Nova Patents
CA2829476C

Gene expression markers for breast cancer prognosis

Abstract

The present invention provides gene sets the expression of which is important in the diagnosis and/or prognosis of breast cancer.

Term

Term ended

Expired 14 January 2024, 2.7 years ago.

  1. Priority
  2. Filed
  3. Granted
  4. Expired
  5. Today

45 claims: 29 independent, 16 dependent

  1. 1
    We claim:1. A method of predicting a likelihood of long-term survival of a breast cancer patient without recurrence of breast cancer, comprising: determining an expression level of an RNA transcript of KRT14, in a fixed, waxembedded breast cancer tumor sample from said patient;normalizing said expression level to obtain a normalized expression level of KRT14;and providing information regarding the likelihood of breast cancer recurrence for said patient, wherein increased normalized expression of KRT14 indicates an increased likelihood of long-term survival without breast cancer recurrence.
  2. 2
    A method of predicting a likelihood of long-term survival of a breast cancer patient without recurrence of breast cancer, comprising:determining an expression level of RNA transcripts of each member of a gene panel comprising KRT14, and MYBL2 in a fixed, wax-embedded breast cancer tumor tissue sample from the patient;normalizing said expression levels to obtain a normalized expression levels of each member of the gene panel;and providing information regarding the likelihood of breast cancer recurrence for said patient, wherein increased normalized expression of KRT14 indicates an increased likelihood of long-term survival without breast cancer recurrence, and wherein increased normalized expression of MYBL2 indicates a reduced likelihood of long-term survival without breast cancer recurrence.
  3. 4
    The method of any one of claims 1 to 3, wherein the breast cancer is estrogen-receptor positive breast cancer. 125 CA 2829476 2017-12-01
  4. 5
    The method of any one of claims 1 to 4, wherein the RNA transcript expression level is determined by quantitative reverse-transcription polymerase chain reaction (qRT-PCR).
  5. 6
    The method of any one of claims 2-5, wherein the gene panel further comprises one or more of KRT5, KRT17, and KRT19.
  6. 7
    The method of any one of claims 1 to 6, further comprising the step of preparing a report indicating that the patient has an increased or decreased likelihood of long-term survival without breast cancer recurrence.
  7. 9
    A method of preparing a personalized genomics profile for a patient, comprising the steps of:(a) subjecting RNA extracted from a fixed, wax-embedded breast tissue sample from the patient to gene expression analysis;(b) determining an expression level of an RNA transcript of KRT14, wherein the expression level is normalized against at least one control gene to obtain normalized data, and optionally is compared to expression levels found in a breast cancer reference tissue set;and (c) creating a report including a prediction of the likelihood of long-term survival without breast cancer recurrence for said patient, wherein increased normalized expression of KRT14 indicates an increased likelihood of long-term survival without breast cancer recurrence.
  8. 10
    A method of preparing a personalized genomics profile for a patient, comprising the steps of:(a) subjecting RNA extracted from a fixed, wax-embedded breast tissue sample from the patient to gene expression analysis;(b) determining expression levels of RNA transcripts of each of a panel of genes comprising KRT14 and MYBL2, wherein the expression levels are normalized against at least 126 CA 2829476 2017-12-01 one control gene to obtain normalized data, and optionally are compared to expression levels found in a breast cancer reference tissue set;and (c) creating a report including a prediction of the likelihood of long-term survival without breast cancer recurrence for said patient, wherein increased normalized expression of KRT14 indicates an increased likelihood of long-term survival without breast cancer recurrence, and wherein increased normalized expression of MYBL2 indicates an reduced likelihood of long-term survival without breast cancer recurrence,
  9. 13
    The method of any one of claims 9 to 12, wherein the gene panel further comprises one or more of KRT5, KRT17, and KRT19.
  10. 14
    The method of any one of claims 9 to 13, wherein the breast cancer is estrogen-receptor positive breast cancer.
  11. 15
    The method of any one of claims 9 to 14, wherein the RNA transcript expression level is determined by quantitative reverse-transcription polymerase chain reaction (qRT-l’CR).
  12. 16
    A method of predicting the likelihood of long-term survival of a breast cancer patient without the recurrence of breast cancer, comprising:isolating RNA from a fixed, wax-embedded tissue sample obtained from a breast tumor of the patient;reverse transcribing an RNA transcript of KRT14 to produce a cDNA of KRT14;amplifying the cDNA of KRT14 to produce an amplicon of the RNA transcript of KRT14;assaying a level of the amplicon of the RNA transcript of KRT14;127 CA 2829476 2017-12-01 normalizing said level against a level of an amplicon of at least one reference RNA transcript in said tissue sample to provide a normalized KRT14 amplicon level;comparing the normalized KRT14 amplicon level to a normalized KRT14 amplicon level in reference breast tumor samples;and predicting the likelihood of long-term survival without the recurrence of breast cancer, wherein increased normalized KRT14 amplicon level is indicative of an increased likelihood of long-term survival without recurrence of breast cancer.
  13. 20
    The method of any one of claims 16 to 19, wherein the level of the amplicon of the RNA transcript of KRT14 is a threshold cycle (Ct) value and the normalized KRT14 amplicon level is a normalized Ct value.
  14. 21
    The method of any one of claims 16 to 20, further comprising the step of preparing a report indicating that the patient has an increased or decreased likelihood of long-term survival without breast cancer recurrence.
  15. 22
    The method of any one of claims 16 to 21, wherein the reference breast cancer samples comprise at least 40 breast cancer samples.
  16. 23
    The method of any one of claims 16 to 22, wherein the gene panel further comprises one or more of KRT5, KRT17, and KRT19. 128 CA 2829476 2017-12-01
  17. 24
    A method of predicting a likelihood of long-term survival of a breast cancer patient without recurrence of breast cancer, comprising:determining an expression level of RNA transcripts in breast tissue from the patient of each member of a gene panel comprising KRT14, and MYBL2, wherein the expression level of the RNA transcript of MYBL2 is obtained by reverse transcription with at least one primer comprising the nucleotide sequence of SEQ ID NO: 18, SEQ ID NO: 24, and SEQ ID NO: 27;normalizing said expression levels to obtain a normalized expression levels of each member of the gene panel;and providing information regarding the likelihood of breast cancer recurrence for said patient, wherein increased normalized expression of KRT14 indicates an increased likelihood of long-term survival without breast cancer recurrence, and wherein increased normalized expression of MYBL2 indicates a reduced likelihood of long-term survival without breast cancer recurrence.
  18. 27
    The method of any one of claims 24 to 26, wherein the breast cancer is estrogenreceptor positive breast cancer.
  19. 28
    The method of any one of claims 24 to 27, wherein the RNA transcript expression level is determined by quantitative reverse-transcription polymerase chain reaction (qRT-PCR).
  20. 29
    The method of any one of claims 24 to 28, wherein the gene panel further comprises one or more of KRT5, KRT17, and KRT19.
  21. 30
    A method of preparing a personalized genomics profile for a patient, comprising the steps of:(a) subjecting RNA extracted from breast tissue from the patient to gene expression analysis;129 CA 2829476 2017-12-01 (b) determining expression levels of RNA transcripts of each of a panel of genes comprising KRT14 and MYBL2, wherein the expression level of the RNA transcript of MYBL2 is obtained by reverse transcription with at least one primer comprising the nucleotide sequence of SEQ ID NO: 18, SEQ ID NO: 24, and SEQ ID NO: 27, and wherein the expression levels are normalized against at least one control gene to obtain normalized data, and optionally are compared to expression levels found in a breast cancer reference tissue set;and (c) creating a report including a prediction of the likelihood of long-term survival without breast cancer recurrence for said patient, wherein increased normalized expression of KRT14 indicates an increased likelihood of long-term survival without breast cancer recurrence, and wherein increased normalized expression of MYBL2 indicates an reduced likelihood of long-term survival without breast cancer recurrence.
  22. 34
    The method of any one of claims 30 to 33, wherein the gene panel further comprises one or more of KRT5, KRT17, and KRT19.
  23. 35
    The method of any one of claims 30 to 34, wherein the RNA transcript expression level is determined by quantitative reverse-transcription polymerase chain reaction (qRT-PCR).
  24. 36
    The method of any one of claims 30 to 35, wherein the breast cancer is estrogenreceptor positive breast cancer.
  25. 37
    A method of predicting the likelihood of long-term survival of a breast cancer patient without the recurrence of breast cancer, comprising:isolating RNA from a tissue sample obtained from a breast tumor of the patient;130 CA 2829476 2017-12-01 reverse transcribing RNA transcripts of a panel of genes comprising KRT14 and MYBL2 to produce a cDNAs of the panel of genes, wherein reverse transcribing the RNA transcript of MYBL2 is performed with at least one primer comprising the nucleotide sequence of SEQ ID NO: 18, SEQ ID NO: 24, and SEQ ID NO: 27;amplifying the cDNAs to produce amplicons of the RNA transcripts;assaying levels of the amplicons of the RNA transcripts;normalizing said levels against a level of an amplicon of at least one reference RNA transcript in said tissue sample to provide normalized amplicon levels of the panel of genes comprising KRT14 and MYBL2;comparing the normalized amplicon levels to a normalized amplicon levels of the same genes in reference breast tumor samples;and predicting the likelihood of long-term survival without the recurrence of breast cancer, wherein increased normalized KRT14 and MYBL2 amplicon levels are indicative of a reduced likelihood of long-term survival without recurrence of breast cancer.
  26. 41
    The method of any one of claims 37 to 40, wherein the level of the amplicon of the RNA transcripts are threshold cycle (Ct) values and the normalized amplieon levels are normalized Ct values. 131 CA 2829476 2017-12-01
  27. 42
    The method of any one of claims 37 to 41, further comprising the step of preparing a report indicating that the patient has an increased or decreased likelihood of long-term survival without breast cancer recurrence.
  28. 43
    The method of any one of claims 37 to 42, wherein the reference breast cancer samples comprise at least 40 breast cancer samples.
  29. 44
    The method of any one of claims 37 to 43, wherein the gene panel further comprises one or more of KRT5, KRT17, and KRT19.
Independent claims29