are there not the survival time data of colon cancer in CPTAC to do the survival analysis ?
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there are not the survival time data of colon cancer in CPTAC to do the survival analysis
We actually do provide followup data for the colon cancer dataset. It is in the "followup" table:
import cptac
colon_dataset = cptac.Colon()
followup_table = colon_dataset.get_followup()
I have printed below a list of the columns that are in the followup table for the colon cancer dataset. The column names may be different from the column names in the followup tables for other datasets, but you should be able to find the same types of information as in other datasets. Does that answer your question?
Short Title
Event
Modified Time
Modified By
Status
CRF Name
Date of Last Contact (Do not answer if patient is deceased)
Vital Status (at time of last contact)
Date of Death
Tumor Status (at time of last contact or death)
Was a Review of the Initial Pathological Findings Done?
Was the Pathology Review consistent with the Diagnosis?
Adjuvant Post-Operative Radiation Therapy
Adjuvant Post-Operative Pharmaceutical Therapy
Adjuvant Post-Operative Targeted Molecular Therapy
New Tumor Event After Initial Treatment
Method Of Diagnosis of New Tumor Event
Other Method Of Diagnosis of New Tumor Event
If No New Tumor Event, explain how it was confirmed.
Type of New Tumor Event
Anatomic Site of New Tumor Event
Other Site of New Tumor Event
Date of New Tumor Event After Initial Treatment
Additional Surgery for New Tumor Event
Date of of Additional Surgery for New Tumor Event
Residual Tumor after surgery for New Tumor Event (AJCC 7th Edition)
Additional Radiation Therapy Treatment of New Tumor Event
Additional Pharmaceutical Therapy Treatment of New Tumor Event
Additional Targeted Molecular Therapy Treatment of New Tumor Event
Radiation Type
Location of Radiation Treatment
Number of Days from Date of Initial Pathologic Diagnosis to the Date Radiation Therapy Started
Total Dose
Units
Total Number of Fractions
Radiation Treatment Ongoing
Number of Days from Date of Initial Pathologic Diagnosis to the Date Radiation Therapy Ended
Measure of Best Response of Radiation Treatment
Was Patient Treated on a Clinical Trial?
Drug Name (Brand or Generic)
Clinical Trial Drug Classification
Pharmaceutical Type
Number of Days from Date of Initial Pathologic Diagnosis to Date of Therapy Start
Therapy Ongoing
Number of Days from Date of Initial Pathologic Diagnosis to Date of Therapy End
Measure of Best Response of Pharmaceutical Treatment
What Type of Malignancy was This?
Primary Site of Disease
Laterality of the Disease
Histological Type
Number of Days from Date of Initial Pathologic Diagnosis of the Tumor Submitted for CPTAC to the Date of Initial Diagnosis of Other Malignancy
Did the patient have surgery for this malignancy?
Type of Surgery
Number of Days from Date of Initial Pathologic Diagnosis of the Tumor Submitted for CPTAC to the Date of Surgical Resection for this Other Malignancy
Did the patient receive pharmaceutical therapy for this malignancy?
Extent of Pharmaceutical Therapy
Drug Name(s) (Brand or Generic)
Number of Days from Date of Initial Pathologic Diagnosis of the Tumor Submitted for CPTAC to Date Pharmaceutical Therapy Started for this Other Malignancy
Did the patient receive radiation therapy for this malignancy?
Extent of Radiation Therapy
If the patient received locoregional radiation, was the radiation therapy received in the same field as the tumor submitted for CPTAC?
Number of Days from Date of Initial Pathologic Diagnosis of the Tumor Submitted to CPTAC to Date Radiation Therapy Started for this Other Malignancy
Was the patient staged using FIGO?
FIGO Staging System (Gynecologic Tumors Only)
FIGO Stage
Was the patient staged using AJCC?
AJCC Cancer Staging Edition
Pathologic Spread: Primary Tumor (pT)
Pathologic Spread: Lymph Nodes (pN)
Distant Metastases (M)
AJCC Tumor Stage
i see your colon follow up data, i think the data can't calculate the cancer patients' survival time, i hope you can check your colon follow up data
The Colon data is finalized. Unfortunately, we only had funding for 1 year of follow up.
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On Wed, May 27, 2020 at 2:47 AM zihaoxingstudy1 @.***> wrote: [image: colon_follow_up] https://user-images.githubusercontent.com/58220227/82997220-abd99e80-a038-11ea-8170-81344ab8346a.PNG i see your colon follow up data, i think the data can't calculate the cancer patients' survival time, i hope you can check your colon follow up data — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#10 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAS55IJHHLQEBHVQ4D2G2UTRTTHSJANCNFSM4NKL64CA .
can we use the TCGA colon clinical survival time data?
TCGA is a different set of tumors. see the Colon paper (shown in the cptac.list_datasets()). https://www.ncbi.nlm.nih.gov/pubmed/31031003