Precision Medicine: Big Data Bioinformatics in Oncology & Virology

NGS in the clinic: from research studies to precision medicine! 

The interest and the potential of precision diagnostics and personalized therapy are now becoming a reality with large scale data analysis being carried out to understand and adopt Next Generation Sequencing (NGS) in biomedical research and even making it into the clinic. In this age of “personalized medicine,” no single indicator determines a patient’s fate or optimal treatment. Instead, advanced approaches adopted by many clinicians are starting to include a number of complex test results used routinely to develop and adjust a coherent clinical plan. The precision and comprehensiveness of information that Next Generation Sequencing screening yields from a sample make this single test an increasingly attractive option for integrated reporting.

With the decreasing cost of NGS and the increasingly broad range of applications, this technology has transformed biomedical research, the biotech industry, and now is increasingly becoming popular in clinical use. NGS applications are used for the identification of germline and somatic pathogenic variants, measurement of gene expression, detection of methylation patterns on DNA and even studies of microbial communities on human skin, in the gut, lungs, and other organs. Many companies are rushing into this space relying on NGS for diagnostics, therapeutics, and clinical trials. Some of the major players operating in the market include established companies like Roche Diagnostics, Novartis AG, Agilent Technologies, and Qiagen. And these companies are on a major push to expand their global presence in every major region: North America, Europe (Germany, UK, France, Spain, Italy and Rest of Europe), Asia-Pacific (China, Japan, India, Australia and Rest of APAC).

In oncology, precision medicine has become established with targeted therapies prescribed using the patient’s genetic makeup (genomic variants in a tumor or patterns of gene expression). But this data turns out to be much more interesting than the several examples of targeted therapies that are starting to show promise. It turns out, the whole body responds to internal and external pathogens, stresses, and age-related pressures in ways that can be measured using precise molecular profiling with NGS technologies. These methods are routinely used to detect and characterize oncolytic pathogens, study changes in the microbiome, and a stressed or weakened immune system. Ultimately, this rich and precise data offers us a realistic picture with amazing resolution. Moreover, the technological advances in high-performance computing and user-friendly cloud-based tools are making the data and their utility accessible to an ever-increasing number of highly skilled workers in the clinical, biotechnology, pharmaceutical, and research industries. 

To learn about these technologies and see the advantages of utilizing NGS for personalized medical use and clinical research, we have started offering OmicsLogic resources designed for students, researchers & faculty to get trained in the analysis of NGS data and gain experience using bioinformatics to answer key research questions in the biomedical field. Our upcoming “Bioinformatics for Precision Medicine” program is a unique opportunity to learn about the role of NGS Data Analysis in different areas like oncology and infectious diseases. Participants will learn to apply statistical analysis and Machine Learning (ML) that enable the use of Molecular Precision to Address Pressing Challenges of the Future of Medicine.

In this program, we will have 10 online interactive sessions covering important topics in precision medicine. The program will start on June 16, 2020. We will begin by speaking about the molecular processes related to cancer biology that lead to changes in organs, tissues, and cells and the molecular factors in tumor development and metastasis. Then, we will to look into clinical and molecular data in oncology studies to study and analyze the phenotype-genotype relationship.

The NGS data analysis being an essential part of this training does not only provides information about simple, single nucleotide alterations, but it can also provide information on complex variations, such as insertions and deletions, copy number alterations, and structural variants. In the sessions followed by the introduction, we will start working on these different omics datatypes to understand the variation at the cellular and molecular levels.

The implementation of genomics level information is very useful to understand – not only cancer but many other life-threatening diseases. After going through five sessions in June covering topics relevant to understanding precision oncology, we will transition to gain deeper insights into the role of Bioinformatics for infectious diseases. Taking examples from the current COVID-19 pandemic,  while polymerase chain reaction (PCR) technology has been at the forefront of diagnostics, sequencing has been at the forefront of understanding the SARS-CoV-2 virus responsible for the disease. Next-generation Sequencing of COVID-19 patients is important for identifying genetic factors that may impact susceptibility, disease severity, immune response, and risk of reinfection. One of the benefits of learning and utilizing data-driven approaches will help you transition to personalized medicine; which is becoming more and more important and a standard of care in many developed markets.

The sessions in July will include a comprehensive and in-depth analysis of NGS data in Virology and will also the role of the Oncolytic viruses in cancer.

This research-based program, which is a part of the “Omicslogic Summer Bioinformatics Training” has been designed by experts with years of experience in both industry and academia.

Our online omicslogic programs are designed for everyone to learn bioinformatics and each of these programs includes access to various important resources that plays a critical role in the overall progress of the participants. Being part of this program, the participants will have access to : 

Educational Access to Edu.T-Bioinfo Platform. (https://edu.t-bio.info/)
Access to learning NGS data analysis (Online Bioinformatics Courses & Project).
Introduction to Bioinformatics, Introduction to genomics, Introduction to Metagenomics & Transcriptomics Data analysis, Genomics data analysis.

Academic Access to the Server.T-Bioinfo Platform. (https://server.t-bio.info/)
Access to perform create Bioinformatics Pipelines for Big Data, Learn to prepare a Workflow based on Data type, Select the right References and Databases, Do gene expression and differential gene expression analysis, Principal Component Analysis and Use of Machine Learning, Interpreting Evolutionary relationships, Visualising and Interpreting Results, and do Reproducible Bioinformatics Analysis.

Bioinformatics Educational Projects: This course will additionally give you access to Oncology and Infectious Disease specialization Projects. (*one project per participant based on the course progress) 

Data analysis from Open Source repositories and Tools: During this program, we will utilize a number of best-known resources available publicly for Oncology & Infectious diseases. You can find most of the resources explained in our blog post.
1. https://edu.t-bio.info/blog/2020/04/21/virology-genomics-resources/
2. https://edu.t-bio.info/blog/2020/02/05/where-can-i-find-a-good-rna-seq-dataset-on-cancer/

Certificates & Recognition : The program includes certification for Participation & Excellence.The certificate of excellence will be provided to students who exceed the progress expectations and complete the Online courses & Propose a Novel Bioinformatics project NGS Data analysis. 

Olga recently completed the Bioinformatics for Precision Oncology program where she took online courses on cancer biology that can be studied by analyzing multi-omics data types. As a result of completing multiple courses and developing a research project which she had a chance to present to program mentors, she received a certificate of excellence for the program. You can also improve your understanding of precision medicine and gain practical experience in bioinformatics by completing this training.

If you have not yet registered, please create an account on this portal for free https://edu.t-bio.info/. Once you are registered, you can join the program by completing the payment on this link: https://edu.t-bio.info/membership-checkout/?level=31. The Registration Fee is $75 (~5690 rupees)

If you have any questions, please reach out to us by email: marketing@pine.bio