CHENNAI, 1 st May 2023: Indian Institute of Technology Madras (IIT Madras) Researchers have
developed a Machine Learning-based computational tool for better detection of cancer-causing
tumours in the brain and spinal cord. Called ‘GBMDriver’ (GlioBlastoma Mutiforme Drivers), this
tool is publicly available online.
Glioblastoma is a fast and aggressively growing tumour in the brain and spinal cord. Although
there has been research undertaken to understand this tumour, therapeutic options remain
limited with an expected survival rate of less than two years from the initial diagnosis.
It is important to evaluate the functional consequences of variants in proteins, which are
involved in Glioblastoma to advance the therapeutic options for patients. However, functional
validations to identify driver mutations (disease-causing mutations) from all the observed
variants would be strenuous work.
The GBMDriver was developed specifically to identify driver mutations and passenger mutations
(passenger mutations are neutral mutations) in Glioblastoma. GBMDriver can be accessed
using the following link
- https://web.iitm.ac.in/bioinfo2/GBMDriver/index.html.
In order to develop this web server, a variety of factors such as amino acid properties, di- and
tri-peptide motifs, conservation scores, and Position Specific Scoring Matrices (PSSM) were
taken into account.
In this study, 9386 driver mutations and 8728 passenger mutations in glioblastoma were
analysed. Driver mutations in glioblastoma were identified with an accuracy of 81.99 percent, in
a blind set of 1809 mutants, which is better than existing computational methods. This method is
completely dependent on protein sequence.
This research was led by Prof. M. Michael Gromiha, Department of Biotechnology, IIT Madras.
His team included Ms. Medha Pandey, PhD Student, IIT Madras and two IIT Madras alumni Dr.
P. Anoosha currently in The Ohio State University, Columbus, U.S., and Dr. Dhanusha
Yesudhas who is now at the National Institute of Health, U.S. Their findings were published in
the reputed peer-reviewed journal Briefings in Bioinformatics
(https://doi.org/10.1093/bib/bbac451).
Explaining the key findings of their research, Prof. M. Michael Gromiha, Department of
Biotechnology, IIT Madras, said, “We have identified the important amino acid features for
identifying cancer-causing mutations and achieved the highest accuracy for distinguishing
between driver and neutral mutations. We hope that this tool (GBMDriver) could help to
prioritize driver mutations in glioblastoma and assist in identifying potential therapeutic targets,
thus helping to develop drug design strategies.”
The Key Applications of this research include
- The methodology and features are portable to apply for other diseases.
- This method could serve as one of the important criteria for disease prognosis.
- Valuable resource to identify mutation-specific drug targets to design therapeutic
strategies.
Ms. Medha Pandey, a PhD Student at IIT Madras, said, “Our method showed an accuracy
and AUC of 73.59% and 0.82 respectively on 10-fold cross-validation and 81.99% and 0.87 in a
blind set of 1809 mutants. We envisage that the present method is helpful to prioritize driver
mutations in glioblastoma and assist in identifying therapeutic targets.”
ABOUT IIT MADRAS
Indian Institute of Technology Madras (IITM) was established in 1959 by the Government of India as an
‘Institute of National Importance.’ The activities of the Institute in various fields of Science and Technology
are carried out in 16 academic departments and several advanced interdisciplinary research academic
centres. The Institute offers undergraduate and postgraduate programmes leading to B.Tech., M.Sc.,
M.B.A., M.Tech., M.S., and Ph.D., degrees in a variety of specialisations. IITM is a residential institute
with more than 600 faculty and 9,500 students. Students from 18 countries are enrolled here. IITM fosters
an active entrepreneurial culture with strong curricular support and through the IITM Incubation Cell.
Recognized as an Institution of Eminence (IoE) in 2019, IITM has been ranked No.1 in the ‘Overall’
Category for the fourth consecutive year in India Ranking 2022 released by National Institutional Ranking
Framework, Ministry of Education, Govt. of India. The Institute has also been ranked No.1 in the
‘Engineering Institutions’ category in the same Rankings for seven consecutive years – from 2016 to
2022. It was also adjudged as the ‘Top innovative Institution’ in the country in Atal Ranking of Institutions
on Innovation Achievements (ARIIA) in 2019, 2020 and 2021. ARIIA Ranking was launched by the
Innovation Cell of Ministry of Education.
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