Methods and materials for assessing and treating cancer

Abstract

To provide methods and materials for detecting and / or treating a subject (e.g., a human) having cancer.SOLUTION: In some embodiments, methods and materials for identifying a subject as having cancer (e.g., a localized cancer) are provided in which the presence of member(s) of two or more classes of biomarkers are detected. In some embodiments, methods and materials for identifying a subject as having cancer (e.g., a localized cancer) are provided in which the presence of member(s) of at least one class of biomarkers and the presence of aneuploidy are detected. In some embodiments, methods described herein provide increased sensitivity and / or specificity in the detection of cancer in a subject (e.g. a human).SELECTED DRAWING: None

Claims

1. 1. A method for identifying the presence of pancreatic cancer in a subject, comprising: detecting in a first biological sample from the subject the presence of one or more genetic biomarkers in one or more of the following genes: KRAS, TP53, CDKN2A, or SMAD4; detecting in a second biological sample from the subject the level of one or more of the following protein biomarkers: carbohydrate antigen 19-9 (CA19-9), carcinoembryonic antigen (CEA), hepatocyte growth factor (HGF), or osteopontin (OPN); comparing the detected levels of the one or more protein biomarkers with one or more reference levels of the protein biomarkers; and identifying the presence of pancreatic cancer in the subject if the presence of one or more genetic biomarkers is detected, if the detected levels of the one or more protein biomarkers are greater than the reference levels of the one or more protein biomarkers, or both; The method comprising:

2. 10. The method of claim 1, wherein the first biological sample, the second biological sample, or both, comprise plasma.

3. The method of claim 1 , wherein the first biological sample and the second biological sample are the same.

4. 2. The method of claim 1, which detects the presence of one or more genetic biomarkers in each of KRAS, TP53, CDKN2A and SMAD4.

5. The method according to claim 1, wherein the levels of each of carbohydrate antigen 19-9 (CA19-9), carcinoembryonic antigen (CEA), hepatocyte growth factor (HGF) and osteopontin (OPN) are detected.

6. a. assigning a unique identifier (UID) to each of a plurality of template molecules present in the sample; b. Amplifying each uniquely tagged template molecule to generate a UID family; and c. sequencing the amplification products in duplicate; 2. The method of claim 1, wherein the presence of one or more genetic biomarkers in one or more of KRAS, TP53, CDKN2A, or SMAD4 is detected using a multiplex PCR-based sequencing assay comprising:

7. 13. The method of claim 1, wherein detecting the presence of one or more genetic biomarkers, detecting the levels of one or more protein biomarkers, or both, is performed if the subject is not known to have cancer cells.

8. 10. The method of claim 1, wherein the subject undergoes one or more of the following therapeutic interventions: surgery, adjuvant chemotherapy, neoadjuvant chemotherapy, radiation therapy, immunotherapy, targeted therapy, or immune checkpoint inhibitors.

9. 1. A method for identifying the presence of cancer in a subject, comprising: detecting the presence of one or more genetic biomarkers in one or more of the following genes in a first biological sample from the subject: NRAS, CTNNB1, PIK3CA, FBXW7, APC, EGFR, BRAF, CDKN2A, PTEN, FGFR2, HRAS, KRAS, AKT1, TP53, PPP2R1A, or GNAS; detecting in a second biological sample from the subject the level of one or more of the following protein biomarkers: CA19-9, CEA, HGF, OPN, CA125, prolactin, TIMP-1, or MPO; comparing the detected levels of the one or more protein biomarkers with one or more reference levels of the protein biomarkers; and identifying the presence of cancer in the subject if the presence of one or more genetic biomarkers is detected, if the detected levels of the one or more protein biomarkers are higher than the reference levels of the one or more protein biomarkers, or both; The method comprising:

10. 10. The method of claim 9, wherein the first biological sample, the second biological sample, or both, comprise plasma.

11. 10. The method of claim 9, wherein the first biological sample and the second biological sample are the same.

12. 10. The method of claim 9, wherein the presence of one or more genetic biomarkers in each of NRAS, CTNNB1, PIK3CA, FBXW7, APC, EGFR, BRAF, CDKN2A, PTEN, FGFR2, HRAS, KRAS, AKT1, TP53, PPP2R1A and GNAS is detected.

13. 10. The method of claim 9, wherein the levels of each of CA19-9, CEA, HGF, OPN, CA125, prolactin, TIMP-1 and MPO are detected.

14. a. assigning a unique identifier (UID) to each of a plurality of template molecules present in the sample; b. Amplifying each uniquely tagged template molecule to generate a UID family; and c. sequencing the amplification products in duplicate; 10. The method of claim 9, wherein a multiplex PCR-based sequencing assay is used to detect the presence of one or more genetic biomarkers in one or more of NRAS, CTNNB1, PIK3CA, FBXW7, APC, EGFR, BRAF, CDKN2A, PTEN, FGFR2, HRAS, KRAS, AKT1, TP53, PPP2R1A, or GNAS, comprising:

15. 10. The method of claim 9, wherein the cancer is liver cancer, ovarian cancer, esophageal cancer, gastric cancer, pancreatic cancer, colorectal cancer, lung cancer, breast cancer, or prostate cancer.

16. 10. The method of claim 9, wherein detecting the presence of one or more genetic biomarkers, detecting the levels of one or more protein biomarkers, or both, is performed if the subject is not known to have cancer cells.

17. 10. The method of claim 9, wherein the subject undergoes one or more of the following therapeutic interventions: surgery, adjuvant chemotherapy, neoadjuvant chemotherapy, radiation therapy, immunotherapy, targeted therapy, or immune checkpoint inhibitors.

18. 1. A method for identifying the presence of cancer in a subject, comprising: detecting the presence of one or more genetic biomarkers in one or more of the following genes in a first biological sample from the subject: NRAS, CTNNB1, PIK3CA, FBXW7, APC, EGFR, BRAF, CDKN2A, PTEN, FGFR2, HRAS, KRAS, AKT1, TP53, PPP2R1A, or GNAS; detecting in a second biological sample from the subject the level of one or more of the following protein biomarkers: CA19-9, CEA, HGF, OPN, CA125, AFP, prolactin, TIMP-1, follistatin, G-CSF, or CA15-3; comparing the detected levels of the one or more protein biomarkers with one or more reference levels of the protein biomarkers; and identifying the presence of cancer in the subject if the presence of one or more genetic biomarkers is detected, if the detected levels of the one or more protein biomarkers are higher than the reference levels of the one or more protein biomarkers, or both; The method comprising:

19. 20. The method of claim 18, wherein the first biological sample, the second biological sample, or both, comprise plasma.

20. 20. The method of claim 18, wherein the first biological sample and the second biological sample are the same.

21. 20. The method of claim 18, detecting the presence of one or more genetic biomarkers in each of NRAS, CTNNB1, PIK3CA, FBXW7, APC, EGFR, BRAF, CDKN2A, PTEN, FGFR2, HRAS, KRAS, AKT1, TP53, PPP2R1A and GNAS.

22. 19. The method of claim 18, wherein the levels of each of CA19-9, CEA, HGF, OPN, CA125, AFP, prolactin, TIMP-1, follistatin, G-CSF and CA15-3 are detected.

23. a. assigning a unique identifier (UID) to each of a plurality of template molecules present in the sample; b. Amplifying each uniquely tagged template molecule to generate a UID family; and c. sequencing the amplification products in duplicate; 20. The method of claim 18, wherein a multiplex PCR-based sequencing assay is used to detect the presence of one or more genetic biomarkers in one or more of NRAS, CTNNB1, PIK3CA, FBXW7, APC, EGFR, BRAF, CDKN2A, PTEN, FGFR2, HRAS, KRAS, AKT1, TP53, PPP2R1A, or GNAS.

24. 19. The method of claim 18, wherein the cancer is liver cancer, ovarian cancer, esophageal cancer, gastric cancer, pancreatic cancer, colorectal cancer, lung cancer, breast cancer, or prostate cancer.

25. 20. The method of claim 18, wherein detecting the presence of one or more genetic biomarkers, detecting the levels of one or more protein biomarkers, or both, is performed if the subject is not known to have cancer cells.

26. 20. The method of claim 18, wherein the subject undergoes one or more of the following therapeutic interventions: surgery, adjuvant chemotherapy, neoadjuvant chemotherapy, radiation therapy, immunotherapy, targeted therapy, or immune checkpoint inhibitors.

27. 1. A method for identifying the presence of cancer in a subject, comprising: detecting the presence of one or more genetic biomarkers in one or more of the following genes in a first biological sample from the subject: NRAS, CTNNB1, PIK3CA, FBXW7, APC, EGFR, BRAF, CDKN2A, PTEN, FGFR2, HRAS, KRAS, AKT1, TP53, PPP2R1A, or GNAS; detecting in a second biological sample from the subject the level of one or more of the following protein biomarkers: CA19-9, CEA, HGF, OPN, CA125, AFP, prolactin, TIMP-1, or CA15-3; comparing the detected levels of the one or more protein biomarkers with one or more reference levels of the protein biomarkers; and identifying the presence of cancer in the subject if the presence of one or more genetic biomarkers is detected, if the detected levels of the one or more protein biomarkers are higher than the reference levels of the one or more protein biomarkers, or both; The method comprising:

28. 28. The method of claim 27, wherein the first biological sample, the second biological sample, or both, comprise plasma.

29. 28. The method of claim 27, wherein the first biological sample and the second biological sample are the same.

30. 28. The method of claim 27, detecting the presence of one or more genetic biomarkers in each of NRAS, CTNNB1, PIK3CA, FBXW7, APC, EGFR, BRAF, CDKN2A, PTEN, FGFR2, HRAS, KRAS, AKT1, TP53, PPP2R1A and GNAS.

31. 28. The method of claim 27, wherein the levels of each of CA19-9, CEA, HGF, OPN, CA125, AFP, prolactin, TIMP-1 and CA15-3 are detected.

32. a. assigning a unique identifier (UID) to each of a plurality of template molecules present in the sample; b. Amplifying each uniquely tagged template molecule to generate a UID family; and c. sequencing the amplification products in duplicate; 28. The method of claim 27, wherein a multiplex PCR-based sequencing assay is used to detect the presence of one or more genetic biomarkers in one or more of NRAS, CTNNB1, PIK3CA, FBXW7, APC, EGFR, BRAF, CDKN2A, PTEN, FGFR2, HRAS, KRAS, AKT1, TP53, PPP2R1A, or GNAS.

33. 28. The method of claim 27, wherein the cancer is liver cancer, ovarian cancer, esophageal cancer, gastric cancer, pancreatic cancer, colorectal cancer, lung cancer, breast cancer, or prostate cancer.

34. 28. The method of claim 27, wherein detecting the presence of one or more genetic biomarkers, detecting the levels of one or more protein biomarkers, or both, is performed if the subject is not known to have cancer cells.

35. 28. The method of claim 27, wherein the subject undergoes one or more of the following therapeutic interventions: surgery, adjuvant chemotherapy, neoadjuvant chemotherapy, radiation therapy, immunotherapy, targeted therapy, or immune checkpoint inhibitors.

36. 1. A method for identifying the presence of bladder cancer or upper tract urothelial cancer in a subject, comprising: detecting in a first biological sample from the subject the presence of one or more genetic biomarkers in one or more of the following genes: TP53, PIK3CA, FGFR3, KRAS, ERBB2, CDKN2A, MLL, HRAS, MET, or VHL; detecting the presence of at least one mutation in the TERT promoter in a second biological sample from the subject; detecting the presence of aneuploidy in a third biological sample obtained from the subject; and identifying the presence of bladder cancer or upper tract urothelial cancer in the subject if the presence of one or more genetic biomarkers is detected, if the presence of at least one mutation in the TERT promoter is detected, if the presence of aneuploidy is detected, or a combination thereof; The method comprising:

37. The first biological sample and the second biological sample are the same; The first biological sample and the third biological sample are the same; The second biological sample and the third biological sample are the same; or The first biological sample, the second biological sample, and the third biological sample are the same.

37. The method of claim 36.

38. 38. The method of claim 37, wherein the first biological sample, the second biological sample, or the third biological sample is a urine sample.

39. 37. The method of claim 36, which detects the presence of an aneuploidy in one or more of chromosome arms 5q, 8q, or 9p.

40. 37. The method of claim 36, detecting the presence of one or more genetic biomarkers in each of TP53, PIK3CA, FGFR3, KRAS, ERBB2, CDKN2A, MLL, HRAS, MET and VHL.

41. a. assigning a unique identifier (UID) to each of a plurality of template molecules present in the sample; b. Amplifying each uniquely tagged template molecule to generate a UID family; and c. sequencing the amplification products in duplicate; 37. The method of claim 36, wherein a multiplex PCR-based sequencing assay is used to detect the presence of one or more genetic biomarkers in one or more of TP53, PIK3CA, FGFR3, KRAS, ERBB2, CDKN2A, MLL, HRAS, MET, or VHL.

42. 37. The method of claim 36, wherein if the subject is not known to have cancer cells, detecting the presence of one or more genetic biomarkers, detecting the presence of the at least one mutation in the TERT promoter, or detecting the presence of aneuploidy is performed.

43. 37. The method of claim 36, wherein the subject undergoes one or more of the following therapeutic interventions: surgery, adjuvant chemotherapy, neoadjuvant chemotherapy, radiation therapy, immunotherapy, targeted therapy, or immune checkpoint inhibitors.

44. 1. A method for identifying the presence of ovarian or endometrial cancer in a subject, comprising: detecting the presence of one or more genetic biomarkers in one or more of the following genes in a first biological sample from the subject: NRAS, PTEN, FGFR2, KRAS, POLE, AKT1, TP53, RNF43, PPP2R1A, MAPK1, CTNNB1, PIK3CA, FBXW7, PIK3R1, APC, EGFR, BRAF, or CDKN2A; detecting the presence of aneuploidy in a second biological sample obtained from the subject; and identifying the presence of ovarian or endometrial cancer in said subject if the presence of one or more genetic biomarkers is detected, if the presence of aneuploidy is detected, or both; The method comprising:

45. 45. The method of claim 44, wherein the first biological sample and the second biological sample are the same.

46. 46. ​​The method of claim 45, wherein the first biological sample or the second biological sample is a cervical sample or an endometrial sample.

47. 45. The method of claim 44, wherein the method detects the presence of an aneuploidy in one or more of chromosome arms 4p, 7q, 8q, or 9q.

48. 45. The method of claim 44, detecting the presence of one or more genetic biomarkers in each of NRAS, PTEN, FGFR2, KRAS, POLE, AKT1, TP53, RNF43, PPP2R1A, MAPK1, CTNNB1, PIK3CA, FBXW7, PIK3R1, APC, EGFR, BRAF, and CDKN2A.

49. a. assigning a unique identifier (UID) to each of a plurality of template molecules present in the sample; b. Amplifying each uniquely tagged template molecule to generate a UID family; and c. sequencing the amplification products in duplicate; 45. The method of claim 44, wherein a multiplex PCR-based sequencing assay is used to detect the presence of one or more genetic biomarkers in one or more of NRAS, PTEN, FGFR2, KRAS, POLE, AKT1, TP53, RNF43, PPP2R1A, MAPK1, CTNNB1, PIK3CA, FBXW7, PIK3R1, APC, EGFR, BRAF, or CDKN2A.

50. 45. The method of claim 44, further comprising detecting the presence of at least one genetic biomarker in one or more of the following genes in a circulating tumor DNA (ctDNA) sample obtained from the subject: AKT1, APC, BRAF, CDKN2A, CTNNB1, EGFR, FBXW7, FGFR2, GNAS, HRAS, KRAS, NRAS, PIK3CA, PPP2R1A, PTEN, or TP53.

51. 45. The method of claim 44, wherein if the subject is not known to have cancer cells, detecting the presence of one or more genetic biomarkers or detecting the presence of aneuploidy is performed.

52. 45. The method of claim 44, wherein the subject undergoes one or more of the following therapeutic interventions: surgery, adjuvant chemotherapy, neoadjuvant chemotherapy, radiation therapy, immunotherapy, targeted therapy, or immune checkpoint inhibitors.

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