LifeOmic

10-12-2021

LifeOmic is a healthcare IT startup focused on improving health and healthcare options and outcomes through sharing complex genomic data sets. LifeOmic’s platform is called the Precision Health Cloud (PHC). The KTB is working with LifeOmic and has uploaded the entire whole genome sequencing data sets from 450 KTB tissue donors into the LifeOmic platform. Researchers can access and analyze this data inside the PHC.

Last year, LifeOmic and the KTB coordinated to submit a poster to the San Antonio Breast Cancer Symposium (click here to view poster). The collaboration helped support our unwritten promise to stay in contact and in touch with our donors, volunteers, researchers, friends, and financial supporters abreast of what is happening at the KTB. Understanding how hereditary, lifestyle and demographic risk factors influence the development of breast cancer is critical for its prevention and treatment. For this purpose, the Komen Tissue Bank serves as the world’s primary repository for normal breast tissue and blood samples from healthy women (~5,500 tissue + blood donors and ~4,500 blood-only donors). In addition, the KTB has received mammograms, H&E images and additional longitudinal health and wellness data from its donors via ongoing annual surveys. Whole genome sequencing has also recently been completed on a subset of 500 donors, including ~125 initially healthy donors who later went on to develop breast cancer.

To make these disparate, multi-modal data accessible to the larger research community and add advanced precision health analytics capabilities to the KTB database, LifeOmic’s Precision Health Cloud (PHC), a secure healthcare-compliant cloud platform, was chosen to host the KTB data moving forward. The PHC provides browsing and querying capabilities across all data including genomic, demographic, histology, donor surveys, and scanned images. Data from donors can be viewed individually as well as analyzed across cohorts of interest. Computation resources, such as informatics workflows and machine learning infrastructure, are available on the same secure environment to leverage the power of cloud computing without having to download large files. This is in addition to visual and custom analytics using Jupyter Notebooks accessible to collaborators.

All available KTB data from ~10,000 donors was loaded into the PHC including data collected at the time of donation and subsequent follow-up questionnaire responses. Additional imaging and genomic data loaded into the PHC include approximately 12,000 mammogram images, 5,000 H&E images, 5,000 ancestry-informative genotypes and 500 VCF and BAM files from whole genome sequencing. A timeline view of each donor shows important milestones over her lifetime. All genetic variants were annotated upon ingestion into the PHC with functional effect on genes, population allele frequency, ClinVar clinical significance and in silico predictions for functional impact.

H&E and/or mammogram images can be viewed directly in the PHC. A built-in image viewer allows researchers to analyze images in the cloud without the need to download large files. Approximately 5,000 H&E images and more than 12,00 mammogram images are available to view.

This new platform will allow researchers to view and access complex data that has been generated from the analysis of samples from the Komen Tissue Bank.  This will continue to support the KTB’s goal of moving research forward through use of all types of samples and data, including research that can be accomplished using data without ever accessing actual tissue samples.