National DNA Day 2020

Photo by Louis Reed on Unsplash

National DNA Day is this month, and to celebrate I wanted to highlight some examples of how the LifeOmic Precision Health Cloud (PHC) has played a role in advancing the study of genomics.

Partnerships

We have been extremely fortunate to establish partnerships with organizations that are leading the way in the field of genomics and medicine.

• Susan G. Komen Tissue Bank — In January, we announced a new partnership with the Susan G. Komen Tissue Bank. Through this partnership, the Komen Tissue Bank will utilize the PHC for genomic, clinical, and imaging data aggregation and analysis.
• AdventHealth — We announced this new partnership in October of last year. With the WholeMe project, AdventHealth will use the PHC to analyze the results of ten-thousand DNA tests from the residents of Florida.
• Indiana University/Regenstrief Institute — We continue to make great progress with our oldest partnership by delivering a platform for the Precision Health Initiative.

Community Standards

LifeOmic is a member of the Global Alliance for Genomics and Health (GA4GH) organization. This is a group of 500+ organizations that are trying to accelerate the potential of research and medicine to advance human health. There are several GA4GH work streams that develop standards and tools for sharing genomic data and information. We always try to adhere to standards when possible to encourage interoperability and data sharing. The following are some examples of how we have adopted some GA4GH standards:

• Genomics API — This API standard has been retired, but we still provide an implementation of the Variants API with the PHC. It integrates nicely with igv.js which we also provide to our users for providing a familiar interface for visualizing genome data.
• Task Execution Service (TES) — The PHC provides a TES implementation to allow our users to run Docker based tools against their data.
• Data Repository Service (DRS) — The PHC Provides a DRS implementation to provide a cloud agnostic way to reference data objects.
• Htsget — The PHC has a htsget implementation that can be used to access BAM files in a more modern client/server fashion.

We have plans this year to expand on this list in the areas of automation, tools, and service discovery.

New PHC Features

We continue to add new functionality to the PHC to provide a world class platform for conducting genomic research.

• Last year I gave a presentation on how we built a system that can handle ingesting and indexing large volumes of genomic data. We have already started to outgrow parts of this solution and are actively working on a second iteration of it. Look for a future post on this blog that describes the changes we made and how it will allow us to index and search across this data faster than we can today.
• We released an updated version of the Omics Explorer. This is an interface that allows one to analyze data across different omic data-sources and cross reference those with clinical knowledge-bases. The data can be filtered across several different facets to allow one to quickly find items of interest.

The Omics Explorer provides a unified view for analyzing omic data such as RNA and DNA variants.

The Omics Explorer showing gene expression data compared against TCGA.

Uncertain Times

This year’s DNA Day is falling during an unprecedented time with the current COVID-19 epidemic. One possible bright spot that is emerging is a change in how scientific research is performed and with how data is shared. Processes and data silos that may have slowed things down are being revamped to allow research to move at faster speed. At LifeOmic, we feel that the PHC is well positioned to help power this new way of performing research. Please contact us if you are interested in learning more.