February 29, 2024

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Scaling Singapore’s Genetic Databank using analytics and AI

Image Credits: A*STAR, Press Release

A pregnant mother wanting to test for Down’s Syndrome in her unborn baby without invasive testing. A doctor trying to make a call on the optimal drug and dosage for a safer and more effective treatment. These are some of the people that the Singapore National Precision Medicine (SG-NPM) programme aims to help.

Established in 2017, the vision of this 10-year effort is to enable a healthcare strategy that is tailored to Singapore’s population diversity through precision medicine – a move that can revolutionise how healthcare is delivered.

Precision medicine takes individual variations in genetics, environmental and lifestyle factors into account, allowing doctors to more accurately predict which treatment and prevention strategies will work in different groups of people. Enabled by tools to analyse data on a large scale and with DNA sequencing becoming more affordable, precision medicine can improve healthcare by giving doctors a more detailed understanding of each patient.

Central to the effort is the Centre for Big data and Integrative Genomics (c-BIG), a collaboration between four A*STAR research institutes – the Genome Institute of Singapore (GIS), the Bioinformatics Institute (BII), the Institute of High Performance Computing (IHPC) and the Institute for Infocomm Research (I2R).

These efforts are coordinated under A*STAR’s Artificial Intelligence, Analytics And Informatics Horizontal Technology Programme Office (AI3 HTPO), which catalyses the development and application of A*STAR’s broad range data science, AI capabilities and technologies for a wide range of industry sectors.

“The first step was to build an IT infrastructure to securely store, analyse and share genomics data at scale to produce and distribute a reference catalogue that captures the genetic variation of 10,000 healthy Singaporeans,” said Dr Shyam Prabhakar, Associate Director, Spatial and Single Cell Systems at A*STAR’s GIS.

This first phase of the NPM has been completed, where the researchers have created the world’s largest genetic databank of Asian populations, which has three Asian populations: Chinese, Indian, and Malay represented. The time is now ripe for Phase 2, which will be to scale up the database.

“The next step is to extend the generation of genetic and phenotypic diversity data to 100,000 healthy Singaporeans in NPM Phase 2, drawing on the capabilities of A*STAR and our ecosystem partners,” said Prof Patrick Tan, Executive Director of GIS, and Executive Director of PRECISE (Precision Health Research Singapore).

“The richness of the data provided by the database, combined with our knowledge of Asian genetics accumulated over the years, means that the clinical applications of genomics are vast.”

This genetic databank is useful for analysis to reveal patterns, trends, and associations, and especially to identify millions of novel Asian-specific genetic variants. Understanding the actual genetic makeup of the Asian population allows the tailoring of products and medicines for this specific market.

For example, genomics can be found at the core of diagnostic tests, such as the use of non-invasive prenatal testing (NIPT) in pregnancy to identify children who may be born with debilitating or fatal genetic defects. Similarly, knowing the genetic variants that an individual carries can be used to estimate their likelihood of suffering from diseases such as diabetes or schizophrenia. Genomics can also be used to guide targeted treatments, such as administering the right drug in the right dose, relevant in pharmacogenomics (PGx), the study of how genes can influence responses to drugs.

Custom-built tech

The c-BIG initiative has contributed to delivering that vision through a variety of technologies and ecosystems. Leveraging the data storage and computing power capability from the National Supercomputing Centre, the team was able to deploy state-of-the-art genome analytics algorithms at an industrial scale to uncover the genetic variants of each individual.

A custom-built secured cloud-based big-data infrastructure has also been developed to enable and facilitate controlled programmatic and web-based graphical interface data access and analysis capabilities to Singapore’s biomedical research community. As the programme grows in the next phase, c-BIG will continue to scale by building on next-level data management, analytics and artificial intelligence (AI).

“The custom data sharing services built by c-BIG will enable secure mining of the resource, and thus pave the way for the discovery of new research insights and actionable clinical findings,” said Dr Nicolas Bertin, Chief Architect of the c-BIG’s NPM infrastructure.

As the team looks to tackle the new scalability challenges posed in NPM Phase 2, researchers are already working to source new types of data to enable richer integrative analyses, including methylation and single-cell expression signals.

The addition of new data types and scaling up of the databank will empower researchers and medical professionals to better understand the inherited diseases in Asian populations. This would pave the way to develop new treatments and ways to predict and diagnose diseases and enable more effective and efficient healthcare services for both Singapore and Asian populations.

PARTNER

Qlik’s vision is a data-literate world, where everyone can use data and analytics to improve decision-making and solve their most challenging problems. A private company, Qlik offers real-time data integration and analytics solutions, powered by Qlik Cloud, to close the gaps between data, insights and action. By transforming data into Active Intelligence, businesses can drive better decisions, improve revenue and profitability, and optimize customer relationships. Qlik serves more than 38,000 active customers in over 100 countries.

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CTC Global Singapore, a premier end-to-end IT solutions provider, is a fully owned subsidiary of ITOCHU Techno-Solutions Corporation (CTC) and ITOCHU Corporation.

Since 1972, CTC has established itself as one of the country’s top IT solutions providers. With 50 years of experience, headed by an experienced management team and staffed by over 200 qualified IT professionals, we support organizations with integrated IT solutions expertise in Autonomous IT, Cyber Security, Digital Transformation, Enterprise Cloud Infrastructure, Workplace Modernization and Professional Services.

Well-known for our strengths in system integration and consultation, CTC Global proves to be the preferred IT outsourcing destination for organizations all over Singapore today.

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Planview has one mission: to build the future of connected work. Our solutions enable organizations to connect the business from ideas to impact, empowering companies to accelerate the achievement of what matters most. Planview’s full spectrum of Portfolio Management and Work Management solutions creates an organizational focus on the strategic outcomes that matter and empowers teams to deliver their best work, no matter how they work. The comprehensive Planview platform and enterprise success model enables customers to deliver innovative, competitive products, services, and customer experiences. Headquartered in Austin, Texas, with locations around the world, Planview has more than 1,300 employees supporting 4,500 customers and 2.6 million users worldwide. For more information, visit www.planview.com.

SUPPORTING ORGANISATION

SIRIM is a premier industrial research and technology organisation in Malaysia, wholly-owned by the Minister​ of Finance Incorporated. With over forty years of experience and expertise, SIRIM is mandated as the machinery for research and technology development, and the national champion of quality. SIRIM has always played a major role in the development of the country’s private sector. By tapping into our expertise and knowledge base, we focus on developing new technologies and improvements in the manufacturing, technology and services sectors. We nurture Small Medium Enterprises (SME) growth with solutions for technology penetration and upgrading, making it an ideal technology partner for SMEs.

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HashiCorp provides infrastructure automation software for multi-cloud environments, enabling enterprises to unlock a common cloud operating model to provision, secure, connect, and run any application on any infrastructure. HashiCorp tools allow organizations to deliver applications faster by helping enterprises transition from manual processes and ITIL practices to self-service automation and DevOps practices. 

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IBM is a leading global hybrid cloud and AI, and business services provider. We help clients in more than 175 countries capitalize on insights from their data, streamline business processes, reduce costs and gain the competitive edge in their industries. Nearly 3,000 government and corporate entities in critical infrastructure areas such as financial services, telecommunications and healthcare rely on IBM’s hybrid cloud platform and Red Hat OpenShift to affect their digital transformations quickly, efficiently and securely. IBM’s breakthrough innovations in AI, quantum computing, industry-specific cloud solutions and business services deliver open and flexible options to our clients. All of this is backed by IBM’s legendary commitment to trust, transparency, responsibility, inclusivity and service.

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