Translating data into clinical information using bioinformatics

Bioinformatics – the use of computing resources to interrogate biological data – is an approach that can be applied to many different fields, from clinical diagnostics and population genomics to precision medicine. With increasingly large data repositories such as the UK Biobank and the Cancer Genome Atlas providing researchers with rich and extensive datasets, bioinformatics strategies are needed to guide how this data is used to enable scientists to translate the information obtained into information that can benefit patients. .

Seven Bridges is a leading biomedical data company specializing in software and data analytics. They aim to help researchers extract more information from complex datasets through the power of bioinformatics.

Technology networks caught up Dr. Brandi Davis-DusenberyScientific Director of Seven Bridges, to learn how bioinformatics can be used as part of a holistic approach to healthcare and how it could bring the concept of personalized medicine to life.

Katie Brighton (KB): What areas of research are already benefiting from the use of bioinformatics approaches? Are there areas of research that you think could benefit from this in the near future?

Brandi Davis-Dusenbery (BD-D): Bioinformatics is a highly interdisciplinary field that leverages aspects of multiple disciplines, including biology, computer science, and statistics, with the goal of increasing understanding of complex biological systems from extremely complex biological data. At Seven Bridges, we believe in a “Science First” approach to enable robust and powerful discovery efforts and the development of impactful solutions to the problems we face. This includes efforts in the areas of diagnosis, disease treatment, clinical strategy, or even conservation programs within the ecology. Bioinformatics already allows researchers in human genomics, biology, proteomics and chemoinformatics to explore the complex relationships between the biology of complex disease states, molecular data and clinical data. It’s an exciting time to tackle complex issues with equally complex yet simple analyses.

KB: Are there any applications of bioinformatics in healthcare that you can tell me about?

BD-D: Bioinformatics pushes our concept of direct-to-consumer medicine and precision medicine to the here and now rather than to a distant science fiction future. In recent years, wearable health technologies have moved from the clinic, where they allowed better blood sugar monitoring for diabetics, to the mainstream where smartwatches can continuously track heart rate and ECG patterns to identify and alert patients. individuals from life-threatening cardiac events. These amazing advances empower people to take charge of their health journey. As technology improves and clinical trials explore the impact that continuous health monitoring can have on individuals and populations, we expect to see increased demand for bioinformatics capabilities that enable the collection, analysis and interpretation of reams of biological data generated.

Bioinformaticians strive to help clinicians and researchers evolve their processes to have a greater impact on patients in their healthcare journeys. In particular, with the rapid and on-site expansion of whole genome sequencing capabilities in healthcare settings, we are seeing an increase in applications of bioinformatics to accelerate turnaround times for critical diagnostic evaluations, genetic testing in newborns with health crises to the identification of precision treatment regimens in cancer patients.

KB: What impact do phenotypic and genomic data repositories have on preclinical and clinical research?

BD-D: With the creation of deeper clinical and epidemiological repositories leveraged against the rapidly growing genomic repositories available to researchers, we see the potential for enormous impacts rippling through pipelines from bench to bedside – from from data-driven diagnosis and treatment to further refinement of clinical trial cohorts via molecular and genomic sub-phenotyping to improve clinical trial endpoints.

Both the UK Biobank and the Cancer Genome Atlas have enabled extensive studies to elucidate the pathology of the disease and have spawned thousands of peer-reviewed publications, adding to the collective knowledge of the scientific community. This body of work has in turn led to breakthroughs in the field of oncology that have led to the development of precision medicine-focused diagnostics for solid tumors that help inform the use of targeted therapies. Every day, researchers strive to translate findings from these rich datasets into actionable therapies for patients. In the past, the lack of flexibility and scalability of computing resources has significantly hampered the ability of researchers to derive new information from ever-growing genomic repositories.

Seven Bridges identified these pinch points in discovery pipelines and solved them. Today, we support broad research efforts by providing a robust cloud-based workspace infrastructure, a shared interface to support global collaboration, easy-to-access tailored data and tools, and a considerable scale to realize the value of these ever-growing repositories. With the technology in place to help deliver the analytical side of the research equation, further impact could be achieved through the adoption and compliance of community data standards to streamline and effectively manage the flow and interpretation data from these repositories. We hope to support institutions as they evolve data standards to foster the ever-increasing impact of their work in communities.

KB: How can computing support multiomics research?

BD-D: Biological systems are incredibly complex. Developing tools to shed light on the many cellular and physiological pathways is essential to the development of human health interventions. To move from genotype to phenotype, we need to understand the continuum from the cell at the molecular level to understanding the body at the physiological level. Data to be interrogated and cross-examined include those from genomics, transcriptomics, proteomics, metabolomics, clinical observations, etc.

This level of interaction and data overlay is inherently complex, diverse and difficult to query, even more so in a workspace or location; yet this is precisely where the insights occur. Seven Bridges enables IT to be put to good use in this research space through the development of robust and unified data standards, data governance, integration and harmonization of all sets of data, and provides a robust cloud-based platform on which to perform these queries. .

KB: What are the challenges encountered in the field of IT? How does Seven Bridges aim to overcome these challenges?

BD-D: The challenges of bioinformatics and biomedicine are numerous.

One of the main challenges is the lack of diversity and democratization of data. Most biobank and population-level datasets tend to be monochromatic, lacking representation of diverse racial, ethnic, and socioeconomic profiles. While some institutions are taking steps to address the lack of diversity, the field is still developing the methodology to generate and use the information available through the analysis of diverse genomes. Seven Bridges answers the demands of researchers by addressing the need for genome-wide reference graphs that can capture this genomic variability. We can characterize genetically distinct populations by analyzing large representative cohorts. These graph-based pangenome references can be used to improve both read alignment and variant calling accuracy while maintaining standards compatibility and without incurring additional computational overhead.

Our pangenome analysis workflow is one of the most accurate state-of-the-art INDEL callers and is also capable of identifying structural variations that unlock the potential to more accurately identify known genetic INDELs in diverse populations. It can also help identify disease-causing mutations in more cases of genetic disorders. We strive to realize the potential of these advances in graph technology within bioinformatics. We seek to create diagnostic workflows that would benefit patients who suffer from any of the thousands of known diseases that are triggered as a result of INDEL mutations. We have shared our results showing the significant impact of pangenome references on population analysis and disease diagnosis in various publications and scientific meetings.

Another significant challenge faced by healthcare researchers is the lack of data standards for indexing and formatting these large, diverse and disparate datasets. There is wide variation between phenotypic data sources and with the growing need to group and harmonize variables across datasets, interoperability – and industry supported data standards that can bring these together different data – is of utmost importance.

KB: What does the future of Seven Bridges look like?

BD-D: We compare our future prospects to the overwhelmingly optimistic outlook created by advances in data acquisition (i.e. a $200 genome!) across the multiomics spectrum. We look forward to increasing availability of rich clinical and phenotyping data to interrogate against these primary data sources, expanded understanding and development of diverse representation in our datasets, and increased applicability and clinical uses. of this data and the products derived therefrom.

Seven Bridges is uniquely positioned to both understand the power of these tools and how best to put these tools into the hands of researchers by leveraging our understanding of their particular research space challenges and opportunities.

The completion of the human genome sequence launched a revolution in research into genetic variability, pathway biology, drug and diagnostic discovery and development. Datasets are bigger, better, richer and more complete. As a community, and particularly at Seven Bridges, we are sitting in the midst of an extremely exciting inflection point in this revolution. Now is a good time for all of us to step up and start asking and answering the big questions.

Dr. Brandi Davis-Dusenbery was talking to Katie Brighton, Science Writer for Technology Networks.

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