The Cancer Discovery Hub (CDH) is a newly established one-stop molecular diagnostic core consisting of different molecular profiling platforms from genomics, epigenomics, to immunomics. Previously known as the Integrated Genomics Platform and housed at the National Cancer Centre Singapore, our lab has built up the expertise and skillset in multi-omic technologies that are gaining increasing scientific importance and relevance. In particular, the CDH has established a wide range of state-of-the-art, research-grade assays trusted by clinician-researchers and scientists, including single cell sequencing, spatial transcriptomics and multi-omic profiling. Our services have been successfully employed by clients and collaborators internationally including those from Singapore, Thailand, China, Taiwan and South Korea.
Our core capabilities include:
NGS library preparation - includes a range of services including tissue processing, DNA/RNA extraction and QC, custom target capture and amplicon sequencing. Provides direct liaison with established third-party NGS vendors to achieve project goals. Custom epigenetics assays e.g. ChIP-seq and DNA methylation sequencing, are also available on case-by-case basis.
NanoString nCounter MAX system - utilizes a novel digital colour-coded barcode technology that is based on direct multiplexed measurement of gene expression and offers high levels of precision and sensitivity (<1 copy per cell). Molecular "barcodes" and single molecule imaging are used to detect and count hundreds of unique transcripts in a single reaction, making it particularly suitable for profiling of single cells and formalin-fixed, paraffin-embedded (FFPE) samples where RNA is usually degraded. Importantly, this system enables the determination of disease-related gene signatures, including a 18-gene “Tumor Inflammation Signature” score that measures a pre-existing but suppressed adaptive immune response within tumor – a potential pan-cancer biomarker for response to cancer immunotherapy.
Silicon Biosystems DEPArray - allows trapping, manipulation, and recovery of selected individual cells for downstream analysis of live or fixed cells, including next generation sequencing applications.
10X Chromium and Visium - for high throughput single cell transcriptomic analysis and spatial transcriptomics, respectively. Importantly, the Visium system represents the state-of-the-art technology that is able to combine spatially-resolved whole transcriptome analysis with morphological context, complementing single cell gene expression information. This will enable a more complete view of disease complexity and allow the discovery of novel biomarkers.
Tumor models - To further translate bench research to pre-clinical and clinical studies, we have also developed patient-derived xenograft (PDX) and organoid creation capabilities, which play an important role in pre-clinical studies and testing. These models allow investigators to overcome issues faced with 2-dimensional cell line models, which often poorly recapitulates genetic and epigenetic heterogeneity of the actual tumor. Organoid models, in particular, enable faster generation of tumor models compared to xenograft models, while preserving the 3-dimensional nature of in vivo tumor physiology. This allows their rapid employment in personalized medicine protocols for therapeutic testing. Furthermore, coupled with the molecular profiling platforms above, this will accelerate novel biomarker discovery for implementation in the clinic. Due to the complexity of creating these models, do contact us for a project feasibility consultation.
Functional assays - we support common molecular/cell biology research assays including Western blot, polymerase chain reaction, immunofluorescence, immunohistochemistry, cell-based assays etc. on a case-by-case basis.
Other capabilties:
Laser capture microdissection - enables isolation of different cell types in a tissue sample, particularly important for studies requiring purity of a cell type and addressing the issue of heterogeneity.
Qiagen GeneReader NGS system - a fully integrated NGS workflow purpose-built to assay its actionable cancer panel. The system also includes QIAcube for DNA extraction and library preparation, as well as QIAGEN Clinical Insight (QCI) platform that combines tools from CLC bio and Ingenuity for analysis of raw data from the GeneReader.
Fluidigm’s C1 Single-Cell Auto Prep System - automatic capture of individual cells from small tissue quantities, including FFPE samples. Allows nucleic acid to be extracted and channelled for genomic or transcriptomics studies.
For more information, contact us today!
Dr Jason Chan
Clinical Director, Cancer Discovery Hub
National Cancer Centre Singapore