Going digital: Singaporean genes go big

Clinicians are increasingly using genomics- the study of human DNA, to diagnose and treat cancer and other diseases.

Even though the human genome was sequenced in 2000- much remains to be known about how it encodes our development- physiology- and disease dynamics.

With most prior genomic research performed on Caucasian subjects- incomplete information and potential inaccuracies arise when genomics is used to diagnose and treat Singaporean patients.

In addition- the dramatic expansion in the complexity and size of genomic datasets presents a challenge in using genomes for diagnosis. The size of genomic datasets is projected to expand a thousand-fold over the next ten years and the current infrastructure may be unable to cope with the data expansion.

Singapore’s newly established Centre for Big Data and Integrative Genomics (c-BIG) was formed to tackle these challenges.

Launched on 10 November 2016- the facility is a collaboration between four A*STAR research institutes – the Genome Institute of Singapore (GIS)- the Bioinformatics Institute (BII)- the Institute for Infocomm Research (I2R) and the Institute of High Performance Computing (IHPC).

Big data analytics within c-BIG utilises powerful data storage and management facilities at the IHPC, the National Supercomputing Centre (NSCC)- and in public cloud systems.

To “localise” genomic medicine- c-BIG supports the GIS’ Platinum Genome Project. This project aims to create gold-standard reference genomes sourced from Singapore’s three main ethnic groups. In a larger-scale project- called SG10K- new algorithms are invented to build a database of 10,000 local genomes covering the majority of Singaporeans’ genetic diversity.

The disease impact of genetic mutations identified in these and other projects will be interpreted using BII’s algorithms- which are based on models of how they affect protein structure.

Besides constructing large local databases of “healthy” genomes- c-BIG is also creating a data analytics and data-sharing portal for cancer genomes. This initiative- named OncoSG- will support large local cancer programs with a collaborative platform. Through OncoSG- clinicians can gain access to rapid biomedical insights by comparing data from individual patients to matching cases in a database.

In the infectious disease space- c-BIG projects focus on profiling thousands of bacterial and viral strains- studying how they affect local patients- and how they spread across borders. When Singapore suffered from a streptococcal outbreak in early 2015- researchers from GIS built an infrastructure to analyse 2,000 strains of the bacteria within a week. With c-BIG’s big data infrastructure in place- researchers will be able to obtain similar results in just six hours.

c-BIG’s big data infrastructure also offers huge potential in viral research. In 2009- BII successfully developed FluServer, a public online tool that analyses sequences of the influenza virus - and is used by the World Health Organization for flu surveillance in 113 countries worldwide.

BII also supports Singapore’s Ministry of Health in analysing important viral infections- such as Hepatitis C outbreaks in hospitals, Norovirus in army camps- and the recent Zika outbreak.

With c-BIG- researchers will be able to track more viral outbreaks and check if mutations can lead to virulence.

To pilot a federated data-sharing model island-wide, c-BIG has developed CHORUS- a genomic database that allows clinical annotation and case-matching while preserving patient confidentiality.

The consortium also facilitates collaboration between genomic researchers and academic medical centres in Singapore to integrate clinical and genomic data – a specialty area of I2R. This allows physicians to make use of data analytics to make more effective decisions- such as when to intubate or administer red blood cell transfusions.

By utilising data-driven genomics to profile local genes and pave the way towards making genomic information a force for improved patient care and cost savings, c-BIG’s formation is in line with the Committee of the Future Economy’s (CFE’s) goal of improving Singapore’s digital capabilities.