PLATFORM TECHNOLOGIES

The Genome Institute of Singapore has a wide range of technologies used in modern genomic and cellular biology investigations. Advanced research methods, and the dedicated equipment designed to perform these methods, allow for new approaches to tackle challenging and new biological questions, opening up new vistas for exploration. With our technology platforms, we support genomics research across multiple A*STAR institutes, universities, hospitals, industries as well as international partners.

NEXT GENERATION SEQUENCING

Established over a decade ago, the GIS Next Generation Sequencing Platform has evolved to become the largest and most productive academic sequencing facility in Singapore. GIS’ team of scientists also developed the first protein-mediated interactome protocol, ChIA-PET. As an endpoint service to a wide range of applications that answer different biological questions, the sequencing platform is critical to the ability to generate data from whole genome sequencing to RNA-sequencing, ChIP-sequencing, exome sequencing and more.

With a fleet of Illumina HiSeq and PacBio sequencers, the platform generates massive amounts of data – up to 150 teraBytes or 200 gigabases per year. These include 400 million reads per flowcell, in as short as a one-day turnaround. This state-of the-art sequencing platform is constantly updating itself with the newest technologies, to maintain its top spot as a sequencing service in Singapore. Not only does the platform look to produce reliable sequencing data in a high throughput manner, it is also expanding its capabilities with new machines to produce longer reads and allow miniaturised sample preparations.

Besides housing the newest and most capable sequencers, the sequencing group also automates parts of the process with liquid handlers.

Group Leader

KHOR Chiea Chuen


GENOTYPING

High throughput, next generation genomic technologies are revolutionising the manner in which research in the field of human heredity is being carried out. As a national institute for genetic and genomic research, sustaining capability and high-level expertise in these technologies is a key strategic priority of GIS in maintaining its position as one of the leading research institutes in the field.

Being the national flagship institute for genomic research in Singapore, we specialise in a very broad selection of array technology from Illumina and Affymetrix to empower our discovery efforts into the underlying genetic causes of human diseases (both common and rare). We also undertake focused genotyping using the Sequenom and Taqman systems for validation purposes. With dedicated automation and quality control pipelines, we support a wide range of experimental protocols for human genetic research.

We aim to bring together genomics and analysis services to support practising clinicians and scientists from both Singapore and abroad wanting to leverage on the latest technologies in genomics for their research. We collaborate with GIS multi-disciplinary research teams in human genetics, cancer biology and stratified oncology, stem cells, and with researchers across America, Asia and Europe.

Group Leader

KHOR Chiea Chuen


HIGH THROUGHPUT PHENOMICS

The Centre for High Throughput Phenomics (CHiP) Platform aims to provide an integrated, state-of-the-art, functional and chemical genomics-based high-throughput/high-content screening (HTS/HCS) platform in Singapore.

High Throughput Screening (HTS) has transformed the way biomedical research is performed by employing laboratory automation and robotics, enabling the functional interrogation of the entire genome and identification of therapeutic drug candidates in a much shorter timeframe than earlier. The application of HTS/HCS will ultimately enable the practice of targeted treatments, a first step towards Personalised Medicine.

The CHiP-GIS has been established as a shared resource for the application of functional and chemical genomic technologies to support the research programs of investigators at GIS and beyond. In doing so, the CHiP-GIS hopes to bring together research scientists, ideas and technologies from all aspects of biomedical research in academia, the clinic and industry.

Manager

PERIYASAMY Giridharan


GIS EFFICIENT RAPID MICROBIAL SEQUENCING (GERMS)

Our pathogen sequencing infrastructure (termed the GERMS platform) is dedicated to all microbial sequencing: viral, bacterial, fungal, and parasitic. Our standard analyses include microbiome (both 16S and metagenomics), whole genome sequencing, transcriptomics, and population diversity analyses (such as for viral populations within a single infected individual); custom analyses are also available. The GERMS Platform has many active collaborations both in Singapore and internationally, which include academic, government, and industrial partners. GERMS offers a complete package for microbial genomics, from project design to sample handling, sequencing, analysis, and interpretation.

COMPUTATIONAL PHENOMICS

The Computational Phenomics Platform (CPP-GIS) provides comprehensive computational support for research and exploration involving functional and chemical genomics-based High-Throughput/High-Content Screening (HTS/HCS). We focus on the development of analysis tools and novel descriptors for complex phenotypes (morphological features) to facilitate drug/therapeutic discovery and functional genomic studies linked to phenotypical outcomes, with important implications in the treatment of human diseases including cancer, neurodegenerative diseases and diabetes.

With a spectrum of expertise in high content image analysis, database development, Artificial Intelligence/machine learning, and system biology/network interference, and through a strong partnership with the CHiP-GIS platform, industry and clinical advocates, CPP-GIS is dedicated to the discovery of biologically relevant molecular probes, novel diagnostic and therapeutic avenues contributing to research programmes and industry partnerships on precision oncology, drug discovery and functional genomics in Singapore and beyond.

Platform Leader

Judice KOH


SINGLE CELL GENOMICS

The GIS Single-Cell Omics Centre (SCOC) is a laboratory located within the Institute dedicated to accelerating the understanding of how individual cells work, and how diagnosis and treatment might be enhanced through insight derived from single cells.

The mission of the SCOC is based on the concept that the cell is the basic building block of life. The human body is composed of billions of individual cells representing thousands of cell-types all intricately communicating with one another. One of the goals of this Centre is to define biological systems at this level, whether in diseased states or normal development, by analysing the transcriptomes and genomes of individual cells. By profiling the transcriptome of many individual cells within a population, one gains unparalleled insight into the diversity of cell types and how they communicate among themselves. Such a level of understanding provides mechanistic insights into how cells self-renew, differentiate, evolve (both between species and within cancers), and respond to infection and/or drug treatments. The Centre allows access to cutting-edge single-cell genomics technologies including 10x Genomics, WaferGen and Fluidigm.

The Centre features 10x Chromium controller produced by 10x Genomics which allows efficient processing of thousands of single cells for multiple downstream applications. The 10x Chromium system enabled applications include single cell gene expression, single cell immune profiling, whole genome/exome sequencing, single cell CNV and single cell ATAC-seq. The Centre is also equipped with WaferGen ICELL8™ Single-Cell System, which allows single cell mRNA sequencing and image acquisition of captured cells.

The Centre also features advanced microfluidic technologies produced by Fluidigm enabling single cell transcriptomics and genomics. Equipment within the Centre includes two C1™ Single-Cell Auto Prep Systems, which automatically capture individual cells from small tissue quantities. The nucleic acids produced on this system and generated from individual cells can subsequently be analysed by high throughput real-time PCR on the two Fluidigm BioMark™ HD Systems housed in the Centre or by NextGen sequencing machines located within GIS.

Head

Shyam PRABHAKAR

Manager

SAMYDURAI Sudhagar

 

Genome Innovation

The Genome Innovation Laboratory is a platform built on the theme of making genomics accessible. We provide services to test, optimise and run genomics protocols, especially those that utilise high-throughput sequencing as a readout. Our particular interests are in up-and-coming, novel approaches. Working closely with clinicians, researchers and the GIS Next Generation Sequencing Platform (NGSP), we aim for broad coverage of genomic technologies with high quality results. Our recent projects include techniques for sensitive variant detection in the context of liquid biopsies, as well as being a testbed for long-read sequencing using Nanopore technologies.

Head

Sarah NG

GENOME ANALYTICS CORE

The GIS Genome Analytics Core platform provides efficient genome analytics capabilities that modern genomics research builds upon. Rapid advances in genome sequencing technologies and the exponential growing data throughput make scalable analytics and data management solutions critical. By providing these services, the Genome Analytics Core platform enables researchers to focus on the science, rather than details of computational platforms and systems.

The platform has access to a variety of high-performance compute platforms, including an in-house cluster with petabyte-scale storage, the National Supercomputing Centre (NSCC) Singapore, as well as leading public cloud service providers with data centres in Singapore. This hybrid compute environment allows the platforms to deliver the most efficient solutions to researchers.

The platform is embedded within GIS and can thus leverage on the scientific expertise of in-house computational research groups and is closely aligned with the scientific goals behind analytics. The platform is further tightly integrated into national programmes, for example, the National Precision Medicine Programme.

Leveraging on open community and industry standards, the platform provides integrated and end-to-end solutions from raw genomic data to custom analytics and applications. As of 2018 primary and secondary analysis services are offered to the wider community through the Integrated Genomics Analytics Platform (iGAP).

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