, each obtained from a training breast cancer patient of a plurality of training breast cancer patients whose clinical and follow-up data are available for at least five years after initial diagnosis, according to the degree of similarity between a second expression profile comprising the nucleic acid levels of expression of said at least five genes in each of said tumor samples and a second good prognosis expression profile, wherein said second good prognosis expression profile comprises the mean nucleic acid level of expression of each of said at least five genes in tumor samples from training breast cancer patients in said plurality of training breast cancer patients who have no distant metastases within five years of initial diagnosis, to obtain a rank-ordered list, said degree of similarity being expressed as a similarity value;

(ii) selecting a particular number or percentage of false negatives for classifying said plurality of training breast cancer patients, wherein a false negative is a training breast cancer patient for whom the second expression profile predicts that said training breast cancer patient will have no distant metastases within the first five years after initial diagnosis, but who has had a distant metastasis within five years after initial diagnosis;

(iii) determining a threshold similarity value, wherein training breast cancer patients from whom tumor samples having a similarity value above said threshold similarity value in said rank ordered list are predicted as having no distant metastases within the first five years after initial diagnosis, and wherein among said training breast cancer patients predicted as having no distant metastases the number or percentage of training breast cancer patients who are false negatives is less than said particular number or percentage selected in said step (ii);

(iv) selecting said threshold similarity value determined in step (iii) as said first threshold similarity value; and

(v) selecting a second similarity value by a method comprising determining which of the tumor samples taken from breast cancer patients having a distant metastasis within five years after initial diagnosis in said rank ordered list has the greatest similarity value, and selecting said greatest similarity value as said second threshold similarity value.

11. The method of claim 9, wherein said first expression profile comprises log intensity values for each of the respective genes listed in Table 6, and said first good prognosis profile comprises the mean log intensity values that are listed in Table 7, and wherein said first threshold similarity value is 0.4 and said second threshold similarity value is 0.636.

12. The method of claim 1, wherein said nucleic acid level of expression of each gene of said at least five genes is a relative nucleic acid level of expression of said gene in said cell sample versus the nucleic acid level of expression of said gene in a reference pool.

13. The method of claim 1, wherein said step (a) further comprises before said step (a2):

(i) rank ordering in descending order a plurality of breast cancer tumor samples, each obtained from a training breast cancer patient of a plurality of training breast cancer patients for whom clinical and follow-up data are available for at least five years after initial diagnosis, according to the degree of similarity between a second expression profile comprising the nucleic acid levels of expression of said at least five genes in each of said tumor samples and a second good prognosis expression profile comprising the mean nucleic acid level of expression of each of said at least five genes in tumor samples from training breast cancer patients in said plurality of training breast cancer patients who have no distant metastases within five years of initial diagnosis, to obtain a rank-ordered list, said degree of similarity being expressed as a similarity value;

(ii) selecting a particular number or percentage of false negatives for classifying said plurality of training breast cancer patients, wherein a false negative is a training breast cancer patient for whom the second expression profile comprising the nucleic acid levels of said at least five genes predicts that said training breast cancer patient will have no distant metastases within the first five years after initial diagnosis, but who has had a distant metastasis within five years after initial diagnosis;

(iii) determining a threshold similarity value, wherein training breast cancer patients whose tumor samples having a similarity value above said threshold similarity value in said rank ordered list are predicted as having no distant metastases within the first five years after initial diagnosis, and wherein among said training breast cancer patients predicted as having no distant metastases the number or percentage of training breast cancer patients who are false negatives is less than said particular number or percentage selected in said step (ii);

(iv) selecting said threshold similarity value determined in step (iii) as said first threshold similarity value; and

(v) selecting a second similarity value by a method comprising determining which of the tumor samples taken from breast cancer patients having a distant metastasis within five years after initial diagnosis in said rank ordered list has the greatest similarity value, and selecting said greatest similarity value as said second threshold similarity value.

31. The method of claim 12 or 30, wherein said reference pool is derived from a normal breast cell line.

32. The method of claim 12 or 30, wherein said reference pool is derived from a breast cancer cell line.

33. The method of claim 12 or 30, wherein said relative nucleic acid level of expression is represented as a log ratio.

14. A method of assigning a treatment to a breast cancer patient, wherein said breast cancer patient is a human breast cancer patient, comprising:

(a) determining the lymph node status for said breast cancer patient;

(b) determining the nucleic acid levels of expression of at least five genes listed in Table 5 in a clinically relevant cell sample from said breast cancer patient, thereby generating a first expression profile comprising the nucleic acid levels of expression of said at least five genes in said cell sample;

(c) classifying said breast cancer patient as having a prognosis selected from the group consisting of a first prognosis, a second prognosis, and a third prognosis by a method comprising

(c1) determining the similarity between said first expression profile and a first good prognosis expression profile comprising the nucleic acid levels of expression of said at least five genes to obtain a patient similarity value, wherein said nucleic acid levels of expression in said good prognosis expression profile represent the nucleic acid levels of expression of said genes in breast cancer patients having no distant metastases within five years of initial diagnosis; and

(c2) classifying said breast cancer patient as having said first prognosis if said patient similarity value exceeds a second similarity threshold value, said second prognosis if said patient similarity value exceeds a first similarity threshold value but does not exceed said second similarity threshold value, and said third prognosis if said patient similarity value does not exceed said first similarity threshold value, wherein said second similarity threshold value indicates greater similarity to said first good prognosis expression profile than does said first similarity threshold value; and

(d) assigning said breast cancer patient a treatment without adjuvant chemotherapy if the breast cancer patient is lymph node negative and is classified as having said first prognosis or said second prognosis, or assigning said breast cancer patient a treatment with adjuvant chemotherapy if said breast cancer patient (d1) is lymph node positive and is classified as having said first prognosis, said second prognosis, or said third prognosis, or (d2) is lymph node negative and is classified as having said third prognosis.

15. The method of claim 14, in which said treatment without adjuvant chemotherapy comprises adjuvant hormonal therapy if said breast cancer patient is lymph node negative and is classified as having said second prognosis.

16. The method of claim 14, wherein said classifying step (c) further comprises before said step (c2):

(i) rank ordering in descending order a plurality of breast cancer tumor samples, each obtained from a different training breast cancer patient of a plurality of training breast cancer patients for whom clinical and follow-up data are available for at least five years after initial diagnosis, according to the degree of similarity between a second expression profile comprising the nucleic acid levels of expression of said at least five genes in each of said tumor samples and a second good prognosis expression profile, said second good prognosis expression profile comprising the nucleic acid levels of expression of said genes that represent the nucleic acid levels of expression of said genes in tumor samples from training breast cancer patients in said plurality of training breast cancer patients who have no distant metastases within five years of initial diagnosis, said degree of similarity being expressed as a similarity value;

(ii) selecting a particular number or percentage of false negatives for classifying said plurality of training breast cancer patients, wherein a false negative is a training breast cancer patient for whom the second expression profile predicts that said training breast cancer patient will have no distant metastases within the first five years after initial diagnosis, but who has had a distant metastasis within the first five years after initial diagnosis;

(iii) determining a threshold similarity value, wherein training breast cancer patients whose tumor samples having a similarity value above said threshold similarity value in said rank ordered list are predicted as having no distant metastases within the first five years after initial diagnosis, and wherein among said training breast cancer patients predicted as having no distant metastases the number or percentage of training breast cancer patients who are false negatives is not greater than said particular number or percentage selected in step (ii);

(iv) selecting said threshold similarity value determined in step (iii) as said first threshold similarity value; and

(v) selecting a second similarity value, greater than said first similarity value, as said second threshold similarity value.

17. The method of claim 14 which further comprises determining the estrogen receptor (ER) status of said breast cancer patient, wherein if said breast cancer patient is ER positive and lymph node negative, said treatment assigned to said breast cancer patient additionally comprises adjuvant hormonal therapy.

18. The method of claim 14, wherein said breast cancer patient is 52 years of age or younger.

19. The method of claim 14 or 18, wherein said breast cancer patient has stage I or stage II breast cancer.

20. The method of claim 14, wherein said breast cancer patient is premenopausal.

21. The method of claim 14, wherein said patient similarity value is a correlation coefficient between said first expression profile and said first good prognosis expression profile, and wherein said determining in step (c1) is carried out by a method comprising determining said correlation coefficient.

22. The method of claim 14, wherein said at least five genes are at least 10 genes listed in Table 5.

23. The method of claim 14, wherein said at least five genes are at least 20 genes listed in Table 5.

24. The method of claim 14, wherein said at least five genes are at least 30 genes listed in Table 5.

25. The method of claim 14, wherein said at least five genes are at least 40 genes listed in Table 5.

26. The method of claim 14, wherein said at least five genes are at least 50 genes listed in Table 5.

27. The method of claim 14, wherein said at least five genes are all genes listed in Table 6.

28. The method of claim 14, wherein said first threshold similarity value and said second threshold similarity value are selected by a method comprising:

(i) rank ordering in descending order a plurality of breast cancer tumor samples, each obtained from a training breast cancer patient of a plurality of training breast cancer patients for whom clinical and follow-up data are available for at least five years after initial diagnosis by the degree of similarity between a second expression profile comprising the nucleic acid levels of expression of said at least five genes in each of said tumor samples and a second good prognosis expression profile, wherein said second good prognosis expression profile comprises the mean nucleic acid level of expression of each of said at least five genes in tumor samples from training breast cancer patients in said plurality of training breast cancer patients who have no distant metastases within five years of initial diagnosis, to obtain a rank-ordered list, said degree of similarity being expressed as a similarity value;

(ii) selecting a particular number or percentage of false negatives for classifying said plurality of training breast cancer patients, wherein a false negative is a training breast cancer patient for whom the second expression profile comprising the nucleic acid levels of said at least five genes in said cell sample predicts that said training breast cancer patient will have no distant metastases within the first five years after initial diagnosis, but who has had a distant metastasis within the first five years after initial diagnosis;

(iii) determining a threshold similarity value, wherein training breast cancer patients whose tumor samples having a similarity value above said threshold similarity value in said rank ordered list are predicted as having no distant metastases within the first five years after initial diagnosis, and wherein among said training breast cancer patients predicted as having no distant metastases the number or percentage of training breast cancer patients who are false negatives is less than said particular number or percentage selected in said step (ii);

(iv) selecting said threshold similarity value determined in step (iii) as said first threshold similarity value; and

(v) selecting a second similarity value by a method comprising determining which of the tumor samples taken from breast cancer patients having a distant metastasis within the first five years after initial diagnosis in said rank ordered list has the greatest similarity value, and selecting said greatest similarity value as said second threshold similarity value.

29. The method of claim 27, wherein said first expression profile comprises log intensity values for each of the respective genes listed in Table 6, and said first good prognosis profile comprises the mean log intensity values that are listed in Table 7, and wherein said first threshold similarity value is 0.4 and said second threshold similarity value is 0.636.

30. The method of claim 14, wherein said nucleic acid level of expression of each gene of said at least five genes in said first expression profile is a relative nucleic acid level of expression of said gene in said cell sample versus the nucleic acid level of expression of said gene in a reference pool.