AI Article Synopsis
- The study focuses on analyzing gene expression levels in melanoma patients to aid clinical decision-making, although current tools are mainly designed for geneticists rather than physicians.
- It highlights the incorporation of immune system-targeting drugs in melanoma treatment and the creation of a database to collect and analyze gene expression data using Python and Apache Spark for scalability.
- The tool VIGLA-M offers visual analysis of gene expression levels and is accessible online, with promising initial findings indicating its potential for understanding patient evolution, though more extensive tests are needed.
Article Abstract
Background: The analysis of gene expression levels is used in many clinical studies to know how patients evolve or to find new genetic biomarkers that could help in clinical decision making. However, the techniques and software available for these analyses are not intended for physicians, but for geneticists. However, enabling physicians to make initial discoveries on these data would benefit in the clinical assay development.
Results: Melanoma is a highly immunogenic tumor. Therefore, in recent years physicians have incorporated immune system altering drugs into their therapeutic arsenal against this disease, revolutionizing the treatment of patients with an advanced stage of the cancer. This has led us to explore and deepen our knowledge of the immunology surrounding melanoma, in order to optimize the approach. Within this project we have developed a database for collecting relevant clinical information for melanoma patients, including the storage of patient gene expression levels obtained from the NanoString platform (several samples are taken from each patient). The Immune Profiling Panel is used in this case. This database is being exploited through the analysis of the different expression profiles of the patients. This analysis is being done with Python, and a parallel version of the algorithms is available with Apache Spark to provide scalability as needed.
Conclusions: VIGLA-M, the visual analysis tool for gene expression levels in melanoma patients is available at http://khaos.uma.es/melanoma/ . The platform with real clinical data can be accessed with a demo user account, physician, using password physician_test_7634 (if you encounter any problems, contact us at this email address: mailto: khaos@lcc.uma.es). The initial results of the analysis of gene expression levels using these tools are providing first insights into the patients' evolution. These results are promising, but larger scale tests must be developed once new patients have been sequenced, to discover new genetic biomarkers.
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Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472185 | PMC |
| http://dx.doi.org/10.1186/s12859-019-2695-7 | DOI Listing |
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