Abstract
Background The affordability of next-generation genomic sequencing and the improvement of medical data management have contributed largely to the evolution of biological analysis from both a clinical and research perspective. Precision medicine is a response to these advancements that places individuals into better-defined subsets based on shared clinical and genetic features. The identification of personalized diagnosis and treatment options is dependent on the ability to draw insights from large-scale, multi-modal analysis of biomedical datasets. Driven by a real use case, we premise that platforms that support precision medicine analysis should maintain data in their optimal data stores, should support distributed storage and query mechanisms, and should scale as more samples are added to the system.
Results We extended a genomics-based columnar data store, GenomicsDB, for ease of use within a distributed analytics platform for clinical and genomic data integration, known as the ODA framework. The framework supports interaction from an i2b2 plugin as well as a notebook environment. We show that the ODA framework exhibits worst-case linear scaling for array size (storage), import time (data construction), and query time for an increasing number of samples. We go on to show worst-case linear time for both import of clinical data and aggregate query execution time within a distributed environment.
Conclusions This work highlights the integration of a distributed genomic database with a distributed compute environment to support scalable and efficient precision medicine queries from a HIPAA-compliant, cohort system in a real-world setting. The ODA framework is currently deployed in production to support precision medicine exploration and analysis from clinicians and researchers at UCLA David Geffen School of Medicine.
Footnotes
melvin{at}omicsautomation.com, wrighth{at}omicsautomation.com, brian{at}omicsautomation.com, nalini{at}omicsautomation.com, gans{at}omicsautomation.com, cdenny{at}ucla.edu
List of abbreviations
- 1000g
- 1000 Genomes Project
- Amazon S3
- Amazon Simple Storage Service
- API
- Application Programming Interface
- AtLAs
- University of California, Los Angeles Biobank
- AWS
- Amazon Web Services
- CRC
- Clinical Research Chart (from i2b2)
- dbSNP
- Single Nucleotide Polymorphism Database
- EHR
- Electronic Health Record
- EMR
- Elastic Map Reduce
- EMRFS
- Elastic MapReduce File System
- ETL
- Extract, transform, and load
- GATK
- Genomics Analysis Toolkit
- GNU
- GNU’s Not Linux
- HDFS
- Hadoop Distributed File System
- HIPAA
- Health Insurance Portability and Accountability Act of 1996
- HTSLIB
- Samtools High-Throughput Sequencing Library
- I2B2
- Informatics for Integrating Biology and the Bedside
- JNI
- Java Native Interface
- ODA
- Omics Data Automation
- POSIX
- Portable Operating System Interface
- RDD
- Resilient Distributed Dataset
- REST
- Representational State Transfer
- SSL
- Secure Sockets Layer
- UCLA
- University of California, Los Angeles
- VCF
- Variant Call Format
- WES
- Whole Exome Sequencing
- XML
- eXtensible Markup Language