To enable rapid turnaround times for clinical variant curation, CSIRO created a cloud-native annotation framework for genomic variant annotation that is scalable to large cohorts.

An individual’s genome can inform diagnostic and treatment choices, however prioritising the actionable variants amongst the patient’s millions of genetic mutations is resource intensive. In-fact, annotating a genome with clinical information and known functionality is currently as time-consuming as reading the genome itself, severely lengthening turn-around-times for clinical tests. Furthermore, with genomic information used for a wide range of application domains, relevant annotation sources can vary dramatically requiring a highly flexible framework able to focus on the relevant information.

In collaboration with Pathology Queensland and QIMR Berghofer, we have created a fully cloud-native architecture that enables the rapid and flexible annotation of genomic variants, called Serverless VEP. Utilising AWS function compute, it is fully serverless and can be automatically deployed in a user’s cloud-account.  The framework can run over patient-individual VCF files or large cohort VCF files.

Value Proposition

Fast and cost-effective solution irrespective of data sizes

Serverless VEP is estimated to be 99% faster than traditional VEP implementations as it can massively-parallelize the annotation task. When not queried the cloud set-up does not incur cost making it sustainable for small Pathology labs or research institutes.

Customising to needed workflows

The framework has an orchestration engine that allows the selective execution of provided and external annotations plugins, making workflows highly customisable.

Easily extendable to query add-ons

As each component is an independent module, it can be easily exchanged to allow additional functionality, such as a FHIR-based phenotype filtering step.


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