Request for Approval / Acknowledgment for Academic Use of TCGA Database in Breast Cancer Genomic Research
Sushma Sushma
Respected Sir/Madam,
Greetings from Aditya Bangalore Institute of Pharmacy Education and Research (ABIPER), Bengaluru, India.
I hope this message finds you well.
I am writing to formally seek approval/acknowledgment for the academic use of The Cancer Genome Atlas (TCGA) Database in our research study titled:
“Decoding the Somatic Mutational Architecture of Breast Cancer Through Large-Scale TCGA Genomic Mining: An In-Silico Translational Oncology Study.”
This study is being conducted as part of a Pharm.D academic research project under the Department of Pharmacy Practice at ABIPER.
Purpose of Database Utilization
The proposed research aims to perform a comprehensive in-silico analysis of somatic mutations in breast cancer using TCGA-BRCA datasets. Specifically, the study will focus on:
• Characterization of somatic mutational landscapes
• Identification of recurrent driver mutations
• Evaluation of tumour mutational burden (TMB)
• Mutational signature analysis
• Subtype-specific genomic heterogeneity
• Survival correlation and prognostic modelling
• Translational mapping to therapeutic targets
Nature of Use
We respectfully acknowledge that the TCGA database is publicly accessible and intended for research use. Nevertheless, as part of good academic and ethical research practice, we wish to obtain formal approval/acknowledgment for its utilization.
We assure that:
• Data will be used strictly for academic and non-commercial research purposes
• No attempt will be made to re-identify individuals
• All datasets are de-identified and handled responsibly
• Proper citation and acknowledgment of TCGA/GDC/cBioPortal will be provided
• No redistribution or unauthorized modification of data will occur
• Analyses will comply with TCGA Data Usage Policies
Study Context
• Study Type: Retrospective in-silico genomic mining
• Data Source: TCGA-BRCA cohort via Genomic Data Commons (GDC) / cBioPortal
• No patient recruitment or intervention
• No direct human/animal experimentation
• Focus on computational and translational oncology analysis
The study intends to bridge genomic discoveries with precision oncology and clinical pharmacy perspectives.
Request
In view of the above, we kindly request your approval/acknowledgment for the academic use of TCGA datasets in this research study.
Your support will significantly strengthen the ethical compliance and scientific rigor of our work.
Investigator Details
Dr. Muchukota Sushma, Pharm.D, Ph.D
Associate Professor
Department of Pharmacy Practice
Aditya Bangalore Institute of Pharmacy Education and Research
Bengaluru, Karnataka, India
Student Investigator(s):
Chetana M V (Pharm.D)
Salim AL Abdullah (Pharm.D)
We would be grateful for your positive consideration.
Thank you for your time and support.
Please find the Protocol
With regards,
Dr. Muchukota Sushma, Pharm.D, BBM, RPh, LLB(Hons) Ph.D.
Associate Professor,
Department of Pharmacy Practice,
Aditya Bangalore Institute of Pharmacy Education & Research (ABIPER), Bangalore.
📧 Email: sushma...@gmail.com | dr.muchuk...@adityapharmacy.in
📱 Mobile: +91 6300599865
Jessica Singh
Hi Dr. Sushma,
Thank you for your detailed message and for outlining your study so clearly. No formal approval or acknowledgment is required from cBioPortal for academic use of TCGA datasets. The data are publicly available for research use through the Genomic Data Commons and other portals. As long as you comply with the TCGA / GDC data use policies, you may proceed with your study.
If you used cBioPortal as part of your analysis workflow, we ask that you cite the cBioPortal platform papers listed in our documentation here:
https://docs.cbioportal.org/user-guide/faq/#how-do-i-cite-the-cbioportal
In particular, please cite the following three papers:
1. Cerami et al. The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data. Cancer Discovery. 2012.
2. Gao et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Science Signaling. 2013.
3. de Bruijn et al. Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal. Cancer Research. 2023.
In addition, please ensure that you appropriately cite the TCGA-BRCA cohort and the Genomic Data Commons as the original data sources, following their respective citation guidelines.
If you have any follow-up questions, please reply to all so that the continued conversation is captured on the cBioPortal forum.
We appreciate your attention to proper data usage and wish you the best with your research.
Best,
Jessica
Jessica Singh - Schedule a Meeting with me
Solutions Consultant - Genomics and Target Discovery Team
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