Genome Institute of Singapore accelerates whole genome processing with Databricks
Genome Institute of Singapore (A*STAR), working with Precision Health Research Singapore (PRECISE) on the National Precision Medicine strategy, used the Databricks Data + AI Platform with Delta Lake and Glow to run joint calling of 10,000 whole genomes in under 72 hours, a 15x improvement over their prior approach, to support population-scale precision medicine research.
Overview
Genome Institute of Singapore (A*STAR), working with Precision Health Research Singapore (PRECISE) on the National Precision Medicine strategy, used the Databricks Data + AI Platform with Delta Lake and Glow to run joint calling of 10,000 whole genomes in under 72 hours, a 15x improvement over their prior approach, to support population-scale precision medicine research.
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Inspect the highlighted sourceThe challenge
Conducting genomic variant discovery for 10,000 individuals was not efficient with the technology GIS had on hand; results generated from smaller sequencing cohorts were unsatisfactory and not comprehensive, and the institute needed a new way to scale and process genomic data to complete 10,000 whole genomes via joint calling.
The solution
GIS used the Databricks Data + AI Platform, with interactive notebooks as the primary interface to set up the analytics pipeline, and incorporated Delta Lake and Glow alongside Apache Spark to enable continuous integration and analytics of new genomes at scale; Databricks led development of a prototype deployed on the Genomics Database.
Reported business value
The platform enabled GIS to run 10,000 genomes in less than 72 hours, a 15x improvement compared to before, and Databricks developed the platform prototype in six weeks versus the six months it used to take; GIS is now moving to sequence the genomes of 100,000 healthy Singaporeans in the next phase.
Sources
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