Method for predicting whether a cancer patient will not benefit from platinum-based chemotherapy agents
A testing method for identification whether a cancer patient is a member of a group or class of cancer patients that are not likely to benefit from administration of a platinum-based chemotherapy agent, e.g., cisplatin, carboplatin or analogs thereof, either alone or in combination with other non-platinum chemotherapy agents, e.g., gemcitabine and paclitaxel. This identification can be made in advance of treatment. The method uses a mass spectrometer obtaining a mass spectrum of a blood-based sample from the patient, and a computer operating as a classifier and using a stored training set comprising class-labeled spectra from other cancer patients.
1 . A method for guiding treatment of a cancer patient, comprising the steps of:
a) obtaining a blood-based sample from the patient;
b) obtaining a mass spectrum of the blood-based sample with the aid of a mass spectrometer;
c) in a programmed computer, (1) performing predefined pre-processing steps on the mass spectrum, (2) obtaining integrated intensity values of selected features at one or more predefined m/z ranges in the mass spectrum after the pre-processing steps are performed and (3) comparing the integrated intensity values with a training set comprising class-labeled mass spectra from blood-based samples of other cancer patients to thereby classifying the mass spectrum with a class label, and
d) if the class label is Poor or the equivalent, the patient is predicted to not benefit from treatment in the form of administration of a platinum-based chemotherapy agent and is thereby guided towards a treatment regimen not containing platinum agents.
2 . The method of claim 1 , wherein in step d) if the class label is Poor or the equivalent, the patient is predicted to not benefit from treatment in the form of administration of a combination of a non-platinum chemotherapy agent and a platinum-based chemotherapy agent and the patient is guided towards treatment regimen not containing platinum agents.
3 . The method of claim 1 , wherein the training set comprises class-labeled spectra from cancer patients, the class labels indicating whether the patients obtained benefit from treatment by administration of an epidermal growth factor receptor inhibitor, the class label Poor or the equivalent assigned to members in the training set for those cancer patients that did not benefit from the administration of an epidermal growth factor receptor inhibitor, the class label Good or the equivalent assigned to members in the training set for those cancer patients that did benefit from the administration of an epidermal growth factor receptor inhibitor.
4 . The method of claim 3 , wherein the class-labeled spectra in the training set are obtained from non-small-cell lung cancer (NSCLC) patients.
5 . The method of claim 1 , wherein the platinum-based chemotherapy agent comprises cisplatin, carboplatin or analogs thereof.
6 . The method of any of claim 1 , wherein the treatment regimen not containing platinum agents comprises gemcitabine or the analog or docetaxel or the analog, and wherein the platinum-based chemotherapy agent comprises cisplatin or analogs thereof.
7 . The method of claim 1 , wherein the cancer patient comprises a patient having either ovarian cancer or non-small cell lung cancer.
8 . The method of claim 7 , wherein the platinum-based chemotherapy agent comprises cisplatin, carboplatin or analogs thereof.
9 . The method of claim 7 , wherein the treatment regimen not containing platinum agents comprises gemcitabine or the analog or docetaxel or the analog, and wherein the platinum-based chemotherapy agent comprises cisplatin or analogs thereof.
10 . The method of claim 7 , wherein the training set comprises class-labeled spectra from non-small-cell lung cancer (NSCLC) patients, the class labels indicating whether the patients obtained benefit from treatment by administration of an epidermal growth factor receptor inhibitor, the class label Poor assigned to members in the training set for those NSCLC patients that did not benefit from the administration of an epidermal growth factor receptor inhibitor.
11 . The method of claim 1 , wherein the cancer patient has either colorectal cancer or head and neck cancer.
12 . A method for guiding treatment of a patient having either non-small-cell lung cancer, ovarian cancer, head and neck cancer, breast cancer or colorectal cancer, comprising the steps of:
a) obtaining a blood-based sample from the patient;
b) obtaining a mass spectrum of the blood-based sample with the aid of a mass spectrometer;
c) in a programmed computer, (1) performing predefined pre-processing steps on the mass spectrum, (2) obtaining integrated intensity values of selected features at one or more predefined m/z ranges in the mass spectrum after the pre-processing steps are performed and (3) comparing the integrated intensity values with a training set comprising class-labeled mass spectra from blood-based samples of other cancer patients to thereby classifying the mass spectrum with a class label,
wherein the wherein the training set comprises class-labeled spectra from cancer patients, the class labels indicating whether the patients obtained benefit from treatment by administration of an epidermal growth factor receptor inhibitor, the class label Poor or the equivalent assigned to members in the training set for those cancer patients that did not benefit from the administration of an epidermal growth factor receptor inhibitor, the class label Good or the equivalent assigned to members in the training set for those cancer patients that did benefit from the administration of an epidermal growth factor receptor inhibitor, and
d) if the class label for the blood-based sample of the patient classified by the programmed computer in step c) 3) is Poor or the equivalent, the patient is predicted to not benefit from treatment in the form of administration of a platinum-based chemotherapy agent and is thereby guided towards a treatment regimen not containing platinum agents.
13 . The method of claim 12 , wherein the treatment regimen not containing platinum agents comprises gemcitabine or the analog or docetaxel or the analog, and wherein the platinum-based chemotherapy agent comprises cisplatin or analogs thereof.