Translating Data Into Clinical Insights With Bioinformatics
Bioinformatics – the use of computational 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 ever-growing large data repositories such as the UK Biobank and the Cancer Genome Atlas providing researchers with rich, extensive data sets, bioinformatics strategies are needed to guide how these data are used to enable scientists to translate information gained into insights that can benefit patients.
Seven Bridges is a leading biomedical data company that specializes in software and data analytics. They aim to help researchers extract more information from complex data sets through the power of bioinformatics.
Technology Networks caught up with Dr. Brandi Davis-Dusenbery, chief scientific officer of Seven Bridges, to find out how bioinformatics can be used as part of a holistic approach to healthcare, and how it could bring the concept of personalized medicine to reality.
Katie Brighton (KB): Which areas of research are already benefiting from employing bioinformatics approaches? Are there research fields that you feel could benefit in the near future?
Brandi Davis-Dusenbery (BD-D): Bioinformatics is a highly interdisciplinary field that leverages aspects of several disciplines including biology, computer science and statistics, with the goal of increasing understanding of complex biological systems from vastly complicated biological data. At Seven Bridges we believe in a “Science First” approach to empower robust and powerful discovery efforts along with the development of impactful solutions to the problems we face. This includes efforts across diagnostics, disease treatment, clinical strategy or even conservation programs within ecology. Bioinformatics already enables researchers in human genomics, biology, proteomics and cheminformatics to explore the complex relationships between the biology of complex disease states, molecular data and clinical data. It’s an exciting time to address complex problems with equally complex but straightforward analyses.
KB: Are there applications of bioinformatics within healthcare that you can tell me about?
BD-D: Bioinformatics is pushing our concept of direct-to-consumer medicine and precision medicine to the here and now rather than a far-flung sci-fi future. In recent years, wearable health tech has moved from the clinic, where it enabled better monitoring of diabetics’ blood glucose levels, to the mainstream consumer where smartwatches can continuously track heart rate and ECG patterns to identify and alert individuals to potentially fatal cardiac events. These amazing advancements allow people to take their health journey into their own hands. As technology improves and clinical trials explore the impact that continuous health monitoring can have on individuals and populations, we expect to see greater demand for the bioinformatics capabilities that enable the collection, analysis and interpretation of the reams of biological data being generated.
Bioinformaticians strive to support clinicians and researchers in evolving their processes to drive higher impacts to patients in their healthcare journeys. In particular, with rapid, onsite whole genome sequencing capabilities expanding across healthcare institutions, we see increasing applications for bioinformatics to drive faster turnaround times for critical diagnostic assessments, from genetic testing in newborns suffering health crises to identifying 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 being made available to researchers, we see the potential for huge impacts to reverberate across bench-to-bedside pipelines – from data-driven diagnosis and treatment to greater refinement of clinical trial cohorts via molecular and genomic sub-phenotyping to improve clinical trial endpoints.
The UK Biobank and the Cancer Genome Atlas have both enabled deep studies to elucidate disease pathology and spawned thousands of peer-reviewed publications enriching the collective knowledge of the scientific community. This body of work has in turn driven breakthroughs in the oncology space 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 are striving to translate findings from these rich datasets into actionable therapeutics for patients. In the past, the lack of flexibility and scalability in computational resources greatly hindered researchers’ ability to derive new insights in ever-growing genomic repositories.
Seven Bridges recognized these pinch-points in discovery pipelines and addressed them. Today we support vast research efforts by providing robust cloud-based workspace infrastructure, a shared interface to support global collaboration, easy-to-access, bespoke data and tools and tremendous scale to realize the value of these ever-growing repositories. With the technology in place to help deliver on the analytics side of the research equation, additional impact could be had through the adoption and compliance of community data standards to efficiently streamline and manage the flow and interpretation of the data from these repositories. We hope to support institutions in their evolution of data standards to drive the ever-increasing impact of their work across communities.
KB: How can informatics support multiomics research?
BD-D: Biological systems are incredibly complex. Developing tools to shine light on the many cellular and physiological pathways are critical to developing interventions in human health. To move from genotype to phenotype, we must 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 includes that from genomics, transcriptomics, proteomics, metabolomics, clinical observations and so on.
This level of data interplay and overlay is inherently complex, diverse and challenging to interrogate, even more so in one workspace or place; yet that is precisely where insights occur. Seven Bridges enables informatics to be utilized to great advantage in this research space through the development of robust and unified data standards, data governance, integration and harmonization across all data sets, and it provides a robust cloud-based platform on which to perform these interrogations.
KB: What are the challenges faced in the informatics field? How does Seven Bridges aim to overcome these challenges?
BD-D: There are many challenges facing the bioinformatics and biomedical fields.
One key challenge is the lack of diversity and democratization of data. Most biobank and population-scale data sets tend to be monochromatic, lacking in representation of various 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 utilize insights available through the analysis of diverse genomes. Seven Bridges is meeting researchers’ demands by addressing the need for pangenome 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 retaining 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 able to identify structural variation that unlocks the potential to more accurately identify known genetic INDELs in diverse populations. It can also help identify pathogenic mutations in more instances of genetic disorders. We are working to realize the potential of these advancements in graph technology within bioinformatics. We are looking 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 diagnoses in various scientific publications and meetings.
Another significant challenge faced by researchers across the healthcare industry is the lack of data standards around indexing and formatting these large, diverse and disparate datasets. There is great variation across phenotypic data sources and with the growing need to pool and harmonize variables across datasets, interoperability – and industry-supported data standards that can bring together these different data – is of utmost importance.
KB: What does the future look like for Seven Bridges?
BD-D: We benchmark our future outlook against the tremendously optimistic outlook created by advances in data acquisition (i.e. a $200 genome!) across the multiomics spectrum. We look forward to an increasing availability of rich clinical and phenotyping data to interrogate against these primary data sources, the broadened understanding and development of diverse representation in our data sets and the increased applicability and approved clinical uses of these data and products derived from them.
Seven Bridges is uniquely poised in both the understanding of the power of these tools and the best way to put those 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 kicked off a revolution in research on genetic variability, pathway biology, drug and diagnostic discovery and development. Datasets are larger, higher quality, richer and more comprehensive. As a community, and especially at Seven Bridges, we sit squarely in the midst of a tremendously exciting inflection point in that revolution. It's a good time for all of us to jump in and start asking and answering the big questions.
Dr. Brandi Davis-Dusenbery was speaking to Katie Brighton, Scientific Copywriter for Technology Networks.